Search to RefSeqBP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-008862
(1757 letters)
Database: RefSeq49_BP.fasta
33,088 sequences; 17,681,374 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001076920.1| nuclear receptor ROR-gamma [Bos taurus]. 852 0.0
Alignment gi|NP_001179790.1| nuclear receptor ROR-alpha [Bos taurus]. 447 e-125
Alignment gi|XP_002690894.1| PREDICTED: RAR-related orphan receptor A [Bo... 447 e-125
Alignment gi|NP_001179587.1| nuclear receptor ROR-beta [Bos taurus]. 406 e-113
Alignment gi|XP_002689697.1| PREDICTED: RAR-related orphan receptor B [Bo... 406 e-113
Alignment gi|XP_610586.3| PREDICTED: nuclear receptor subfamily 1, group ... 129 8e-30
Alignment gi|XP_002698802.1| PREDICTED: nuclear receptor subfamily 1, gro... 129 1e-29
Alignment gi|NP_001071568.1| nuclear receptor subfamily 1 group D member ... 125 2e-28
Alignment gi|NP_776827.1| COUP transcription factor 2 [Bos taurus]. 123 5e-28
Alignment gi|NP_001124228.1| retinoic acid receptor, gamma [Bos taurus]. 117 2e-26
>ref|NP_001076920.1| nuclear receptor ROR-gamma [Bos taurus].
Length = 506
Score = 852 bits (2200), Expect = 0.0
Identities = 426/495 (86%), Positives = 431/495 (87%)
Frame = +3
Query: 201 TQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC 380
+QIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC
Sbjct: 24 SQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC 83
Query: 381 QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGAQG 560
QHCRLQKCLALGMSRDAVK GRMSKKQRDSLHAEV +PP GAQG
Sbjct: 84 QHCRLQKCLALGMSRDAVKLGRMSKKQRDSLHAEVQKQLQQRQQQQREQAAKTPPMGAQG 143
Query: 561 ADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYSNSLVKAGLNGASYHLE 740
AD LAC DLPEASACPP LLRAP CGPSYSNSL K GLNGASYHLE
Sbjct: 144 ADTLACTLGLPDGQLPLGSSPDLPEASACPPSLLRAPGCGPSYSNSLAKTGLNGASYHLE 203
Query: 741 YSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGEPGRGPDSYCSPSFRSTPEAP 920
YSPERGKAEGRENFYG GSQLAPDR GLH EDPR PGLGEPGRG DSY +PSFRSTPE P
Sbjct: 204 YSPERGKAEGRENFYGIGSQLAPDRGGLHSEDPRRPGLGEPGRGLDSYFTPSFRSTPEVP 263
Query: 921 YASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWERCAHR 1100
YASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMW RCAHR
Sbjct: 264 YASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWGRCAHR 323
Query: 1101 LTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGKYG 1280
LTEAIQYVVEFAKRL GFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADN TVFFE
Sbjct: 324 LTEAIQYVVEFAKRLPGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNDTVFFE---- 379
Query: 1281 GMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQLQ 1460
GCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQLQ
Sbjct: 380 --------GCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQLQ 431
Query: 1461 YNLELAFHHHLCKTHRQGILAKLPPKGKLRSLCSQHVEKLQTFQHLHPIVVQVAFPPLYK 1640
NLELAFHHHLCKTHRQGILAKLPPKGKLRSLCSQHVEKLQTFQHLHPIVVQ AFPPLYK
Sbjct: 432 CNLELAFHHHLCKTHRQGILAKLPPKGKLRSLCSQHVEKLQTFQHLHPIVVQAAFPPLYK 491
Query: 1641 ELFSTEIESSDGLSE 1685
ELFSTEIES +GLS+
Sbjct: 492 ELFSTEIESPEGLSK 506
>ref|NP_001179790.1| nuclear receptor ROR-alpha [Bos taurus].
Length = 523
Score = 447 bits (1150), Expect = e-125
Identities = 242/495 (48%), Positives = 319/495 (64%), Gaps = 7/495 (1%)
Frame = +3
Query: 201 TQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC 380
+QIE+IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N YSC RQ+NC IDRTSRNRC
Sbjct: 66 SQIEIIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNATYSCPRQKNCLIDRTSRNRC 125
Query: 381 QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGAQG 560
QHCRLQKCLA+GMSRDAVKFGRMSKKQRDSL+AEV
Sbjct: 126 QHCRLQKCLAVGMSRDAVKFGRMSKKQRDSLYAEVQKHRMQQQQRDHQQQPGE------- 178
Query: 561 ADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYS---NSLVKAGLNGASY 731
A+PL P+Y+ N L + + ++Y
Sbjct: 179 AEPLT-----------------------------------PTYNISANGLTELHDDLSNY 203
Query: 732 HLEYSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGE--PGRGPDSYCSPSFRS 905
++PE KA+ + + Q +PD+ GL + + + P G YCS F +
Sbjct: 204 IDGHTPEGSKADSAVSSFYLDIQPSPDQSGLDINGIKPEPICDYTPASGFFPYCS--FTN 261
Query: 906 TPEAPYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWE 1085
+P S+ E+EHL QN+ KS+ +TCQ E+L + F +EE+ YQ K MW+
Sbjct: 262 GETSPTVSMAELEHLAQNISKSHLETCQYLREELQQITWQTFLQEEIENYQNKQREVMWQ 321
Query: 1086 RCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFF 1265
CA ++TEAIQYVVEFAKR+ GFMELCQNDQIVLLKAG++EVV +RMCRA+++ N+TV+F
Sbjct: 322 LCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYF 381
Query: 1266 EGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRK 1445
+GKY ++F++LGC + IS +F+F +SL ++ +EDEIAL++A VL++A+R LQEK K
Sbjct: 382 DGKYASPDVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVK 441
Query: 1446 VEQLQYNLELAFHHHLCKTHRQ-GILAKLPPK-GKLRSLCSQHVEKLQTFQHLHPIVVQV 1619
+E+LQ ++LA H L K HR+ GIL KL K LR+LC +H EKL F+ ++P +V++
Sbjct: 442 IEKLQQKIQLALQHVLQKNHREDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRL 501
Query: 1620 AFPPLYKELFSTEIE 1664
FPPLYKELF++E E
Sbjct: 502 HFPPLYKELFTSEFE 516
>ref|XP_002690894.1| PREDICTED: RAR-related orphan receptor A [Bos taurus].
Length = 523
Score = 447 bits (1150), Expect = e-125
Identities = 242/495 (48%), Positives = 319/495 (64%), Gaps = 7/495 (1%)
Frame = +3
Query: 201 TQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC 380
+QIE+IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N YSC RQ+NC IDRTSRNRC
Sbjct: 66 SQIEIIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNATYSCPRQKNCLIDRTSRNRC 125
Query: 381 QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGAQG 560
QHCRLQKCLA+GMSRDAVKFGRMSKKQRDSL+AEV
Sbjct: 126 QHCRLQKCLAVGMSRDAVKFGRMSKKQRDSLYAEVQKHRMQQQQRDHQQQPGE------- 178
Query: 561 ADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYS---NSLVKAGLNGASY 731
A+PL P+Y+ N L + + ++Y
Sbjct: 179 AEPLT-----------------------------------PTYNISANGLTELHDDLSNY 203
Query: 732 HLEYSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGE--PGRGPDSYCSPSFRS 905
++PE KA+ + + Q +PD+ GL + + + P G YCS F +
Sbjct: 204 IDGHTPEGSKADSAVSSFYLDIQPSPDQSGLDINGIKPEPICDYTPASGFFPYCS--FTN 261
Query: 906 TPEAPYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWE 1085
+P S+ E+EHL QN+ KS+ +TCQ E+L + F +EE+ YQ K MW+
Sbjct: 262 GETSPTVSMAELEHLAQNISKSHLETCQYLREELQQITWQTFLQEEIENYQNKQREVMWQ 321
Query: 1086 RCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFF 1265
CA ++TEAIQYVVEFAKR+ GFMELCQNDQIVLLKAG++EVV +RMCRA+++ N+TV+F
Sbjct: 322 LCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYF 381
Query: 1266 EGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRK 1445
+GKY ++F++LGC + IS +F+F +SL ++ +EDEIAL++A VL++A+R LQEK K
Sbjct: 382 DGKYASPDVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVK 441
Query: 1446 VEQLQYNLELAFHHHLCKTHRQ-GILAKLPPK-GKLRSLCSQHVEKLQTFQHLHPIVVQV 1619
+E+LQ ++LA H L K HR+ GIL KL K LR+LC +H EKL F+ ++P +V++
Sbjct: 442 IEKLQQKIQLALQHVLQKNHREDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRL 501
Query: 1620 AFPPLYKELFSTEIE 1664
FPPLYKELF++E E
Sbjct: 502 HFPPLYKELFTSEFE 516
>ref|NP_001179587.1| nuclear receptor ROR-beta [Bos taurus].
Length = 459
Score = 406 bits (1044), Expect = e-113
Identities = 231/499 (46%), Positives = 306/499 (61%), Gaps = 11/499 (2%)
Frame = +3
Query: 195 MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRN 374
MR QIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N +YSC RQ+NC IDRT+RN
Sbjct: 1 MRAQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNASYSCPRQRNCLIDRTNRN 60
Query: 375 RCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGA 554
RCQHCRLQKCLALGMSRDAVKFGRMSKKQR
Sbjct: 61 RCQHCRLQKCLALGMSRDAVKFGRMSKKQR------------------------------ 90
Query: 555 QGADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYSNSLVKAGLNG---A 725
D L EA A A G S SN L + LN
Sbjct: 91 ---DSLYAEVQKHQQRLQEQRQQQSGEAEAL------ARVYGSSISNGL--SNLNNEASG 139
Query: 726 SYHLEYSPERGKAEGRENFYGTGSQLAPDRCGLHF---EDPRHPGLGEPGRGPDSYCSPS 896
+Y + + K+EG N Q +PD+ GL + + + + P+ + S
Sbjct: 140 TYANGHVIDLPKSEGYYNV--DSGQPSPDQSGLDMTGIKQIKQEPIYDLTSVPNLFTYSS 197
Query: 897 FRSTPEAPYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWE 1076
F + AP +++EI+ + QN+ KS+ +TCQ +E+L + + EE+ YQ KS
Sbjct: 198 FNNGQLAPGITMSEIDRIAQNIIKSHLETCQYTMEELHQLAWQTHTYEEIKAYQSKSREA 257
Query: 1077 MWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHT 1256
+W++CA ++T AIQYVVEFAKR++GFMELCQNDQI+LLK+G +EVVLVRMCRA+N N+T
Sbjct: 258 LWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNT 317
Query: 1257 VFFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQE 1436
V FEGKYGGM++F+ALG +L++ FDF+++L +L+ +E+EIAL+++ VLI+ +R L E
Sbjct: 318 VLFEGKYGGMQMFKALGSDDLVNEAFDFAKNLCSLQLTEEEIALFSSAVLISPDRAWLIE 377
Query: 1437 KRKVEQLQYNLELAFHHHLCKTHRQG-----ILAKLPPKGKLRSLCSQHVEKLQTFQHLH 1601
RKV++LQ + A H + K H ++AK+P + ++C+ H EKLQ F+ H
Sbjct: 378 PRKVQKLQEKIYFALQHVIQKNHLDDETLAKLIAKIP---TITAVCNLHGEKLQVFKQSH 434
Query: 1602 PIVVQVAFPPLYKELFSTE 1658
P +V FPPLYKELF+ +
Sbjct: 435 PDIVNTLFPPLYKELFNPD 453
>ref|XP_002689697.1| PREDICTED: RAR-related orphan receptor B [Bos taurus].
Length = 459
Score = 406 bits (1044), Expect = e-113
Identities = 231/499 (46%), Positives = 306/499 (61%), Gaps = 11/499 (2%)
Frame = +3
Query: 195 MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRN 374
MR QIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N +YSC RQ+NC IDRT+RN
Sbjct: 1 MRAQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNASYSCPRQRNCLIDRTNRN 60
Query: 375 RCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGA 554
RCQHCRLQKCLALGMSRDAVKFGRMSKKQR
Sbjct: 61 RCQHCRLQKCLALGMSRDAVKFGRMSKKQR------------------------------ 90
Query: 555 QGADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYSNSLVKAGLNG---A 725
D L EA A A G S SN L + LN
Sbjct: 91 ---DSLYAEVQKHQQRLQEQRQQQSGEAEAL------ARVYGSSISNGL--SNLNNEASG 139
Query: 726 SYHLEYSPERGKAEGRENFYGTGSQLAPDRCGLHF---EDPRHPGLGEPGRGPDSYCSPS 896
+Y + + K+EG N Q +PD+ GL + + + + P+ + S
Sbjct: 140 TYANGHVIDLPKSEGYYNV--DSGQPSPDQSGLDMTGIKQIKQEPIYDLTSVPNLFTYSS 197
Query: 897 FRSTPEAPYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWE 1076
F + AP +++EI+ + QN+ KS+ +TCQ +E+L + + EE+ YQ KS
Sbjct: 198 FNNGQLAPGITMSEIDRIAQNIIKSHLETCQYTMEELHQLAWQTHTYEEIKAYQSKSREA 257
Query: 1077 MWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHT 1256
+W++CA ++T AIQYVVEFAKR++GFMELCQNDQI+LLK+G +EVVLVRMCRA+N N+T
Sbjct: 258 LWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNT 317
Query: 1257 VFFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQE 1436
V FEGKYGGM++F+ALG +L++ FDF+++L +L+ +E+EIAL+++ VLI+ +R L E
Sbjct: 318 VLFEGKYGGMQMFKALGSDDLVNEAFDFAKNLCSLQLTEEEIALFSSAVLISPDRAWLIE 377
Query: 1437 KRKVEQLQYNLELAFHHHLCKTHRQG-----ILAKLPPKGKLRSLCSQHVEKLQTFQHLH 1601
RKV++LQ + A H + K H ++AK+P + ++C+ H EKLQ F+ H
Sbjct: 378 PRKVQKLQEKIYFALQHVIQKNHLDDETLAKLIAKIP---TITAVCNLHGEKLQVFKQSH 434
Query: 1602 PIVVQVAFPPLYKELFSTE 1658
P +V FPPLYKELF+ +
Sbjct: 435 PDIVNTLFPPLYKELFNPD 453
>ref|XP_610586.3| PREDICTED: nuclear receptor subfamily 1, group D, member 2 [Bos
taurus].
Length = 585
Score = 129 bits (324), Expect = 8e-30
Identities = 76/188 (40%), Positives = 116/188 (61%), Gaps = 7/188 (3%)
Frame = +3
Query: 1062 KSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYN 1241
KS E+WE + T A++ VVEFAKR+ GF +L Q+DQ+ LLKAG EV++VR ++
Sbjct: 402 KSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFD 461
Query: 1242 ADNHTV-FFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINAN 1418
A TV F GK ++ ++G +L++S+F+FS L+AL+ S++E++L+TA+VL++A+
Sbjct: 462 AKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSAD 521
Query: 1419 RPGLQEKRKVEQLQYNLELAFHHHLCKTHRQ------GILAKLPPKGKLRSLCSQHVEKL 1580
R G++ VE LQ L A + K H +L KLP LRSL + H E+L
Sbjct: 522 RSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLP---DLRSLNNMHSEEL 578
Query: 1581 QTFQHLHP 1604
F+ +HP
Sbjct: 579 LAFK-VHP 585
Score = 127 bits (320), Expect = 2e-29
Identities = 58/113 (51%), Positives = 78/113 (69%), Gaps = 1/113 (0%)
Frame = +3
Query: 150 AKKDGSPVGKAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAY- 326
+K V K+H V + V+ CK+CGD +SG HYGV CEGCKGFFRRS Q N+ Y
Sbjct: 86 SKSSAPGVTKSHSGVTKFSGMVLLCKVCGDVASGFHYGVHACEGCKGFFRRSIQQNIQYK 145
Query: 327 SCTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV 485
C + +NC I R +RNRCQ CR +KCL++GMSRDAV+FGR+ K+++ + E+
Sbjct: 146 KCLKNENCSIMRMNRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRMLIEM 198
>ref|XP_002698802.1| PREDICTED: nuclear receptor subfamily 1, group D, member 2 [Bos
taurus].
Length = 585
Score = 129 bits (323), Expect = 1e-29
Identities = 76/188 (40%), Positives = 116/188 (61%), Gaps = 7/188 (3%)
Frame = +3
Query: 1062 KSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYN 1241
KS E+WE + T A++ VVEFAKR+ GF +L Q+DQ+ LLKAG EV++VR ++
Sbjct: 402 KSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFD 461
Query: 1242 ADNHTV-FFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINAN 1418
A TV F GK ++ ++G +L++S+F+FS L+AL+ S++E++L+TA+VL++A+
Sbjct: 462 AKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLLSAD 521
Query: 1419 RPGLQEKRKVEQLQYNLELAFHHHLCKTHRQ------GILAKLPPKGKLRSLCSQHVEKL 1580
R G++ VE LQ L A + K H +L KLP LRSL + H E+L
Sbjct: 522 RSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLP---DLRSLNNMHSEEL 578
Query: 1581 QTFQHLHP 1604
F+ +HP
Sbjct: 579 LAFK-VHP 585
Score = 127 bits (320), Expect = 2e-29
Identities = 58/113 (51%), Positives = 78/113 (69%), Gaps = 1/113 (0%)
Frame = +3
Query: 150 AKKDGSPVGKAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAY- 326
+K V K+H V + V+ CK+CGD +SG HYGV CEGCKGFFRRS Q N+ Y
Sbjct: 86 SKSSAPGVTKSHSGVTKFSGMVLLCKVCGDVASGFHYGVHACEGCKGFFRRSIQQNIQYK 145
Query: 327 SCTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV 485
C + +NC I R +RNRCQ CR +KCL++GMSRDAV+FGR+ K+++ + E+
Sbjct: 146 KCLKNENCSIMRMNRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRMLIEM 198
>ref|NP_001071568.1| nuclear receptor subfamily 1 group D member 1 [Bos taurus].
Length = 613
Score = 125 bits (313), Expect = 2e-28
Identities = 61/124 (49%), Positives = 84/124 (67%), Gaps = 8/124 (6%)
Frame = +3
Query: 138 GPPP-----AKKDGSPVG--KAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFF 296
G PP A +D + V K+ ++ + V+ CK+CGD +SG HYGV CEGCKGFF
Sbjct: 98 GSPPGGLQVALEDSNRVSPSKSTSNITKLNGMVLLCKVCGDVASGFHYGVHACEGCKGFF 157
Query: 297 RRSQQCNVAYS-CTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSL 473
RRS Q N+ Y C + +NC I R +RNRCQ CR +KCL++GMSRDAV+FGR+ K+++ +
Sbjct: 158 RRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRM 217
Query: 474 HAEV 485
AE+
Sbjct: 218 LAEM 221
Score = 122 bits (307), Expect = 8e-28
Identities = 74/189 (39%), Positives = 115/189 (60%), Gaps = 8/189 (4%)
Frame = +3
Query: 1050 GYQRKSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMC 1229
G +++ E+WE + T A++ VVEFAK + GF +L Q+DQ+ LLKAG EV++VR
Sbjct: 425 GRSGRTVQEIWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFA 484
Query: 1230 RAYNADNHTVFFEGK--YGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALV 1403
+N + TV F + Y EL A+G +L++++FDFS L++L +E+E+ L+TA+V
Sbjct: 485 SLFNVKDQTVMFLSRTTYSLQEL-GAMGMGDLLNAMFDFSEKLNSLALTEEELGLFTAVV 543
Query: 1404 LINANRPGLQEKRKVEQLQYNL-----ELAFHHHLCKTHR-QGILAKLPPKGKLRSLCSQ 1565
L++A+R G++ VEQLQ L L + +T R +L KLP LR+L +
Sbjct: 544 LVSADRSGMENSASVEQLQETLLRALRALVLKNRPSETSRFTKLLLKLP---DLRTLNNM 600
Query: 1566 HVEKLQTFQ 1592
H EKL +F+
Sbjct: 601 HSEKLLSFR 609
>ref|NP_776827.1| COUP transcription factor 2 [Bos taurus].
Length = 414
Score = 123 bits (309), Expect = 5e-28
Identities = 63/136 (46%), Positives = 80/136 (58%), Gaps = 22/136 (16%)
Frame = +3
Query: 120 QLHPIPGPPP----------------------AKKDGSPVGKAHGSVMRTQIEVIPCKIC 233
Q P+PGPPP A G P G GS + Q + I C +C
Sbjct: 25 QAPPVPGPPPGAPHTPQTPGQGGPASTPAQTAAGGQGGPGGP--GSDKQQQQQHIECVVC 82
Query: 234 GDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQHCRLQKCLAL 413
GDKSSG HYG TCEGCK FF+RS + N++Y+C +NCPID+ RN+CQ+CRL+KCL +
Sbjct: 83 GDKSSGKHYGQFTCEGCKSFFKRSVRRNLSYTCRANRNCPIDQHHRNQCQYCRLKKCLKV 142
Query: 414 GMSRDAVKFGRMSKKQ 461
GM R+AV+ GRM Q
Sbjct: 143 GMRREAVQRGRMPPTQ 158
>ref|NP_001124228.1| retinoic acid receptor, gamma [Bos taurus].
Length = 458
Score = 117 bits (294), Expect = 2e-26
Identities = 50/81 (61%), Positives = 64/81 (79%)
Frame = +3
Query: 219 PCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQHCRLQ 398
PC +C DKSSG HYGV +CEGCKGFFRRS Q N+ Y+C R +NC I++ +RNRCQ+CRLQ
Sbjct: 89 PCFVCNDKSSGYHYGVSSCEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQ 148
Query: 399 KCLALGMSRDAVKFGRMSKKQ 461
KC +GMS++AV+ R KK+
Sbjct: 149 KCFEVGMSKEAVRNDRNKKKK 169
Score = 81.3 bits (199), Expect = 3e-15
Identities = 56/188 (29%), Positives = 93/188 (49%), Gaps = 8/188 (4%)
Frame = +3
Query: 921 YASLTEIEHLVQNVCKSYRDT----CQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWER 1088
Y ++E L+ V K++++T CQL ++ A ++ + +W++
Sbjct: 180 YELSPQLEELITKVSKAHQETFPSLCQL----------GKYTTNSSADHRVQLDLGLWDK 229
Query: 1089 CAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFE 1268
+ T+ I +VEFAKRL GF L DQI LLKA ++++++R+C Y + T+ F
Sbjct: 230 FSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFS 289
Query: 1269 GKYGGMELFRA----LGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQE 1436
G+ L R G L +F F+ L L + E L +A+ LI +R L+E
Sbjct: 290 ---DGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEE 346
Query: 1437 KRKVEQLQ 1460
KV++LQ
Sbjct: 347 PEKVDKLQ 354
Database: RefSeq49_BP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 17,681,374
Number of sequences in database: 33,088
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33088
Number of Hits to DB: 69,953,018
Number of extensions: 2078490
Number of successful extensions: 11692
Number of sequences better than 1.0e-05: 69
Number of HSP's gapped: 11556
Number of HSP's successfully gapped: 96
Length of query: 585
Length of database: 17,681,374
Length adjustment: 108
Effective length of query: 477
Effective length of database: 14,107,870
Effective search space: 6729453990
Effective search space used: 6729453990
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 36 (18.5 bits)
Search to RefSeqCP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-008862
(1757 letters)
Database: RefSeq49_CP.fasta
33,336 sequences; 18,874,504 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_540323.2| PREDICTED: similar to RAR-related orphan recept... 841 0.0
Alignment gi|XP_535503.2| PREDICTED: similar to RAR-related orphan recept... 447 e-125
Alignment gi|XP_541280.2| PREDICTED: similar to Nuclear receptor ROR-beta... 405 e-113
Alignment gi|XP_862760.1| PREDICTED: similar to Orphan nuclear receptor N... 129 9e-30
Alignment gi|XP_862737.1| PREDICTED: similar to nuclear receptor subfamil... 129 9e-30
Alignment gi|XP_542763.2| PREDICTED: similar to Orphan nuclear receptor N... 129 9e-30
Alignment gi|XP_862785.1| PREDICTED: similar to Orphan nuclear receptor N... 126 6e-29
Alignment gi|XP_543634.2| PREDICTED: similar to Retinoic acid receptor ga... 117 3e-26
Alignment gi|XP_849260.1| PREDICTED: similar to Retinoic acid receptor ga... 117 3e-26
Alignment gi|NP_001003093.1| peroxisome proliferator-activated receptor a... 117 3e-26
>ref|XP_540323.2| PREDICTED: similar to RAR-related orphan receptor C isoform a [Canis
familiaris].
Length = 518
Score = 841 bits (2173), Expect = 0.0
Identities = 416/495 (84%), Positives = 430/495 (86%)
Frame = +3
Query: 201 TQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC 380
+QIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNV YSCTRQQNCPIDRTSRNRC
Sbjct: 24 SQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVVYSCTRQQNCPIDRTSRNRC 83
Query: 381 QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGAQG 560
QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV +PPAG QG
Sbjct: 84 QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVQKQLQRQQQQQRGQVAKTPPAGGQG 143
Query: 561 ADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYSNSLVKAGLNGASYHLE 740
ADPLAC DLPEA+ACPPGLLRAP G SY +SL KAG + ASYHLE
Sbjct: 144 ADPLACPIGLPDGQLPLGSSPDLPEAAACPPGLLRAPGSGSSYPSSLAKAGPDRASYHLE 203
Query: 741 YSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGEPGRGPDSYCSPSFRSTPEAP 920
YSP+RGKAE FYGTGSQL+ +RC LHFED R PGL EPGRGPD+YCSPS S EA
Sbjct: 204 YSPQRGKAEASGGFYGTGSQLSLERCALHFEDARPPGLEEPGRGPDTYCSPSSHSALEAS 263
Query: 921 YASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWERCAHR 1100
YASL E EHLVQNVCKSYR+TCQLRLEDLLRQR NIFSREEVA YQRKSMWEMWERCAHR
Sbjct: 264 YASLMETEHLVQNVCKSYRETCQLRLEDLLRQRPNIFSREEVASYQRKSMWEMWERCAHR 323
Query: 1101 LTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGKYG 1280
LTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGKYG
Sbjct: 324 LTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGKYG 383
Query: 1281 GMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQLQ 1460
GMELFRALGCSELISSIFDFSRSLS+LRFSEDEIALYTALVLINANRPGLQEKRKVEQLQ
Sbjct: 384 GMELFRALGCSELISSIFDFSRSLSSLRFSEDEIALYTALVLINANRPGLQEKRKVEQLQ 443
Query: 1461 YNLELAFHHHLCKTHRQGILAKLPPKGKLRSLCSQHVEKLQTFQHLHPIVVQVAFPPLYK 1640
+NLE AFHHHL +THRQGILAKLPPKGKLRSLCSQHVEKL TFQHLHPIVVQ FPPLYK
Sbjct: 444 HNLEQAFHHHLYRTHRQGILAKLPPKGKLRSLCSQHVEKLHTFQHLHPIVVQATFPPLYK 503
Query: 1641 ELFSTEIESSDGLSE 1685
ELFSTEIES +GLSE
Sbjct: 504 ELFSTEIESPEGLSE 518
>ref|XP_535503.2| PREDICTED: similar to RAR-related orphan receptor A isoform d [Canis
familiaris].
Length = 497
Score = 447 bits (1150), Expect = e-125
Identities = 242/494 (48%), Positives = 318/494 (64%), Gaps = 7/494 (1%)
Frame = +3
Query: 204 QIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQ 383
QIE+IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N YSC RQ+NC IDRTSRNRCQ
Sbjct: 41 QIEIIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNATYSCPRQKNCLIDRTSRNRCQ 100
Query: 384 HCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGAQGA 563
HCRLQKCLA+GMSRDAVKFGRMSKKQRDSL+AEV A
Sbjct: 101 HCRLQKCLAVGMSRDAVKFGRMSKKQRDSLYAEVQKHRMQQQQRDHQQQPGE-------A 153
Query: 564 DPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYS---NSLVKAGLNGASYH 734
+PL P+Y+ N L + + ++Y
Sbjct: 154 EPLT-----------------------------------PTYNISANGLTELHEDLSNYI 178
Query: 735 LEYSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGE--PGRGPDSYCSPSFRST 908
++PE KA+ + + Q +PD+ GL + + + P G YCS F +
Sbjct: 179 DGHTPEGSKADSAVSSFYLDIQPSPDQSGLDINGIKPEPICDYTPASGFFPYCS--FTNG 236
Query: 909 PEAPYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWER 1088
+P S+ E+EHL QN+ KS+ +TCQ E+L + F +EE+ YQ K MW+
Sbjct: 237 ETSPTVSMAELEHLAQNISKSHLETCQYLREELQQITWQTFLQEEIESYQNKQREVMWQL 296
Query: 1089 CAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFE 1268
CA ++TEAIQYVVEFAKR+ GFMELCQNDQIVLLKAG++EVV +RMCRA+++ N+TV+F+
Sbjct: 297 CAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYFD 356
Query: 1269 GKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKV 1448
GKY ++F++LGC + IS +F+F +SL ++ +EDEIAL++A VL++A+R LQEK K+
Sbjct: 357 GKYASPDVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKI 416
Query: 1449 EQLQYNLELAFHHHLCKTHRQ-GILAKLPPK-GKLRSLCSQHVEKLQTFQHLHPIVVQVA 1622
E+LQ ++LA H L K HR+ GIL KL K LR+LC +H EKL F+ ++P +V++
Sbjct: 417 EKLQQKIQLALQHVLQKNHREDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRLH 476
Query: 1623 FPPLYKELFSTEIE 1664
FPPLYKELF++E E
Sbjct: 477 FPPLYKELFTSEFE 490
>ref|XP_541280.2| PREDICTED: similar to Nuclear receptor ROR-beta (Nuclear receptor
RZR-beta) [Canis familiaris].
Length = 459
Score = 405 bits (1042), Expect = e-113
Identities = 231/499 (46%), Positives = 305/499 (61%), Gaps = 11/499 (2%)
Frame = +3
Query: 195 MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRN 374
MR QIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N +YSC RQ+NC IDRT+RN
Sbjct: 1 MRAQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNASYSCPRQRNCLIDRTNRN 60
Query: 375 RCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGA 554
RCQHCRLQKCLALGMSRDAVKFGRMSKKQR
Sbjct: 61 RCQHCRLQKCLALGMSRDAVKFGRMSKKQR------------------------------ 90
Query: 555 QGADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYSNSLVKAGLNG---A 725
D L EA A A G SN L GL+G
Sbjct: 91 ---DSLYAEVQKHQQRLQEQRQQQSGEAEAL------ARVYGGGISNGL--GGLHGEAGG 139
Query: 726 SYHLEYSPERGKAEGRENFYGTGSQLAPDRCGLHF---EDPRHPGLGEPGRGPDSYCSPS 896
+Y + + K+EG N Q +PD+ GL + + + + P+ + S
Sbjct: 140 TYANGHVIDLPKSEGYYNV--DSGQPSPDQSGLDMTGIKQIKQEPIYDLTSVPNLFTYSS 197
Query: 897 FRSTPEAPYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWE 1076
F + AP ++ EI+ + QN+ KS+ +TCQ +E+L + + EE+ YQ KS
Sbjct: 198 FNNGQLAPGITMGEIDRIAQNIIKSHLETCQYTMEELHQLAWQTHTYEEIKAYQSKSREA 257
Query: 1077 MWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHT 1256
+W++CA ++T AIQYVVEFAKR++GFMELCQNDQI+LLK+G +EVVLVRMCRA+N N+T
Sbjct: 258 LWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNT 317
Query: 1257 VFFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQE 1436
V FEGKYGGM++F+ALG +L++ FDF+++L +L+ +E+EIAL+++ VLI+ +R L E
Sbjct: 318 VLFEGKYGGMQMFKALGSDDLVNEAFDFAKNLCSLQLTEEEIALFSSAVLISPDRAWLIE 377
Query: 1437 KRKVEQLQYNLELAFHHHLCKTHRQG-----ILAKLPPKGKLRSLCSQHVEKLQTFQHLH 1601
RKV++LQ + A H + K H ++AK+P + ++C+ H EKLQ F+ H
Sbjct: 378 PRKVQKLQEKIYFALQHVIQKNHLDDETLAKLIAKIP---TITAVCNLHGEKLQVFKQSH 434
Query: 1602 PIVVQVAFPPLYKELFSTE 1658
P +V FPPLYKELF+ +
Sbjct: 435 PDIVNTLFPPLYKELFNPD 453
>ref|XP_862760.1| PREDICTED: similar to Orphan nuclear receptor NR1D2 (Rev-erb-beta)
(EAR-1R) (Orphan nuclear hormone receptor BD73) isoform 3
[Canis familiaris].
Length = 522
Score = 129 bits (324), Expect = 9e-30
Identities = 76/188 (40%), Positives = 116/188 (61%), Gaps = 7/188 (3%)
Frame = +3
Query: 1062 KSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYN 1241
KS E+WE + T A++ VVEFAKR+ GF +L Q+DQ+ LLKAG EV++VR ++
Sbjct: 339 KSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFD 398
Query: 1242 ADNHTV-FFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINAN 1418
A TV F GK ++ ++G +L++S+F+FS L+AL+ S++E++L+TA+VL++A+
Sbjct: 399 AKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSAD 458
Query: 1419 RPGLQEKRKVEQLQYNLELAFHHHLCKTHRQ------GILAKLPPKGKLRSLCSQHVEKL 1580
R G++ VE LQ L A + K H +L KLP LRSL + H E+L
Sbjct: 459 RSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLP---DLRSLNNMHSEEL 515
Query: 1581 QTFQHLHP 1604
F+ +HP
Sbjct: 516 LAFK-VHP 522
Score = 126 bits (317), Expect = 6e-29
Identities = 57/113 (50%), Positives = 78/113 (69%), Gaps = 1/113 (0%)
Frame = +3
Query: 150 AKKDGSPVGKAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYS 329
+K + K+H V + V+ CK+CGD +SG HYGV CEGCKGFFRRS Q N+ Y
Sbjct: 79 SKSSAPGMTKSHSGVTKFSGMVLLCKVCGDVASGFHYGVHACEGCKGFFRRSIQQNIQYK 138
Query: 330 -CTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV 485
C + +NC I R +RNRCQ CR +KCL++GMSRDAV+FGR+ K+++ + E+
Sbjct: 139 KCLKNENCSIMRMNRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRMLIEM 191
>ref|XP_862737.1| PREDICTED: similar to nuclear receptor subfamily 1, group D, member 2
isoform 2 [Canis familiaris].
Length = 498
Score = 129 bits (324), Expect = 9e-30
Identities = 76/188 (40%), Positives = 116/188 (61%), Gaps = 7/188 (3%)
Frame = +3
Query: 1062 KSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYN 1241
KS E+WE + T A++ VVEFAKR+ GF +L Q+DQ+ LLKAG EV++VR ++
Sbjct: 315 KSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFD 374
Query: 1242 ADNHTV-FFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINAN 1418
A TV F GK ++ ++G +L++S+F+FS L+AL+ S++E++L+TA+VL++A+
Sbjct: 375 AKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSAD 434
Query: 1419 RPGLQEKRKVEQLQYNLELAFHHHLCKTHRQ------GILAKLPPKGKLRSLCSQHVEKL 1580
R G++ VE LQ L A + K H +L KLP LRSL + H E+L
Sbjct: 435 RSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLP---DLRSLNNMHSEEL 491
Query: 1581 QTFQHLHP 1604
F+ +HP
Sbjct: 492 LAFK-VHP 498
Score = 126 bits (317), Expect = 6e-29
Identities = 57/113 (50%), Positives = 78/113 (69%), Gaps = 1/113 (0%)
Frame = +3
Query: 150 AKKDGSPVGKAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYS 329
+K + K+H V + V+ CK+CGD +SG HYGV CEGCKGFFRRS Q N+ Y
Sbjct: 79 SKSSAPGMTKSHSGVTKFSGMVLLCKVCGDVASGFHYGVHACEGCKGFFRRSIQQNIQYK 138
Query: 330 -CTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV 485
C + +NC I R +RNRCQ CR +KCL++GMSRDAV+FGR+ K+++ + E+
Sbjct: 139 KCLKNENCSIMRMNRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRMLIEM 191
>ref|XP_542763.2| PREDICTED: similar to Orphan nuclear receptor NR1D2 (Rev-erb-beta)
(EAR-1R) (Orphan nuclear hormone receptor BD73) isoform 1
[Canis familiaris].
Length = 576
Score = 129 bits (324), Expect = 9e-30
Identities = 76/188 (40%), Positives = 116/188 (61%), Gaps = 7/188 (3%)
Frame = +3
Query: 1062 KSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYN 1241
KS E+WE + T A++ VVEFAKR+ GF +L Q+DQ+ LLKAG EV++VR ++
Sbjct: 393 KSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFD 452
Query: 1242 ADNHTV-FFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINAN 1418
A TV F GK ++ ++G +L++S+F+FS L+AL+ S++E++L+TA+VL++A+
Sbjct: 453 AKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSAD 512
Query: 1419 RPGLQEKRKVEQLQYNLELAFHHHLCKTHRQ------GILAKLPPKGKLRSLCSQHVEKL 1580
R G++ VE LQ L A + K H +L KLP LRSL + H E+L
Sbjct: 513 RSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLP---DLRSLNNMHSEEL 569
Query: 1581 QTFQHLHP 1604
F+ +HP
Sbjct: 570 LAFK-VHP 576
Score = 126 bits (317), Expect = 6e-29
Identities = 57/113 (50%), Positives = 78/113 (69%), Gaps = 1/113 (0%)
Frame = +3
Query: 150 AKKDGSPVGKAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYS 329
+K + K+H V + V+ CK+CGD +SG HYGV CEGCKGFFRRS Q N+ Y
Sbjct: 79 SKSSAPGMTKSHSGVTKFSGMVLLCKVCGDVASGFHYGVHACEGCKGFFRRSIQQNIQYK 138
Query: 330 -CTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV 485
C + +NC I R +RNRCQ CR +KCL++GMSRDAV+FGR+ K+++ + E+
Sbjct: 139 KCLKNENCSIMRMNRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRMLIEM 191
>ref|XP_862785.1| PREDICTED: similar to Orphan nuclear receptor NR1D2 (Rev-erb-beta)
(EAR-1R) (Orphan nuclear hormone receptor BD73) isoform
4 [Canis familiaris].
Length = 405
Score = 126 bits (317), Expect = 6e-29
Identities = 57/113 (50%), Positives = 78/113 (69%), Gaps = 1/113 (0%)
Frame = +3
Query: 150 AKKDGSPVGKAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYS 329
+K + K+H V + V+ CK+CGD +SG HYGV CEGCKGFFRRS Q N+ Y
Sbjct: 79 SKSSAPGMTKSHSGVTKFSGMVLLCKVCGDVASGFHYGVHACEGCKGFFRRSIQQNIQYK 138
Query: 330 -CTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV 485
C + +NC I R +RNRCQ CR +KCL++GMSRDAV+FGR+ K+++ + E+
Sbjct: 139 KCLKNENCSIMRMNRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRMLIEM 191
>ref|XP_543634.2| PREDICTED: similar to Retinoic acid receptor gamma-B (RAR-gamma-B)
isoform 1 [Canis familiaris].
Length = 447
Score = 117 bits (294), Expect = 3e-26
Identities = 50/81 (61%), Positives = 64/81 (79%)
Frame = +3
Query: 219 PCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQHCRLQ 398
PC +C DKSSG HYGV +CEGCKGFFRRS Q N+ Y+C R +NC I++ +RNRCQ+CRLQ
Sbjct: 78 PCFVCNDKSSGYHYGVSSCEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQ 137
Query: 399 KCLALGMSRDAVKFGRMSKKQ 461
KC +GMS++AV+ R KK+
Sbjct: 138 KCFEVGMSKEAVRNDRNKKKK 158
Score = 81.3 bits (199), Expect = 3e-15
Identities = 56/188 (29%), Positives = 93/188 (49%), Gaps = 8/188 (4%)
Frame = +3
Query: 921 YASLTEIEHLVQNVCKSYRDT----CQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWER 1088
Y ++E L+ V K++++T CQL ++ A ++ + +W++
Sbjct: 169 YELSPQLEELITKVSKAHQETFPSLCQL----------GKYTTNSSADHRVQLDLGLWDK 218
Query: 1089 CAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFE 1268
+ T+ I +VEFAKRL GF L DQI LLKA ++++++R+C Y + T+ F
Sbjct: 219 FSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFS 278
Query: 1269 GKYGGMELFRA----LGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQE 1436
G+ L R G L +F F+ L L + E L +A+ LI +R L+E
Sbjct: 279 ---DGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEE 335
Query: 1437 KRKVEQLQ 1460
KV++LQ
Sbjct: 336 PEKVDKLQ 343
>ref|XP_849260.1| PREDICTED: similar to Retinoic acid receptor gamma-A (RAR-gamma-A)
isoform 2 [Canis familiaris].
Length = 478
Score = 117 bits (294), Expect = 3e-26
Identities = 50/81 (61%), Positives = 64/81 (79%)
Frame = +3
Query: 219 PCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQHCRLQ 398
PC +C DKSSG HYGV +CEGCKGFFRRS Q N+ Y+C R +NC I++ +RNRCQ+CRLQ
Sbjct: 109 PCFVCNDKSSGYHYGVSSCEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQ 168
Query: 399 KCLALGMSRDAVKFGRMSKKQ 461
KC +GMS++AV+ R KK+
Sbjct: 169 KCFEVGMSKEAVRNDRNKKKK 189
Score = 81.3 bits (199), Expect = 3e-15
Identities = 56/188 (29%), Positives = 93/188 (49%), Gaps = 8/188 (4%)
Frame = +3
Query: 921 YASLTEIEHLVQNVCKSYRDT----CQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWER 1088
Y ++E L+ V K++++T CQL ++ A ++ + +W++
Sbjct: 200 YELSPQLEELITKVSKAHQETFPSLCQL----------GKYTTNSSADHRVQLDLGLWDK 249
Query: 1089 CAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFE 1268
+ T+ I +VEFAKRL GF L DQI LLKA ++++++R+C Y + T+ F
Sbjct: 250 FSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFS 309
Query: 1269 GKYGGMELFRA----LGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQE 1436
G+ L R G L +F F+ L L + E L +A+ LI +R L+E
Sbjct: 310 ---DGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEE 366
Query: 1437 KRKVEQLQ 1460
KV++LQ
Sbjct: 367 PEKVDKLQ 374
>ref|NP_001003093.1| peroxisome proliferator-activated receptor alpha [Canis lupus
familiaris].
Length = 468
Score = 117 bits (294), Expect = 3e-26
Identities = 56/122 (45%), Positives = 78/122 (63%), Gaps = 1/122 (0%)
Frame = +3
Query: 123 LHPIPGPPPAKKDGSPVGKAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRR 302
L P P P +P G S + IE C+ICGD++SG HYGV CEGCKGFFRR
Sbjct: 72 LSPAPSPSSVTHPAAPGGAEEPSSVALNIE---CRICGDRASGYHYGVHACEGCKGFFRR 128
Query: 303 SQQCNVAY-SCTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHA 479
+ + +AY C R +C I + +RN+CQ+CR KCL++GMS +A++FGRM + ++ L A
Sbjct: 129 TIRLKLAYDKCDR--SCKIQKKNRNKCQYCRFHKCLSVGMSHNAIRFGRMPRSEKAKLKA 186
Query: 480 EV 485
E+
Sbjct: 187 EI 188
Score = 77.8 bits (190), Expect = 3e-14
Identities = 54/220 (24%), Positives = 95/220 (43%), Gaps = 12/220 (5%)
Frame = +3
Query: 996 LEDLLRQRSNIFSREEVAGYQRKSMW-EMWERCAHRLTEAIQYVVEFAKRLSGFMELCQN 1172
+E L + ++ G Q K ++ C E + + EFAK + GF L N
Sbjct: 244 METLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKSIPGFANLDLN 303
Query: 1173 DQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGKYGGMELFRALG--CSELISSIFDFSR 1346
DQ+ LLK G E + + N D V + + E ++L +++ FDF+
Sbjct: 304 DQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAM 363
Query: 1347 SLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQGIL-- 1520
+AL + +I+L+ A ++ +RPGL +E++Q + HL H I
Sbjct: 364 KFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLKLHLQTNHPDNIFLF 423
Query: 1521 -AKLPPKGKLRSLCSQHVEKLQTFQH------LHPIVVQV 1619
L LR L ++H + +Q + LHP++ ++
Sbjct: 424 PKLLQKMADLRQLVTEHAQLVQVIKKTESDAALHPLLQEI 463
Database: RefSeq49_CP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,874,504
Number of sequences in database: 33,336
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33336
Number of Hits to DB: 72,796,926
Number of extensions: 2132778
Number of successful extensions: 12239
Number of sequences better than 1.0e-05: 152
Number of HSP's gapped: 12064
Number of HSP's successfully gapped: 201
Length of query: 585
Length of database: 18,874,504
Length adjustment: 108
Effective length of query: 477
Effective length of database: 15,274,216
Effective search space: 7285801032
Effective search space used: 7285801032
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 36 (18.5 bits)
Search to RefSeqSP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-008862
(1757 letters)
Database: RefSeq49_SP.fasta
24,897 sequences; 11,343,932 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_003355219.1| PREDICTED: nuclear receptor ROR-gamma isofor... 944 0.0
Alignment gi|XP_003355220.1| PREDICTED: nuclear receptor ROR-gamma isofor... 939 0.0
Alignment gi|XP_001928189.3| PREDICTED: nuclear receptor ROR-alpha [Sus s... 450 e-126
Alignment gi|XP_001929656.2| PREDICTED: nuclear receptor ROR-gamma-like [... 174 1e-43
Alignment gi|XP_003358388.1| PREDICTED: nuclear receptor subfamily 1 grou... 129 5e-30
Alignment gi|NP_001177181.1| COUP transcription factor 2 isoform 1 [Sus s... 122 8e-28
Alignment gi|XP_001924421.2| PREDICTED: retinoic acid receptor gamma [Sus... 117 2e-26
Alignment gi|XP_001926863.2| PREDICTED: retinoic acid receptor beta isofo... 116 3e-26
Alignment gi|XP_003123832.1| PREDICTED: COUP transcription factor 1-like ... 115 6e-26
Alignment gi|XP_003354261.1| PREDICTED: COUP transcription factor 1-like ... 115 6e-26
>ref|XP_003355219.1| PREDICTED: nuclear receptor ROR-gamma isoform 1 [Sus scrofa].
Length = 497
Score = 944 bits (2441), Expect = 0.0
Identities = 464/497 (93%), Positives = 464/497 (93%)
Frame = +3
Query: 195 MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRN 374
MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRN
Sbjct: 1 MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRN 60
Query: 375 RCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGA 554
RCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV SPPAGA
Sbjct: 61 RCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVQKQLQQRQQQQREQAAKSPPAGA 120
Query: 555 QGADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYSNSLVKAGLNGASYH 734
QGADPLAC DLPEASACPPGLLRAPSCGPSYSNSLVKAGLNGASYH
Sbjct: 121 QGADPLACPLGLPDGQLPLGSSPDLPEASACPPGLLRAPSCGPSYSNSLVKAGLNGASYH 180
Query: 735 LEYSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGEPGRGPDSYCSPSFRSTPE 914
LEYSPERGKAEGRENFYGTGSQLAPDRCGL FEDPRHPGLGEPGRGPDSYCSPSFRSTPE
Sbjct: 181 LEYSPERGKAEGRENFYGTGSQLAPDRCGLRFEDPRHPGLGEPGRGPDSYCSPSFRSTPE 240
Query: 915 APYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWERCA 1094
APYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWERCA
Sbjct: 241 APYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWERCA 300
Query: 1095 HRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGK 1274
HRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGK
Sbjct: 301 HRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGK 360
Query: 1275 YGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQ 1454
YGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQ
Sbjct: 361 YGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQ 420
Query: 1455 LQYNLELAFHHHLCKTHRQGILAKLPPKGKLRSLCSQHVEKLQTFQHLHPIVVQVAFPPL 1634
LQYNLELAFHHHLCKTHRQGILAKLPPKGKLRSLCSQHVEKLQTFQHLHPIVVQVAFPPL
Sbjct: 421 LQYNLELAFHHHLCKTHRQGILAKLPPKGKLRSLCSQHVEKLQTFQHLHPIVVQVAFPPL 480
Query: 1635 YKELFSTEIESSDGLSE 1685
YKELFSTEIESSDGLSE
Sbjct: 481 YKELFSTEIESSDGLSE 497
>ref|XP_003355220.1| PREDICTED: nuclear receptor ROR-gamma isoform 2 [Sus scrofa].
Length = 518
Score = 939 bits (2427), Expect = 0.0
Identities = 461/495 (93%), Positives = 462/495 (93%)
Frame = +3
Query: 201 TQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC 380
+QIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC
Sbjct: 24 SQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC 83
Query: 381 QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGAQG 560
QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV SPPAGAQG
Sbjct: 84 QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVQKQLQQRQQQQREQAAKSPPAGAQG 143
Query: 561 ADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYSNSLVKAGLNGASYHLE 740
ADPLAC DLPEASACPPGLLRAPSCGPSYSNSLVKAGLNGASYHLE
Sbjct: 144 ADPLACPLGLPDGQLPLGSSPDLPEASACPPGLLRAPSCGPSYSNSLVKAGLNGASYHLE 203
Query: 741 YSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGEPGRGPDSYCSPSFRSTPEAP 920
YSPERGKAEGRENFYGTGSQLAPDRCGL FEDPRHPGLGEPGRGPDSYCSPSFRSTPEAP
Sbjct: 204 YSPERGKAEGRENFYGTGSQLAPDRCGLRFEDPRHPGLGEPGRGPDSYCSPSFRSTPEAP 263
Query: 921 YASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWERCAHR 1100
YASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWERCAHR
Sbjct: 264 YASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWERCAHR 323
Query: 1101 LTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGKYG 1280
LTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGKYG
Sbjct: 324 LTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGKYG 383
Query: 1281 GMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQLQ 1460
GMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQLQ
Sbjct: 384 GMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQLQ 443
Query: 1461 YNLELAFHHHLCKTHRQGILAKLPPKGKLRSLCSQHVEKLQTFQHLHPIVVQVAFPPLYK 1640
YNLELAFHHHLCKTHRQGILAKLPPKGKLRSLCSQHVEKLQTFQHLHPIVVQVAFPPLYK
Sbjct: 444 YNLELAFHHHLCKTHRQGILAKLPPKGKLRSLCSQHVEKLQTFQHLHPIVVQVAFPPLYK 503
Query: 1641 ELFSTEIESSDGLSE 1685
ELFSTEIESSDGLSE
Sbjct: 504 ELFSTEIESSDGLSE 518
>ref|XP_001928189.3| PREDICTED: nuclear receptor ROR-alpha [Sus scrofa].
Length = 468
Score = 450 bits (1157), Expect = e-126
Identities = 243/499 (48%), Positives = 321/499 (64%), Gaps = 7/499 (1%)
Frame = +3
Query: 189 SVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTS 368
+ M+ QIE+IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N YSC RQ+NC IDRTS
Sbjct: 7 AAMKAQIEIIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNATYSCPRQKNCLIDRTS 66
Query: 369 RNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPA 548
RNRCQHCRLQKCLA+GMSRDAVKFGRMSKKQRDSL+AEV
Sbjct: 67 RNRCQHCRLQKCLAVGMSRDAVKFGRMSKKQRDSLYAEVQKHRMQQQQRDHQQQPGE--- 123
Query: 549 GAQGADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYS---NSLVKAGLN 719
A+PL P+Y+ N L + +
Sbjct: 124 ----AEPLT-----------------------------------PTYNISANGLTELHDD 144
Query: 720 GASYHLEYSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGE--PGRGPDSYCSP 893
++Y ++PE KA+ + + Q +PD+ GL + + + P G YCS
Sbjct: 145 LSNYIDGHTPEGSKADSAVSSFYLDIQPSPDQSGLDINGIKPEPICDYTPASGFFPYCS- 203
Query: 894 SFRSTPEAPYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMW 1073
F + +P S+ E+EHL QN+ KS+ +TCQ E+L + F +EE+ YQ K
Sbjct: 204 -FTNGETSPTVSMAELEHLAQNISKSHLETCQYLREELQQITWQTFLQEEIENYQNKQRE 262
Query: 1074 EMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNH 1253
MW+ CA ++TEAIQYVVEFAKR+ GFMELCQNDQIVLLKAG++EVV +RMCRA+++ N+
Sbjct: 263 VMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNN 322
Query: 1254 TVFFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQ 1433
TV+F+GKY ++F++LGC + IS +F+F +SL ++ +EDEIAL++A VL++A+R LQ
Sbjct: 323 TVYFDGKYASPDVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQ 382
Query: 1434 EKRKVEQLQYNLELAFHHHLCKTHRQ-GILAKLPPK-GKLRSLCSQHVEKLQTFQHLHPI 1607
EK K+E+LQ ++LA H L K HR+ GIL KL K LR+LC +H EKL F+ ++P
Sbjct: 383 EKVKIEKLQQKIQLALQHVLQKNHREDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPD 442
Query: 1608 VVQVAFPPLYKELFSTEIE 1664
+V++ FPPLYKELF++E E
Sbjct: 443 IVRLHFPPLYKELFTSEFE 461
>ref|XP_001929656.2| PREDICTED: nuclear receptor ROR-gamma-like [Sus scrofa].
Length = 156
Score = 174 bits (441), Expect = 1e-43
Identities = 78/81 (96%), Positives = 80/81 (98%)
Frame = +3
Query: 195 MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRN 374
MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRN
Sbjct: 1 MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRN 60
Query: 375 RCQHCRLQKCLALGMSRDAVK 437
RCQHCRLQKCLALGMSRD ++
Sbjct: 61 RCQHCRLQKCLALGMSRDGLR 81
>ref|XP_003358388.1| PREDICTED: nuclear receptor subfamily 1 group D member 2 [Sus
scrofa].
Length = 496
Score = 129 bits (324), Expect = 5e-30
Identities = 76/188 (40%), Positives = 116/188 (61%), Gaps = 7/188 (3%)
Frame = +3
Query: 1062 KSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYN 1241
KS E+WE + T A++ VVEFAKR+ GF +L Q+DQ+ LLKAG EV++VR ++
Sbjct: 313 KSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFD 372
Query: 1242 ADNHTV-FFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINAN 1418
A TV F GK ++ ++G +L++S+F+FS L+AL+ S++E++L+TA+VL++A+
Sbjct: 373 AKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSAD 432
Query: 1419 RPGLQEKRKVEQLQYNLELAFHHHLCKTHRQ------GILAKLPPKGKLRSLCSQHVEKL 1580
R G++ VE LQ L A + K H +L KLP LRSL + H E+L
Sbjct: 433 RSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLP---DLRSLNNMHSEEL 489
Query: 1581 QTFQHLHP 1604
F+ +HP
Sbjct: 490 LAFK-VHP 496
Score = 80.9 bits (198), Expect = 2e-15
Identities = 36/67 (53%), Positives = 50/67 (74%), Gaps = 1/67 (1%)
Frame = +3
Query: 288 GFFRRSQQCNVAYS-CTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQR 464
GFFRRS Q N+ Y C + +NC I R +RNRCQ CR +KCL++GMSRDAV+FGR+ K+++
Sbjct: 43 GFFRRSIQQNIQYKKCLKNENCSIMRMNRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREK 102
Query: 465 DSLHAEV 485
+ E+
Sbjct: 103 QRMLIEM 109
>ref|NP_001177181.1| COUP transcription factor 2 isoform 1 [Sus scrofa].
Length = 414
Score = 122 bits (305), Expect = 8e-28
Identities = 62/136 (45%), Positives = 79/136 (58%), Gaps = 22/136 (16%)
Frame = +3
Query: 120 QLHPIPGPPP----------------------AKKDGSPVGKAHGSVMRTQIEVIPCKIC 233
Q P+PGPPP A G P G G + Q + I C +C
Sbjct: 25 QAPPVPGPPPGAPHTPQTPGQGGPASTPAQTAAGGQGGPGGP--GGDKQQQQQHIECVVC 82
Query: 234 GDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQHCRLQKCLAL 413
GDKSSG HYG TCEGCK FF+RS + N++Y+C +NCPID+ RN+CQ+CRL+KCL +
Sbjct: 83 GDKSSGKHYGQFTCEGCKSFFKRSVRRNLSYTCRANRNCPIDQHHRNQCQYCRLKKCLKV 142
Query: 414 GMSRDAVKFGRMSKKQ 461
GM R+AV+ GRM Q
Sbjct: 143 GMRREAVQRGRMPPTQ 158
>ref|XP_001924421.2| PREDICTED: retinoic acid receptor gamma [Sus scrofa].
Length = 429
Score = 117 bits (294), Expect = 2e-26
Identities = 50/81 (61%), Positives = 64/81 (79%)
Frame = +3
Query: 219 PCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQHCRLQ 398
PC +C DKSSG HYGV +CEGCKGFFRRS Q N+ Y+C R +NC I++ +RNRCQ+CRLQ
Sbjct: 60 PCFVCNDKSSGYHYGVSSCEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQ 119
Query: 399 KCLALGMSRDAVKFGRMSKKQ 461
KC +GMS++AV+ R KK+
Sbjct: 120 KCFEVGMSKEAVRNDRNKKKK 140
Score = 81.3 bits (199), Expect = 2e-15
Identities = 56/188 (29%), Positives = 93/188 (49%), Gaps = 8/188 (4%)
Frame = +3
Query: 921 YASLTEIEHLVQNVCKSYRDT----CQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWER 1088
Y ++E L+ V K++++T CQL ++ A ++ + +W++
Sbjct: 151 YELSPQLEELITKVSKAHQETFPSLCQL----------GKYTTNSSADHRVQLDLGLWDK 200
Query: 1089 CAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFE 1268
+ T+ I +VEFAKRL GF L DQI LLKA ++++++R+C Y + T+ F
Sbjct: 201 FSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFS 260
Query: 1269 GKYGGMELFRA----LGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQE 1436
G+ L R G L +F F+ L L + E L +A+ LI +R L+E
Sbjct: 261 ---DGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEE 317
Query: 1437 KRKVEQLQ 1460
KV++LQ
Sbjct: 318 PEKVDKLQ 325
>ref|XP_001926863.2| PREDICTED: retinoic acid receptor beta isoform 1 [Sus scrofa].
Length = 448
Score = 116 bits (291), Expect = 3e-26
Identities = 50/84 (59%), Positives = 64/84 (76%)
Frame = +3
Query: 219 PCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQHCRLQ 398
PC +C DKSSG HYGV CEGCKGFFRRS Q N+ Y+C R +NC I++ +RNRCQ+CRLQ
Sbjct: 80 PCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMIYTCHRDKNCVINKVTRNRCQYCRLQ 139
Query: 399 KCLALGMSRDAVKFGRMSKKQRDS 470
KC +GMS+++V+ R KK+ S
Sbjct: 140 KCFEVGMSKESVRNDRNKKKKEPS 163
Score = 87.8 bits (216), Expect = 2e-17
Identities = 77/276 (27%), Positives = 134/276 (48%), Gaps = 14/276 (5%)
Frame = +3
Query: 891 PSFRSTPEAPYASLTEIEHLVQNVCKSYRDT----CQLRLEDLLRQRSNIFSREEVAGYQ 1058
PS + E+ Y E++ L + + K++++T CQL ++ A ++
Sbjct: 162 PSKQECTES-YEMTAELDDLTEKIRKAHQETFPSLCQL----------GKYTTNSSADHR 210
Query: 1059 RKSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAY 1238
+ +W++ + T+ I +VEFAKRL GF L DQI LLKA ++++++R+C Y
Sbjct: 211 VRLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRY 270
Query: 1239 NADNHTVFFEGKYGGMELFRA----LGCSELISSIFDFSRSLSALRFSEDEIALYTALVL 1406
+ T+ F G+ L R G L +F F+ L L + E L +A+ L
Sbjct: 271 TPEQDTMTFS---DGLTLNRTQMHNAGFGPLTDLVFTFASQLLPLEMDDTETGLLSAICL 327
Query: 1407 INANRPGLQEKRKVEQLQYNLELAFHHHL-----CKTHR-QGILAKLPPKGKLRSLCSQH 1568
I +R L+E KV++LQ L A ++ K H IL K+ LRS+ ++
Sbjct: 328 ICGDRQDLEEPTKVDKLQEPLLEALKIYIRRRRPSKPHMFPKILMKIT---DLRSISAKG 384
Query: 1569 VEKLQTFQHLHPIVVQVAFPPLYKELFSTEIESSDG 1676
E++ T + + + + PPL +E+ +E+S+G
Sbjct: 385 AERVITLK----MEIPGSMPPLIQEM----LENSEG 412
>ref|XP_003123832.1| PREDICTED: COUP transcription factor 1-like isoform 1 [Sus scrofa].
Length = 422
Score = 115 bits (289), Expect = 6e-26
Identities = 54/109 (49%), Positives = 71/109 (65%)
Frame = +3
Query: 135 PGPPPAKKDGSPVGKAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQC 314
PG P G+ ++Q + I C +CGDKSSG HYG TCEGCK FF+RS +
Sbjct: 57 PGAPATPGTAGDKGQGPPGSGQSQ-QHIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRR 115
Query: 315 NVAYSCTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQ 461
N+ Y+C +NCPID+ RN+CQ+CRL+KCL +GM R+AV+ GRM Q
Sbjct: 116 NLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGRMPPTQ 164
>ref|XP_003354261.1| PREDICTED: COUP transcription factor 1-like isoform 1 [Sus scrofa].
Length = 422
Score = 115 bits (289), Expect = 6e-26
Identities = 54/109 (49%), Positives = 71/109 (65%)
Frame = +3
Query: 135 PGPPPAKKDGSPVGKAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQC 314
PG P G+ ++Q + I C +CGDKSSG HYG TCEGCK FF+RS +
Sbjct: 57 PGAPATPGTAGDKGQGPPGSGQSQ-QHIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRR 115
Query: 315 NVAYSCTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQ 461
N+ Y+C +NCPID+ RN+CQ+CRL+KCL +GM R+AV+ GRM Q
Sbjct: 116 NLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGRMPPTQ 164
Database: RefSeq49_SP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 11,343,932
Number of sequences in database: 24,897
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24897
Number of Hits to DB: 45,217,407
Number of extensions: 1345155
Number of successful extensions: 7346
Number of sequences better than 1.0e-05: 51
Number of HSP's gapped: 7280
Number of HSP's successfully gapped: 73
Length of query: 585
Length of database: 11,343,932
Length adjustment: 104
Effective length of query: 481
Effective length of database: 8,754,644
Effective search space: 4210983764
Effective search space used: 4210983764
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)
Search to RefSeqMP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-008862
(1757 letters)
Database: RefSeq49_MP.fasta
30,036 sequences; 15,617,559 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_035411.2| nuclear receptor ROR-gamma [Mus musculus]. 815 0.0
Alignment gi|NP_038674.1| nuclear receptor ROR-alpha [Mus musculus]. 447 e-126
Alignment gi|NP_001036819.1| nuclear receptor ROR-beta isoform 1 [Mus mus... 407 e-113
Alignment gi|NP_666207.3| nuclear receptor ROR-beta isoform 2 [Mus muscul... 405 e-113
Alignment gi|NP_663409.2| nuclear receptor subfamily 1 group D member 1 [... 225 1e-58
Alignment gi|NP_035714.3| nuclear receptor subfamily 1 group D member 2 [... 130 2e-30
Alignment gi|NP_033827.2| COUP transcription factor 2 isoform 1 [Mus musc... 123 4e-28
Alignment gi|NP_001036192.1| retinoic acid receptor gamma isoform 2 [Mus ... 117 2e-26
Alignment gi|NP_035374.3| retinoic acid receptor gamma isoform 1 [Mus mus... 117 2e-26
Alignment gi|NP_035373.1| retinoic acid receptor beta [Mus musculus]. 116 5e-26
>ref|NP_035411.2| nuclear receptor ROR-gamma [Mus musculus].
Length = 516
Score = 815 bits (2104), Expect = 0.0
Identities = 400/495 (80%), Positives = 426/495 (86%)
Frame = +3
Query: 201 TQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC 380
+QIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC
Sbjct: 24 SQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC 83
Query: 381 QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGAQG 560
QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV +PPAG++G
Sbjct: 84 QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVQKQLQQQQQQEQVAK--TPPAGSRG 141
Query: 561 ADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYSNSLVKAGLNGASYHLE 740
AD L DLPEASACPPGLLRA GP YSN+L K + GAS HLE
Sbjct: 142 ADTLTYTLGLSDGQLPLGASPDLPEASACPPGLLRASGSGPPYSNTLAKTEVQGASCHLE 201
Query: 741 YSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGEPGRGPDSYCSPSFRSTPEAP 920
YSPERGKAEGR++ Y T QL RCGL FE+ RHP LGEP +GPDS+C PSF S PE P
Sbjct: 202 YSPERGKAEGRDSIYSTDGQLTLGRCGLRFEETRHPELGEPEQGPDSHCIPSFCSAPEVP 261
Query: 921 YASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWERCAHR 1100
YASLT+IE+LVQNVCKS+R+TCQLRLEDLLRQR+N+FSREEV YQRKSMWEMWERCAH
Sbjct: 262 YASLTDIEYLVQNVCKSFRETCQLRLEDLLRQRTNLFSREEVTSYQRKSMWEMWERCAHH 321
Query: 1101 LTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGKYG 1280
LTEAIQYVVEFAKRLSGFMELCQNDQI+LLKAGAMEVVLVRMCRAYNA+NHTVFFEGKYG
Sbjct: 322 LTEAIQYVVEFAKRLSGFMELCQNDQIILLKAGAMEVVLVRMCRAYNANNHTVFFEGKYG 381
Query: 1281 GMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQLQ 1460
G+ELFRALGCSELISSIFDFS LSAL FSEDEIALYTALVLINANRPGLQEKR+VE LQ
Sbjct: 382 GVELFRALGCSELISSIFDFSHFLSALCFSEDEIALYTALVLINANRPGLQEKRRVEHLQ 441
Query: 1461 YNLELAFHHHLCKTHRQGILAKLPPKGKLRSLCSQHVEKLQTFQHLHPIVVQVAFPPLYK 1640
YNLELAFHHHLCKTHRQG+LAKLPPKGKLRSLCSQHVEKLQ FQHLHPIVVQ AFPPLYK
Sbjct: 442 YNLELAFHHHLCKTHRQGLLAKLPPKGKLRSLCSQHVEKLQIFQHLHPIVVQAAFPPLYK 501
Query: 1641 ELFSTEIESSDGLSE 1685
ELFST++ES +GLS+
Sbjct: 502 ELFSTDVESPEGLSK 516
>ref|NP_038674.1| nuclear receptor ROR-alpha [Mus musculus].
Length = 523
Score = 447 bits (1151), Expect = e-126
Identities = 242/495 (48%), Positives = 319/495 (64%), Gaps = 7/495 (1%)
Frame = +3
Query: 201 TQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC 380
+QIE+IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N YSC RQ+NC IDRTSRNRC
Sbjct: 66 SQIEIIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNATYSCPRQKNCLIDRTSRNRC 125
Query: 381 QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGAQG 560
QHCRLQKCLA+GMSRDAVKFGRMSKKQRDSL+AEV
Sbjct: 126 QHCRLQKCLAVGMSRDAVKFGRMSKKQRDSLYAEVQKHRMQQQQRDHQQQPGE------- 178
Query: 561 ADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYS---NSLVKAGLNGASY 731
A+PL P+Y+ N L + + ++Y
Sbjct: 179 AEPLT-----------------------------------PTYNISANGLTELHDDLSTY 203
Query: 732 HLEYSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGE--PGRGPDSYCSPSFRS 905
++PE KA+ + + Q +PD+ GL + + + P G YCS F +
Sbjct: 204 MDGHTPEGSKADSAVSSFYLDIQPSPDQSGLDINGIKPEPICDYTPASGFFPYCS--FTN 261
Query: 906 TPEAPYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWE 1085
+P S+ E+EHL QN+ KS+ +TCQ E+L + F +EE+ YQ K MW+
Sbjct: 262 GETSPTVSMAELEHLAQNISKSHLETCQYLREELQQITWQTFLQEEIENYQNKQREVMWQ 321
Query: 1086 RCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFF 1265
CA ++TEAIQYVVEFAKR+ GFMELCQNDQIVLLKAG++EVV +RMCRA+++ N+TV+F
Sbjct: 322 LCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYF 381
Query: 1266 EGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRK 1445
+GKY ++F++LGC + IS +F+F +SL ++ +EDEIAL++A VL++A+R LQEK K
Sbjct: 382 DGKYASPDVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVK 441
Query: 1446 VEQLQYNLELAFHHHLCKTHRQ-GILAKLPPK-GKLRSLCSQHVEKLQTFQHLHPIVVQV 1619
+E+LQ ++LA H L K HR+ GIL KL K LR+LC +H EKL F+ ++P +V++
Sbjct: 442 IEKLQQKIQLALQHVLQKNHREDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRL 501
Query: 1620 AFPPLYKELFSTEIE 1664
FPPLYKELF++E E
Sbjct: 502 HFPPLYKELFTSEFE 516
>ref|NP_001036819.1| nuclear receptor ROR-beta isoform 1 [Mus musculus].
Length = 459
Score = 407 bits (1045), Expect = e-113
Identities = 230/497 (46%), Positives = 307/497 (61%), Gaps = 9/497 (1%)
Frame = +3
Query: 195 MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRN 374
MR QIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N +YSC RQ+NC IDRT+RN
Sbjct: 1 MRAQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNASYSCPRQRNCLIDRTNRN 60
Query: 375 RCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGA 554
RCQHCRLQKCLALGMSRDAVKFGRMSKKQR
Sbjct: 61 RCQHCRLQKCLALGMSRDAVKFGRMSKKQR------------------------------ 90
Query: 555 QGADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYSNSLVKAGLNGASYH 734
D L EA A + + S SN + G A+ H
Sbjct: 91 ---DSLYAEVQKHQQRLQEQRQQQSGEAEAL--ARVYSSSISNGLSNLNTETGGTYANGH 145
Query: 735 LEYSPERGKAEGRENFYGTGS-QLAPDRCGLHF---EDPRHPGLGEPGRGPDSYCSPSFR 902
+ P K+EG +Y S Q +PD+ GL + + + + P+ + SF
Sbjct: 146 VIDLP---KSEG---YYSIDSGQPSPDQSGLDMTGIKQIKQEPIYDLTSVPNLFTYSSFN 199
Query: 903 STPEAPYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMW 1082
+ AP +++EI+ + QN+ KS+ +TCQ +E+L + + EE+ YQ KS +W
Sbjct: 200 NGQLAPGITMSEIDRIAQNIIKSHLETCQYTMEELHQLAWQTHTYEEIKAYQSKSREALW 259
Query: 1083 ERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVF 1262
++CA ++T AIQYVVEFAKR++GFMELCQNDQI+LLK+G +EVVLVRMCRA+N N+TV
Sbjct: 260 QQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVL 319
Query: 1263 FEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKR 1442
FEGKYGGM++F+ALG +L++ FDF+++L +L+ +E+EIAL+++ VLI+ +R L E R
Sbjct: 320 FEGKYGGMQMFKALGSDDLVNEAFDFAKNLCSLQLTEEEIALFSSAVLISPDRAWLIEPR 379
Query: 1443 KVEQLQYNLELAFHHHLCKTHRQG-----ILAKLPPKGKLRSLCSQHVEKLQTFQHLHPI 1607
KV++LQ + A H + K H ++AK+P + ++C+ H EKLQ F+ HP
Sbjct: 380 KVQKLQEKIYFALQHVIQKNHLDDETLAKLIAKIP---TITAVCNLHGEKLQVFKQSHPD 436
Query: 1608 VVQVAFPPLYKELFSTE 1658
+V FPPLYKELF+ +
Sbjct: 437 IVNTLFPPLYKELFNPD 453
>ref|NP_666207.3| nuclear receptor ROR-beta isoform 2 [Mus musculus].
Length = 470
Score = 405 bits (1041), Expect = e-113
Identities = 232/509 (45%), Positives = 311/509 (61%), Gaps = 9/509 (1%)
Frame = +3
Query: 159 DGSPVGKAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTR 338
+ P KA G+ QIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N +YSC R
Sbjct: 3 ENQPKTKADGTA---QIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNASYSCPR 59
Query: 339 QQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXX 518
Q+NC IDRT+RNRCQHCRLQKCLALGMSRDAVKFGRMSKKQR
Sbjct: 60 QRNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQR------------------ 101
Query: 519 XXXXXXSPPAGAQGADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYSNS 698
D L EA A + + S SN
Sbjct: 102 ---------------DSLYAEVQKHQQRLQEQRQQQSGEAEAL--ARVYSSSISNGLSNL 144
Query: 699 LVKAGLNGASYHLEYSPERGKAEGRENFYGTGS-QLAPDRCGLHF---EDPRHPGLGEPG 866
+ G A+ H+ P K+EG +Y S Q +PD+ GL + + + +
Sbjct: 145 NTETGGTYANGHVIDLP---KSEG---YYSIDSGQPSPDQSGLDMTGIKQIKQEPIYDLT 198
Query: 867 RGPDSYCSPSFRSTPEAPYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEV 1046
P+ + SF + AP +++EI+ + QN+ KS+ +TCQ +E+L + + EE+
Sbjct: 199 SVPNLFTYSSFNNGQLAPGITMSEIDRIAQNIIKSHLETCQYTMEELHQLAWQTHTYEEI 258
Query: 1047 AGYQRKSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRM 1226
YQ KS +W++CA ++T AIQYVVEFAKR++GFMELCQNDQI+LLK+G +EVVLVRM
Sbjct: 259 KAYQSKSREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRM 318
Query: 1227 CRAYNADNHTVFFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVL 1406
CRA+N N+TV FEGKYGGM++F+ALG +L++ FDF+++L +L+ +E+EIAL+++ VL
Sbjct: 319 CRAFNPLNNTVLFEGKYGGMQMFKALGSDDLVNEAFDFAKNLCSLQLTEEEIALFSSAVL 378
Query: 1407 INANRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQG-----ILAKLPPKGKLRSLCSQHV 1571
I+ +R L E RKV++LQ + A H + K H ++AK+P + ++C+ H
Sbjct: 379 ISPDRAWLIEPRKVQKLQEKIYFALQHVIQKNHLDDETLAKLIAKIP---TITAVCNLHG 435
Query: 1572 EKLQTFQHLHPIVVQVAFPPLYKELFSTE 1658
EKLQ F+ HP +V FPPLYKELF+ +
Sbjct: 436 EKLQVFKQSHPDIVNTLFPPLYKELFNPD 464
>ref|NP_663409.2| nuclear receptor subfamily 1 group D member 1 [Mus musculus].
Length = 615
Score = 225 bits (573), Expect = 1e-58
Identities = 167/525 (31%), Positives = 257/525 (48%), Gaps = 40/525 (7%)
Frame = +3
Query: 138 GPPP-----AKKDGSPVGKAHGSVMRTQIE--VIPCKICGDKSSGIHYGVITCEGCKGFF 296
G PP A +D S V + G+ T++ V+ CK+CGD +SG HYGV CEGCKGFF
Sbjct: 98 GSPPGSLQVAMEDSSRVSPSKGTSNITKLNGMVLLCKVCGDVASGFHYGVHACEGCKGFF 157
Query: 297 RRSQQCNVAYS-CTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSL 473
RRS Q N+ Y C + +NC I R +RNRCQ CR +KCL++GMSRDAV+FGR+ K+++ +
Sbjct: 158 RRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRM 217
Query: 474 HAEVXXXXXXXXXXXXXXXXXS------PPAGAQGADPLACXXXXXXXXXXXXXXXDLPE 635
AE+ P +G+ G P P
Sbjct: 218 LAEMQSAMNLANNQLSSLCPLETSPTPHPTSGSMGPSPPPAPAPTPLVGFSQFPQQLTPP 277
Query: 636 ASACPPGLLR------APSCGPSYSNSLVKAGLNGASYHLEYSPERGKAEGRENFYGTGS 797
S P + A + ++ + K G + +++ ++ A + G
Sbjct: 278 RSPSPEPTMEDVISQVARAHREIFTYAHDKLGTSPGNFNANHASGSPSATTPHRWESQGC 337
Query: 798 QLAPDRCGLHFEDPRHPGLGEPGRGPDSYCSPSFRSTPEAPYASLTEIEHLVQNVCKSY- 974
AP+ L + L +GP SY P++ S P + S + +C ++
Sbjct: 338 PSAPNDNNLLAAQRHNEALNGLRQGPSSY-PPTWPSGP--THHSCHQPNSNGHRLCPTHV 394
Query: 975 -------RDTCQLRLED----LLRQRSNIFSREEVAGYQRKSMWEMWERCAHRLTEAIQY 1121
LR + LL N++ G +++ E+WE + T A++
Sbjct: 395 YSAPEGEAPANSLRQGNTKNVLLACPMNMYPH----GRSGRTVQEIWEDFSMSFTPAVRE 450
Query: 1122 VVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGK--YGGMELF 1295
VVEFAK + GF +L Q+DQ+ LLKAG EV++VR +N + TV F + Y EL
Sbjct: 451 VVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNVKDQTVMFLSRTTYSLQEL- 509
Query: 1296 RALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQLQYNL-- 1469
A+G +L++++FDFS L++L +E+E+ L+TA+VL++A+R G++ VEQLQ L
Sbjct: 510 GAMGMGDLLNAMFDFSEKLNSLALTEEELGLFTAVVLVSADRSGMENSASVEQLQETLLR 569
Query: 1470 ---ELAFHHHLCKTHR-QGILAKLPPKGKLRSLCSQHVEKLQTFQ 1592
L + +T R +L KLP LR+L + H EKL +F+
Sbjct: 570 ALRALVLKNRPSETSRFTKLLLKLP---DLRTLNNMHSEKLLSFR 611
>ref|NP_035714.3| nuclear receptor subfamily 1 group D member 2 [Mus musculus].
Length = 576
Score = 130 bits (328), Expect = 2e-30
Identities = 77/189 (40%), Positives = 117/189 (61%), Gaps = 7/189 (3%)
Frame = +3
Query: 1059 RKSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAY 1238
+KS E+WE + T A++ VVEFAKR+ GF +L Q+DQ+ LLKAG EV++VR +
Sbjct: 392 QKSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLF 451
Query: 1239 NADNHTV-FFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINA 1415
+A TV F GK ++ ++G +L+SS+F+FS L+AL+ S++E++L+TA+VL++A
Sbjct: 452 DAKERTVTFLSGKKYSVDDLHSMGAGDLLSSMFEFSEKLNALQLSDEEMSLFTAVVLVSA 511
Query: 1416 NRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQ------GILAKLPPKGKLRSLCSQHVEK 1577
+R G++ VE LQ L A + K H +L KLP LRSL + H E+
Sbjct: 512 DRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLP---DLRSLNNMHSEE 568
Query: 1578 LQTFQHLHP 1604
L F+ +HP
Sbjct: 569 LLAFK-VHP 576
Score = 125 bits (313), Expect = 1e-28
Identities = 58/117 (49%), Positives = 80/117 (68%), Gaps = 2/117 (1%)
Frame = +3
Query: 141 PPPAKKDGSP-VGKAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCN 317
P K +P + K+H + + V+ CK+CGD +SG HYGV CEGCKGFFRRS Q N
Sbjct: 75 PVKTGKTSAPGMTKSHSGMTKFSGMVLLCKVCGDVASGFHYGVHACEGCKGFFRRSIQQN 134
Query: 318 VAYS-CTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV 485
+ Y C + +NC I R +RNRCQ CR +KCL++GMSRDAV+FGR+ K+++ + E+
Sbjct: 135 IQYKKCLKNENCSIMRMNRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRMLIEM 191
>ref|NP_033827.2| COUP transcription factor 2 isoform 1 [Mus musculus].
Length = 414
Score = 123 bits (309), Expect = 4e-28
Identities = 63/136 (46%), Positives = 80/136 (58%), Gaps = 22/136 (16%)
Frame = +3
Query: 120 QLHPIPGPPP----------------------AKKDGSPVGKAHGSVMRTQIEVIPCKIC 233
Q P+PGPPP A G P G GS + Q + I C +C
Sbjct: 25 QAPPVPGPPPGAPHTPQTPGQGGPASTPAQTAAGGQGGPGGP--GSDKQQQQQHIECVVC 82
Query: 234 GDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQHCRLQKCLAL 413
GDKSSG HYG TCEGCK FF+RS + N++Y+C +NCPID+ RN+CQ+CRL+KCL +
Sbjct: 83 GDKSSGKHYGQFTCEGCKSFFKRSVRRNLSYTCRANRNCPIDQHHRNQCQYCRLKKCLKV 142
Query: 414 GMSRDAVKFGRMSKKQ 461
GM R+AV+ GRM Q
Sbjct: 143 GMRREAVQRGRMPPTQ 158
>ref|NP_001036192.1| retinoic acid receptor gamma isoform 2 [Mus musculus].
Length = 447
Score = 117 bits (294), Expect = 2e-26
Identities = 50/81 (61%), Positives = 64/81 (79%)
Frame = +3
Query: 219 PCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQHCRLQ 398
PC +C DKSSG HYGV +CEGCKGFFRRS Q N+ Y+C R +NC I++ +RNRCQ+CRLQ
Sbjct: 78 PCFVCNDKSSGYHYGVSSCEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQ 137
Query: 399 KCLALGMSRDAVKFGRMSKKQ 461
KC +GMS++AV+ R KK+
Sbjct: 138 KCFEVGMSKEAVRNDRNKKKK 158
Score = 81.3 bits (199), Expect = 2e-15
Identities = 56/188 (29%), Positives = 93/188 (49%), Gaps = 8/188 (4%)
Frame = +3
Query: 921 YASLTEIEHLVQNVCKSYRDT----CQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWER 1088
Y ++E L+ V K++++T CQL ++ A ++ + +W++
Sbjct: 169 YELSPQLEELITKVSKAHQETFPSLCQL----------GKYTTNSSADHRVQLDLGLWDK 218
Query: 1089 CAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFE 1268
+ T+ I +VEFAKRL GF L DQI LLKA ++++++R+C Y + T+ F
Sbjct: 219 FSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFS 278
Query: 1269 GKYGGMELFRA----LGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQE 1436
G+ L R G L +F F+ L L + E L +A+ LI +R L+E
Sbjct: 279 ---DGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEE 335
Query: 1437 KRKVEQLQ 1460
KV++LQ
Sbjct: 336 PEKVDKLQ 343
>ref|NP_035374.3| retinoic acid receptor gamma isoform 1 [Mus musculus].
Length = 458
Score = 117 bits (294), Expect = 2e-26
Identities = 50/81 (61%), Positives = 64/81 (79%)
Frame = +3
Query: 219 PCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQHCRLQ 398
PC +C DKSSG HYGV +CEGCKGFFRRS Q N+ Y+C R +NC I++ +RNRCQ+CRLQ
Sbjct: 89 PCFVCNDKSSGYHYGVSSCEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQ 148
Query: 399 KCLALGMSRDAVKFGRMSKKQ 461
KC +GMS++AV+ R KK+
Sbjct: 149 KCFEVGMSKEAVRNDRNKKKK 169
Score = 81.3 bits (199), Expect = 2e-15
Identities = 56/188 (29%), Positives = 93/188 (49%), Gaps = 8/188 (4%)
Frame = +3
Query: 921 YASLTEIEHLVQNVCKSYRDT----CQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWER 1088
Y ++E L+ V K++++T CQL ++ A ++ + +W++
Sbjct: 180 YELSPQLEELITKVSKAHQETFPSLCQL----------GKYTTNSSADHRVQLDLGLWDK 229
Query: 1089 CAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFE 1268
+ T+ I +VEFAKRL GF L DQI LLKA ++++++R+C Y + T+ F
Sbjct: 230 FSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFS 289
Query: 1269 GKYGGMELFRA----LGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQE 1436
G+ L R G L +F F+ L L + E L +A+ LI +R L+E
Sbjct: 290 ---DGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEE 346
Query: 1437 KRKVEQLQ 1460
KV++LQ
Sbjct: 347 PEKVDKLQ 354
>ref|NP_035373.1| retinoic acid receptor beta [Mus musculus].
Length = 448
Score = 116 bits (291), Expect = 5e-26
Identities = 50/84 (59%), Positives = 64/84 (76%)
Frame = +3
Query: 219 PCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQHCRLQ 398
PC +C DKSSG HYGV CEGCKGFFRRS Q N+ Y+C R +NC I++ +RNRCQ+CRLQ
Sbjct: 80 PCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMIYTCHRDKNCVINKVTRNRCQYCRLQ 139
Query: 399 KCLALGMSRDAVKFGRMSKKQRDS 470
KC +GMS+++V+ R KK+ S
Sbjct: 140 KCFEVGMSKESVRNDRNKKKKEPS 163
Score = 89.0 bits (219), Expect = 1e-17
Identities = 75/273 (27%), Positives = 134/273 (49%), Gaps = 11/273 (4%)
Frame = +3
Query: 891 PSFRSTPEAPYASLTEIEHLVQNVCKSYRDT----CQLRLEDLLRQRSNIFSREEVAGYQ 1058
PS + E+ Y E++ L + + K++++T CQL ++ A ++
Sbjct: 162 PSKQECTES-YEMTAELDDLTEKIRKAHQETFPSLCQL----------GKYTTNSSADHR 210
Query: 1059 RKSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAY 1238
+ +W++ + T+ I +VEFAKRL GF L DQI LLKA ++++++R+C Y
Sbjct: 211 VRLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRY 270
Query: 1239 NADNHTVFFEGKYGGMELFRA----LGCSELISSIFDFSRSLSALRFSEDEIALYTALVL 1406
+ T+ F G+ L R G L +F F+ L L + E L +A+ L
Sbjct: 271 TPEQDTMTFS---DGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICL 327
Query: 1407 INANRPGLQEKRKVEQLQYNLELAFHHHLCKTH--RQGILAKLPPK-GKLRSLCSQHVEK 1577
I +R L+E KV++LQ L A ++ K + + K+ K LRS+ ++ E+
Sbjct: 328 ICGDRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAER 387
Query: 1578 LQTFQHLHPIVVQVAFPPLYKELFSTEIESSDG 1676
+ T + + + + PPL +E+ +E+S+G
Sbjct: 388 VITLK----MEIPGSMPPLIQEM----LENSEG 412
Database: RefSeq49_MP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 15,617,559
Number of sequences in database: 30,036
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 30036
Number of Hits to DB: 60,103,445
Number of extensions: 1722794
Number of successful extensions: 8873
Number of sequences better than 1.0e-05: 74
Number of HSP's gapped: 8754
Number of HSP's successfully gapped: 107
Length of query: 585
Length of database: 15,617,559
Length adjustment: 107
Effective length of query: 478
Effective length of database: 12,403,707
Effective search space: 5928971946
Effective search space used: 5928971946
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 36 (18.5 bits)
Search to RefSeqHP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-008862
(1757 letters)
Database: RefSeq49_HP.fasta
32,964 sequences; 18,297,164 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001001523.1| nuclear receptor ROR-gamma isoform b [Homo s... 863 0.0
Alignment gi|NP_005051.2| nuclear receptor ROR-gamma isoform a [Homo sapi... 857 0.0
Alignment gi|NP_599022.1| nuclear receptor ROR-alpha isoform b [Homo sapi... 451 e-127
Alignment gi|NP_599024.1| nuclear receptor ROR-alpha isoform d [Homo sapi... 450 e-126
Alignment gi|NP_002934.1| nuclear receptor ROR-alpha isoform c [Homo sapi... 448 e-126
Alignment gi|NP_599023.1| nuclear receptor ROR-alpha isoform a [Homo sapi... 447 e-125
Alignment gi|NP_008845.2| nuclear receptor ROR-beta [Homo sapiens]. 259 7e-69
Alignment gi|NP_001138897.1| nuclear receptor subfamily 1 group D member ... 129 9e-30
Alignment gi|NP_005117.3| nuclear receptor subfamily 1 group D member 2 i... 129 9e-30
Alignment gi|NP_068370.1| nuclear receptor subfamily 1 group D member 1 [... 126 6e-29
>ref|NP_001001523.1| nuclear receptor ROR-gamma isoform b [Homo sapiens].
Length = 497
Score = 863 bits (2229), Expect = 0.0
Identities = 427/497 (85%), Positives = 439/497 (88%)
Frame = +3
Query: 195 MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRN 374
MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQ+CN AYSCTRQQNCPIDRTSRN
Sbjct: 1 MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQRCNAAYSCTRQQNCPIDRTSRN 60
Query: 375 RCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGA 554
RCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV +PPAGA
Sbjct: 61 RCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVQKQLQQRQQQQQEPVVKTPPAGA 120
Query: 555 QGADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYSNSLVKAGLNGASYH 734
QGAD L DLPEASACPPGLL+A GPSYSN+L KAGLNGAS H
Sbjct: 121 QGADTLTYTLGLPDGQLPLGSSPDLPEASACPPGLLKASGSGPSYSNNLAKAGLNGASCH 180
Query: 735 LEYSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGEPGRGPDSYCSPSFRSTPE 914
LEYSPERGKAEGRE+FY TGSQL PDRCGL FE+ RHPGLGE G+GPDSY SPSFRSTPE
Sbjct: 181 LEYSPERGKAEGRESFYSTGSQLTPDRCGLRFEEHRHPGLGELGQGPDSYGSPSFRSTPE 240
Query: 915 APYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWERCA 1094
APYASLTEIEHLVQ+VCKSYR+TCQLRLEDLLRQRSNIFSREEV GYQRKSMWEMWERCA
Sbjct: 241 APYASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCA 300
Query: 1095 HRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGK 1274
H LTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADN TVFFEGK
Sbjct: 301 HHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGK 360
Query: 1275 YGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQ 1454
YGGMELFRALGCSELISSIFDFS SLSAL FSEDEIALYTALVLINA+RPGLQEKRKVEQ
Sbjct: 361 YGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQ 420
Query: 1455 LQYNLELAFHHHLCKTHRQGILAKLPPKGKLRSLCSQHVEKLQTFQHLHPIVVQVAFPPL 1634
LQYNLELAFHHHLCKTHRQ ILAKLPPKGKLRSLCSQHVE+LQ FQHLHPIVVQ AFPPL
Sbjct: 421 LQYNLELAFHHHLCKTHRQSILAKLPPKGKLRSLCSQHVERLQIFQHLHPIVVQAAFPPL 480
Query: 1635 YKELFSTEIESSDGLSE 1685
YKELFSTE ES GLS+
Sbjct: 481 YKELFSTETESPVGLSK 497
>ref|NP_005051.2| nuclear receptor ROR-gamma isoform a [Homo sapiens].
Length = 518
Score = 857 bits (2215), Expect = 0.0
Identities = 424/495 (85%), Positives = 437/495 (88%)
Frame = +3
Query: 201 TQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC 380
+QIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQ+CN AYSCTRQQNCPIDRTSRNRC
Sbjct: 24 SQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQRCNAAYSCTRQQNCPIDRTSRNRC 83
Query: 381 QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGAQG 560
QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV +PPAGAQG
Sbjct: 84 QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVQKQLQQRQQQQQEPVVKTPPAGAQG 143
Query: 561 ADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYSNSLVKAGLNGASYHLE 740
AD L DLPEASACPPGLL+A GPSYSN+L KAGLNGAS HLE
Sbjct: 144 ADTLTYTLGLPDGQLPLGSSPDLPEASACPPGLLKASGSGPSYSNNLAKAGLNGASCHLE 203
Query: 741 YSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGEPGRGPDSYCSPSFRSTPEAP 920
YSPERGKAEGRE+FY TGSQL PDRCGL FE+ RHPGLGE G+GPDSY SPSFRSTPEAP
Sbjct: 204 YSPERGKAEGRESFYSTGSQLTPDRCGLRFEEHRHPGLGELGQGPDSYGSPSFRSTPEAP 263
Query: 921 YASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWERCAHR 1100
YASLTEIEHLVQ+VCKSYR+TCQLRLEDLLRQRSNIFSREEV GYQRKSMWEMWERCAH
Sbjct: 264 YASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHH 323
Query: 1101 LTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGKYG 1280
LTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADN TVFFEGKYG
Sbjct: 324 LTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYG 383
Query: 1281 GMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQLQ 1460
GMELFRALGCSELISSIFDFS SLSAL FSEDEIALYTALVLINA+RPGLQEKRKVEQLQ
Sbjct: 384 GMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQ 443
Query: 1461 YNLELAFHHHLCKTHRQGILAKLPPKGKLRSLCSQHVEKLQTFQHLHPIVVQVAFPPLYK 1640
YNLELAFHHHLCKTHRQ ILAKLPPKGKLRSLCSQHVE+LQ FQHLHPIVVQ AFPPLYK
Sbjct: 444 YNLELAFHHHLCKTHRQSILAKLPPKGKLRSLCSQHVERLQIFQHLHPIVVQAAFPPLYK 503
Query: 1641 ELFSTEIESSDGLSE 1685
ELFSTE ES GLS+
Sbjct: 504 ELFSTETESPVGLSK 518
>ref|NP_599022.1| nuclear receptor ROR-alpha isoform b [Homo sapiens].
Length = 556
Score = 451 bits (1161), Expect = e-127
Identities = 247/515 (47%), Positives = 327/515 (63%), Gaps = 7/515 (1%)
Frame = +3
Query: 141 PPPAKKDGSPVGKAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNV 320
PP ++K+ V + M QIE+IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N
Sbjct: 82 PPYSQKEDKEVQTGY---MNAQIEIIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNA 138
Query: 321 AYSCTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXX 500
YSC RQ+NC IDRTSRNRCQHCRLQKCLA+GMSRDAVKFGRMSKKQRDSL+AEV
Sbjct: 139 TYSCPRQKNCLIDRTSRNRCQHCRLQKCLAVGMSRDAVKFGRMSKKQRDSLYAEVQKHRM 198
Query: 501 XXXXXXXXXXXXSPPAGAQGADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCG 680
A+PL
Sbjct: 199 QQQQRDHQQQPGE-------AEPLT----------------------------------- 216
Query: 681 PSYS---NSLVKAGLNGASYHLEYSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPG 851
P+Y+ N L + + ++Y ++PE KA+ + + Q +PD+ GL +
Sbjct: 217 PTYNISANGLTELHDDLSNYIDGHTPEGSKADSAVSSFYLDIQPSPDQSGLDINGIKPEP 276
Query: 852 LGE--PGRGPDSYCSPSFRSTPEAPYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSN 1025
+ + P G YCS F + +P S+ E+EHL QN+ KS+ +TCQ E+L +
Sbjct: 277 ICDYTPASGFFPYCS--FTNGETSPTVSMAELEHLAQNISKSHLETCQYLREELQQITWQ 334
Query: 1026 IFSREEVAGYQRKSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAM 1205
F +EE+ YQ K MW+ CA ++TEAIQYVVEFAKR+ GFMELCQNDQIVLLKAG++
Sbjct: 335 TFLQEEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSL 394
Query: 1206 EVVLVRMCRAYNADNHTVFFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIA 1385
EVV +RMCRA+++ N+TV+F+GKY ++F++LGC + IS +F+F +SL ++ +EDEIA
Sbjct: 395 EVVFIRMCRAFDSQNNTVYFDGKYASPDVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIA 454
Query: 1386 LYTALVLINANRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQ-GILAKLPPK-GKLRSLC 1559
L++A VL++A+R LQEK K+E+LQ ++LA H L K HR+ GIL KL K LR+LC
Sbjct: 455 LFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQHVLQKNHREDGILTKLICKVSTLRALC 514
Query: 1560 SQHVEKLQTFQHLHPIVVQVAFPPLYKELFSTEIE 1664
+H EKL F+ ++P +V++ FPPLYKELF++E E
Sbjct: 515 GRHTEKLMAFKAIYPDIVRLHFPPLYKELFTSEFE 549
>ref|NP_599024.1| nuclear receptor ROR-alpha isoform d [Homo sapiens].
Length = 468
Score = 450 bits (1157), Expect = e-126
Identities = 243/499 (48%), Positives = 321/499 (64%), Gaps = 7/499 (1%)
Frame = +3
Query: 189 SVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTS 368
+ M+ QIE+IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N YSC RQ+NC IDRTS
Sbjct: 7 AAMKAQIEIIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNATYSCPRQKNCLIDRTS 66
Query: 369 RNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPA 548
RNRCQHCRLQKCLA+GMSRDAVKFGRMSKKQRDSL+AEV
Sbjct: 67 RNRCQHCRLQKCLAVGMSRDAVKFGRMSKKQRDSLYAEVQKHRMQQQQRDHQQQPGE--- 123
Query: 549 GAQGADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYS---NSLVKAGLN 719
A+PL P+Y+ N L + +
Sbjct: 124 ----AEPLT-----------------------------------PTYNISANGLTELHDD 144
Query: 720 GASYHLEYSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGE--PGRGPDSYCSP 893
++Y ++PE KA+ + + Q +PD+ GL + + + P G YCS
Sbjct: 145 LSNYIDGHTPEGSKADSAVSSFYLDIQPSPDQSGLDINGIKPEPICDYTPASGFFPYCS- 203
Query: 894 SFRSTPEAPYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMW 1073
F + +P S+ E+EHL QN+ KS+ +TCQ E+L + F +EE+ YQ K
Sbjct: 204 -FTNGETSPTVSMAELEHLAQNISKSHLETCQYLREELQQITWQTFLQEEIENYQNKQRE 262
Query: 1074 EMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNH 1253
MW+ CA ++TEAIQYVVEFAKR+ GFMELCQNDQIVLLKAG++EVV +RMCRA+++ N+
Sbjct: 263 VMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNN 322
Query: 1254 TVFFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQ 1433
TV+F+GKY ++F++LGC + IS +F+F +SL ++ +EDEIAL++A VL++A+R LQ
Sbjct: 323 TVYFDGKYASPDVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQ 382
Query: 1434 EKRKVEQLQYNLELAFHHHLCKTHRQ-GILAKLPPK-GKLRSLCSQHVEKLQTFQHLHPI 1607
EK K+E+LQ ++LA H L K HR+ GIL KL K LR+LC +H EKL F+ ++P
Sbjct: 383 EKVKIEKLQQKIQLALQHVLQKNHREDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPD 442
Query: 1608 VVQVAFPPLYKELFSTEIE 1664
+V++ FPPLYKELF++E E
Sbjct: 443 IVRLHFPPLYKELFTSEFE 461
>ref|NP_002934.1| nuclear receptor ROR-alpha isoform c [Homo sapiens].
Length = 548
Score = 448 bits (1152), Expect = e-126
Identities = 242/499 (48%), Positives = 321/499 (64%), Gaps = 7/499 (1%)
Frame = +3
Query: 189 SVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTS 368
++ + QIE+IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N YSC RQ+NC IDRTS
Sbjct: 87 ALRKAQIEIIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNATYSCPRQKNCLIDRTS 146
Query: 369 RNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPA 548
RNRCQHCRLQKCLA+GMSRDAVKFGRMSKKQRDSL+AEV
Sbjct: 147 RNRCQHCRLQKCLAVGMSRDAVKFGRMSKKQRDSLYAEVQKHRMQQQQRDHQQQPGE--- 203
Query: 549 GAQGADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYS---NSLVKAGLN 719
A+PL P+Y+ N L + +
Sbjct: 204 ----AEPLT-----------------------------------PTYNISANGLTELHDD 224
Query: 720 GASYHLEYSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGE--PGRGPDSYCSP 893
++Y ++PE KA+ + + Q +PD+ GL + + + P G YCS
Sbjct: 225 LSNYIDGHTPEGSKADSAVSSFYLDIQPSPDQSGLDINGIKPEPICDYTPASGFFPYCS- 283
Query: 894 SFRSTPEAPYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMW 1073
F + +P S+ E+EHL QN+ KS+ +TCQ E+L + F +EE+ YQ K
Sbjct: 284 -FTNGETSPTVSMAELEHLAQNISKSHLETCQYLREELQQITWQTFLQEEIENYQNKQRE 342
Query: 1074 EMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNH 1253
MW+ CA ++TEAIQYVVEFAKR+ GFMELCQNDQIVLLKAG++EVV +RMCRA+++ N+
Sbjct: 343 VMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNN 402
Query: 1254 TVFFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQ 1433
TV+F+GKY ++F++LGC + IS +F+F +SL ++ +EDEIAL++A VL++A+R LQ
Sbjct: 403 TVYFDGKYASPDVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQ 462
Query: 1434 EKRKVEQLQYNLELAFHHHLCKTHRQ-GILAKLPPK-GKLRSLCSQHVEKLQTFQHLHPI 1607
EK K+E+LQ ++LA H L K HR+ GIL KL K LR+LC +H EKL F+ ++P
Sbjct: 463 EKVKIEKLQQKIQLALQHVLQKNHREDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPD 522
Query: 1608 VVQVAFPPLYKELFSTEIE 1664
+V++ FPPLYKELF++E E
Sbjct: 523 IVRLHFPPLYKELFTSEFE 541
>ref|NP_599023.1| nuclear receptor ROR-alpha isoform a [Homo sapiens].
Length = 523
Score = 447 bits (1150), Expect = e-125
Identities = 242/495 (48%), Positives = 319/495 (64%), Gaps = 7/495 (1%)
Frame = +3
Query: 201 TQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRC 380
+QIE+IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N YSC RQ+NC IDRTSRNRC
Sbjct: 66 SQIEIIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNATYSCPRQKNCLIDRTSRNRC 125
Query: 381 QHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVXXXXXXXXXXXXXXXXXSPPAGAQG 560
QHCRLQKCLA+GMSRDAVKFGRMSKKQRDSL+AEV
Sbjct: 126 QHCRLQKCLAVGMSRDAVKFGRMSKKQRDSLYAEVQKHRMQQQQRDHQQQPGE------- 178
Query: 561 ADPLACXXXXXXXXXXXXXXXDLPEASACPPGLLRAPSCGPSYS---NSLVKAGLNGASY 731
A+PL P+Y+ N L + + ++Y
Sbjct: 179 AEPLT-----------------------------------PTYNISANGLTELHDDLSNY 203
Query: 732 HLEYSPERGKAEGRENFYGTGSQLAPDRCGLHFEDPRHPGLGE--PGRGPDSYCSPSFRS 905
++PE KA+ + + Q +PD+ GL + + + P G YCS F +
Sbjct: 204 IDGHTPEGSKADSAVSSFYLDIQPSPDQSGLDINGIKPEPICDYTPASGFFPYCS--FTN 261
Query: 906 TPEAPYASLTEIEHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWE 1085
+P S+ E+EHL QN+ KS+ +TCQ E+L + F +EE+ YQ K MW+
Sbjct: 262 GETSPTVSMAELEHLAQNISKSHLETCQYLREELQQITWQTFLQEEIENYQNKQREVMWQ 321
Query: 1086 RCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFF 1265
CA ++TEAIQYVVEFAKR+ GFMELCQNDQIVLLKAG++EVV +RMCRA+++ N+TV+F
Sbjct: 322 LCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYF 381
Query: 1266 EGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRK 1445
+GKY ++F++LGC + IS +F+F +SL ++ +EDEIAL++A VL++A+R LQEK K
Sbjct: 382 DGKYASPDVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVK 441
Query: 1446 VEQLQYNLELAFHHHLCKTHRQ-GILAKLPPK-GKLRSLCSQHVEKLQTFQHLHPIVVQV 1619
+E+LQ ++LA H L K HR+ GIL KL K LR+LC +H EKL F+ ++P +V++
Sbjct: 442 IEKLQQKIQLALQHVLQKNHREDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRL 501
Query: 1620 AFPPLYKELFSTEIE 1664
FPPLYKELF++E E
Sbjct: 502 HFPPLYKELFTSEFE 516
>ref|NP_008845.2| nuclear receptor ROR-beta [Homo sapiens].
Length = 459
Score = 259 bits (661), Expect = 7e-69
Identities = 135/304 (44%), Positives = 202/304 (66%), Gaps = 9/304 (2%)
Frame = +3
Query: 774 ENFYGTGS-QLAPDRCGLHF---EDPRHPGLGEPGRGPDSYCSPSFRSTPEAPYASLTEI 941
E +Y S Q +PD+ GL + + + + P+ + SF + AP ++TEI
Sbjct: 153 EGYYNVDSGQPSPDQSGLDMTGIKQIKQEPIYDLTSVPNLFTYSSFNNGQLAPGITMTEI 212
Query: 942 EHLVQNVCKSYRDTCQLRLEDLLRQRSNIFSREEVAGYQRKSMWEMWERCAHRLTEAIQY 1121
+ + QN+ KS+ +TCQ +E+L + + EE+ YQ KS +W++CA ++T AIQY
Sbjct: 213 DRIAQNIIKSHLETCQYTMEELHQLAWQTHTYEEIKAYQSKSREALWQQCAIQITHAIQY 272
Query: 1122 VVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNHTVFFEGKYGGMELFRA 1301
VVEFAKR++GFMELCQNDQI+LLK+G +EVVLVRMCRA+N N+TV FEGKYGGM++F+A
Sbjct: 273 VVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKA 332
Query: 1302 LGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINANRPGLQEKRKVEQLQYNLELAF 1481
LG +L++ FDF+++L +L+ +E+EIAL+++ VLI+ +R L E RKV++LQ + A
Sbjct: 333 LGSDDLVNEAFDFAKNLCSLQLTEEEIALFSSAVLISPDRAWLIEPRKVQKLQEKIYFAL 392
Query: 1482 HHHLCKTHRQG-----ILAKLPPKGKLRSLCSQHVEKLQTFQHLHPIVVQVAFPPLYKEL 1646
H + K H ++AK+P + ++C+ H EKLQ F+ HP +V FPPLYKEL
Sbjct: 393 QHVIQKNHLDDETLAKLIAKIP---TITAVCNLHGEKLQVFKQSHPEIVNTLFPPLYKEL 449
Query: 1647 FSTE 1658
F+ +
Sbjct: 450 FNPD 453
Score = 189 bits (479), Expect = 9e-48
Identities = 88/97 (90%), Positives = 92/97 (94%)
Frame = +3
Query: 195 MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRN 374
MR QIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQ N +YSC RQ+NC IDRT+RN
Sbjct: 1 MRAQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNASYSCPRQRNCLIDRTNRN 60
Query: 375 RCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV 485
RCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSL+AEV
Sbjct: 61 RCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLYAEV 97
>ref|NP_001138897.1| nuclear receptor subfamily 1 group D member 2 isoform 2 [Homo
sapiens].
Length = 504
Score = 129 bits (324), Expect = 9e-30
Identities = 76/188 (40%), Positives = 116/188 (61%), Gaps = 7/188 (3%)
Frame = +3
Query: 1062 KSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYN 1241
KS E+WE + T A++ VVEFAKR+ GF +L Q+DQ+ LLKAG EV++VR ++
Sbjct: 321 KSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFD 380
Query: 1242 ADNHTV-FFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINAN 1418
A TV F GK ++ ++G +L++S+F+FS L+AL+ S++E++L+TA+VL++A+
Sbjct: 381 AKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSAD 440
Query: 1419 RPGLQEKRKVEQLQYNLELAFHHHLCKTHRQ------GILAKLPPKGKLRSLCSQHVEKL 1580
R G++ VE LQ L A + K H +L KLP LRSL + H E+L
Sbjct: 441 RSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLP---DLRSLNNMHSEEL 497
Query: 1581 QTFQHLHP 1604
F+ +HP
Sbjct: 498 LAFK-VHP 504
Score = 126 bits (317), Expect = 6e-29
Identities = 57/113 (50%), Positives = 78/113 (69%), Gaps = 1/113 (0%)
Frame = +3
Query: 150 AKKDGSPVGKAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYS 329
+K + K+H V + V+ CK+CGD +SG HYGV CEGCKGFFRRS Q N+ Y
Sbjct: 4 SKSSAPGMTKSHSGVTKFSGMVLLCKVCGDVASGFHYGVHACEGCKGFFRRSIQQNIQYK 63
Query: 330 -CTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV 485
C + +NC I R +RNRCQ CR +KCL++GMSRDAV+FGR+ K+++ + E+
Sbjct: 64 KCLKNENCSIMRMNRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRMLIEM 116
>ref|NP_005117.3| nuclear receptor subfamily 1 group D member 2 isoform 1 [Homo
sapiens].
Length = 579
Score = 129 bits (324), Expect = 9e-30
Identities = 76/188 (40%), Positives = 116/188 (61%), Gaps = 7/188 (3%)
Frame = +3
Query: 1062 KSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYN 1241
KS E+WE + T A++ VVEFAKR+ GF +L Q+DQ+ LLKAG EV++VR ++
Sbjct: 396 KSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFD 455
Query: 1242 ADNHTV-FFEGKYGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALVLINAN 1418
A TV F GK ++ ++G +L++S+F+FS L+AL+ S++E++L+TA+VL++A+
Sbjct: 456 AKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSAD 515
Query: 1419 RPGLQEKRKVEQLQYNLELAFHHHLCKTHRQ------GILAKLPPKGKLRSLCSQHVEKL 1580
R G++ VE LQ L A + K H +L KLP LRSL + H E+L
Sbjct: 516 RSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLP---DLRSLNNMHSEEL 572
Query: 1581 QTFQHLHP 1604
F+ +HP
Sbjct: 573 LAFK-VHP 579
Score = 126 bits (317), Expect = 6e-29
Identities = 57/113 (50%), Positives = 78/113 (69%), Gaps = 1/113 (0%)
Frame = +3
Query: 150 AKKDGSPVGKAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYS 329
+K + K+H V + V+ CK+CGD +SG HYGV CEGCKGFFRRS Q N+ Y
Sbjct: 79 SKSSAPGMTKSHSGVTKFSGMVLLCKVCGDVASGFHYGVHACEGCKGFFRRSIQQNIQYK 138
Query: 330 -CTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEV 485
C + +NC I R +RNRCQ CR +KCL++GMSRDAV+FGR+ K+++ + E+
Sbjct: 139 KCLKNENCSIMRMNRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRMLIEM 191
>ref|NP_068370.1| nuclear receptor subfamily 1 group D member 1 [Homo sapiens].
Length = 614
Score = 126 bits (317), Expect = 6e-29
Identities = 62/124 (50%), Positives = 84/124 (67%), Gaps = 8/124 (6%)
Frame = +3
Query: 138 GPPP-----AKKDGSPVG--KAHGSVMRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFF 296
G PP A +D S V K+ ++ + V+ CK+CGD +SG HYGV CEGCKGFF
Sbjct: 97 GSPPGSLQVAMEDSSRVSPSKSTSNITKLNGMVLLCKVCGDVASGFHYGVHACEGCKGFF 156
Query: 297 RRSQQCNVAYS-CTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSL 473
RRS Q N+ Y C + +NC I R +RNRCQ CR +KCL++GMSRDAV+FGR+ K+++ +
Sbjct: 157 RRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRM 216
Query: 474 HAEV 485
AE+
Sbjct: 217 LAEM 220
Score = 124 bits (310), Expect = 4e-28
Identities = 75/189 (39%), Positives = 115/189 (60%), Gaps = 8/189 (4%)
Frame = +3
Query: 1050 GYQRKSMWEMWERCAHRLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMC 1229
G +++ E+WE + T A++ VVEFAK + GF +L Q+DQ+ LLKAG EV++VR
Sbjct: 426 GRSGRTVQEIWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFA 485
Query: 1230 RAYNADNHTVFFEGK--YGGMELFRALGCSELISSIFDFSRSLSALRFSEDEIALYTALV 1403
+N + TV F + Y EL A+G +L+S++FDFS L++L +E+E+ L+TA+V
Sbjct: 486 SLFNVKDQTVMFLSRTTYSLQEL-GAMGMGDLLSAMFDFSEKLNSLALTEEELGLFTAVV 544
Query: 1404 LINANRPGLQEKRKVEQLQYNL-----ELAFHHHLCKTHR-QGILAKLPPKGKLRSLCSQ 1565
L++A+R G++ VEQLQ L L + +T R +L KLP LR+L +
Sbjct: 545 LVSADRSGMENSASVEQLQETLLRALRALVLKNRPLETSRFTKLLLKLP---DLRTLNNM 601
Query: 1566 HVEKLQTFQ 1592
H EKL +F+
Sbjct: 602 HSEKLLSFR 610
Database: RefSeq49_HP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,297,164
Number of sequences in database: 32,964
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 32964
Number of Hits to DB: 71,367,722
Number of extensions: 2083100
Number of successful extensions: 11361
Number of sequences better than 1.0e-05: 142
Number of HSP's gapped: 11176
Number of HSP's successfully gapped: 199
Length of query: 585
Length of database: 18,297,164
Length adjustment: 108
Effective length of query: 477
Effective length of database: 14,737,052
Effective search space: 7029573804
Effective search space used: 7029573804
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 36 (18.5 bits)
Search to Sscrofa10_2
BLASTN 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-008862
(1757 letters)
Database: Sscrofa_10.2.fasta
4582 sequences; 2,808,509,378 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Sscrofa_Chr04 1003 0.0
Sscrofa_Chr08 133 4e-28
Sscrofa_Chr01 78 2e-11
>Sscrofa_Chr04
|| Length = 143465943
Score = 1003 bits (506), Expect = 0.0
Identities = 512/514 (99%)
Strand = Plus / Plus
Query: 429 gctgtcaagtttggccgcatgtccaagaagcaaagggacagcctgcatgctgaggtgcag 488
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106413415 gctgtcaagtttggccgcatgtccaagaagcaaagggacagcctgcatgctgaggtgcag 106413474
Query: 489 aaacagctgcagcagaggcaacagcagcaacgggaacaagcggccaagtcccctcctgca 548
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106413475 aaacagctgcagcagaggcaacagcagcaacgggaacaagcggccaagtcccctcctgca 106413534
Query: 549 ggggcccaaggagcagaccccctcgcctgccccctggggctcccagatgggcagctgccc 608
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106413535 ggggcccaaggagcagaccccctcgcctgccccctggggctcccagatgggcagctgccc 106413594
Query: 609 ctgggctcctcacctgacctgccggaggcctcggcctgtccccccggtctcctgagagcc 668
||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct: 106413595 ctgggctcctcacctgacctgccagaggcctcggcctgtccccccggtctcctgagagcc 106413654
Query: 669 ccaagctgcgggccctcctactccaacagcttggtcaaggctgggctcaatggggcttct 728
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106413655 ccaagctgcgggccctcctactccaacagcttggtcaaggctgggctcaatggggcttct 106413714
Query: 729 taccacctggaatacagccctgagcggggcaaggctgagggcagagagaacttctatggc 788
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106413715 taccacctggaatacagccctgagcggggcaaggctgagggcagagagaacttctatggc 106413774
Query: 789 acaggcagccagctggcccccgacaggtgtggactccattttgaggaccccaggcatcct 848
||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Sbjct: 106413775 acaggcagccagctggcccccgacaggtgtggactccgttttgaggaccccaggcatcct 106413834
Query: 849 gggcttggggaaccaggacggggccctgacagctactgcagccccagtttccgcagtacc 908
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106413835 gggcttggggaaccaggacggggccctgacagctactgcagccccagtttccgcagtacc 106413894
Query: 909 ccagaggcaccttacgcctccctgacagagattg 942
||||||||||||||||||||||||||||||||||
Sbjct: 106413895 ccagaggcaccttacgcctccctgacagagattg 106413928
Score = 438 bits (221), Expect = e-120
Identities = 231/233 (99%), Gaps = 1/233 (0%)
Strand = Plus / Plus
Query: 1525 agctgccacccaaggggaagcttcggagcctgtgcagtcagcacgtggaaaagctgcaaa 1584
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106421316 agctgccacccaaggggaagcttcggagcctgtgcagtcagcacgtggaaaagctgcaaa 106421375
Query: 1585 ccttccagcacctccaccccatcgtggtccaagttgctttccctccactctataaggaac 1644
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106421376 ccttccagcacctccaccccatcgtggtccaagttgctttccctccactctataaggaac 106421435
Query: 1645 tcttcagcactgaaatcgagtcatctgatgggctgtccgagtgacctggaaacaggagtc 1704
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106421436 tcttcagcactgaaatcgagtcatctgatgggctgtccgagtgacctggaaacaggagtc 106421495
Query: 1705 tgttcccttccctagagcctgctggcttacttccccttcgg-cttttcctttc 1756
|||||||||||||||||||||||||||||||||||| |||| |||||||||||
Sbjct: 106421496 tgttcccttccctagagcctgctggcttacttccccctcggccttttcctttc 106421548
Score = 392 bits (198), Expect = e-106
Identities = 198/198 (100%)
Strand = Plus / Plus
Query: 4 ggccacctgtgtggtgcggagcttaaacccccctgcccagaagcattgggggagagctag 63
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106309848 ggccacctgtgtggtgcggagcttaaacccccctgcccagaagcattgggggagagctag 106309907
Query: 64 gtgcagagctgcaggctgaggctctgctgagagggcctcacccccaaccccgctgccagc 123
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106309908 gtgcagagctgcaggctgaggctctgctgagagggcctcacccccaaccccgctgccagc 106309967
Query: 124 tgcaccccatccctggaccaccccccgctaagaaggacgggagcccagtcggcaaagccc 183
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106309968 tgcaccccatccctggaccaccccccgctaagaaggacgggagcccagtcggcaaagccc 106310027
Query: 184 acggctcagtcatgagaa 201
||||||||||||||||||
Sbjct: 106310028 acggctcagtcatgagaa 106310045
Score = 392 bits (198), Expect = e-106
Identities = 198/198 (100%)
Strand = Plus / Plus
Query: 4 ggccacctgtgtggtgcggagcttaaacccccctgcccagaagcattgggggagagctag 63
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106403098 ggccacctgtgtggtgcggagcttaaacccccctgcccagaagcattgggggagagctag 106403157
Query: 64 gtgcagagctgcaggctgaggctctgctgagagggcctcacccccaaccccgctgccagc 123
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106403158 gtgcagagctgcaggctgaggctctgctgagagggcctcacccccaaccccgctgccagc 106403217
Query: 124 tgcaccccatccctggaccaccccccgctaagaaggacgggagcccagtcggcaaagccc 183
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106403218 tgcaccccatccctggaccaccccccgctaagaaggacgggagcccagtcggcaaagccc 106403277
Query: 184 acggctcagtcatgagaa 201
||||||||||||||||||
Sbjct: 106403278 acggctcagtcatgagaa 106403295
Score = 285 bits (144), Expect = 4e-74
Identities = 144/144 (100%)
Strand = Plus / Plus
Query: 286 agggtttcttccgccggagccagcagtgtaacgtggcctactcctgcacccgtcagcaga 345
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106412071 agggtttcttccgccggagccagcagtgtaacgtggcctactcctgcacccgtcagcaga 106412130
Query: 346 actgccccatcgaccgcactagccgaaaccgatgccagcactgccgcctacagaaatgcc 405
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106412131 actgccccatcgaccgcactagccgaaaccgatgccagcactgccgcctacagaaatgcc 106412190
Query: 406 tggccctgggcatgtcccgagatg 429
||||||||||||||||||||||||
Sbjct: 106412191 tggccctgggcatgtcccgagatg 106412214
Score = 270 bits (136), Expect = 2e-69
Identities = 136/136 (100%)
Strand = Plus / Plus
Query: 1063 agtcaatgtgggagatgtgggaacgctgtgcccaccgcctcaccgaggccattcagtacg 1122
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106415305 agtcaatgtgggagatgtgggaacgctgtgcccaccgcctcaccgaggccattcagtacg 106415364
Query: 1123 tggtggagttcgctaagaggctctcgggctttatggagctctgccagaacgaccagatcg 1182
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106415365 tggtggagttcgctaagaggctctcgggctttatggagctctgccagaacgaccagatcg 106415424
Query: 1183 tgctactcaaagcagg 1198
||||||||||||||||
Sbjct: 106415425 tgctactcaaagcagg 106415440
Score = 244 bits (123), Expect = 1e-61
Identities = 123/123 (100%)
Strand = Plus / Plus
Query: 942 gagcacctggtgcagaatgtttgtaagtcttaccgagacacgtgtcagctgcggctggag 1001
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106414143 gagcacctggtgcagaatgtttgtaagtcttaccgagacacgtgtcagctgcggctggag 106414202
Query: 1002 gacctgcttcggcagcgctccaacatcttctcccgagaggaggtggccggctaccagagg 1061
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106414203 gacctgcttcggcagcgctccaacatcttctcccgagaggaggtggccggctaccagagg 106414262
Query: 1062 aag 1064
|||
Sbjct: 106414263 aag 106414265
Score = 224 bits (113), Expect = 1e-55
Identities = 113/113 (100%)
Strand = Plus / Plus
Query: 1194 gcaggagcaatggaagtggtgctggtcaggatgtgccgagcctacaacgctgacaaccac 1253
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106415591 gcaggagcaatggaagtggtgctggtcaggatgtgccgagcctacaacgctgacaaccac 106415650
Query: 1254 acagtcttttttgaaggcaaatacggtggcatggagctgttccgagccttggg 1306
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106415651 acagtcttttttgaaggcaaatacggtggcatggagctgttccgagccttggg 106415703
Score = 222 bits (112), Expect = 5e-55
Identities = 112/112 (100%)
Strand = Plus / Plus
Query: 1305 ggctgcagcgagctcatcagctccatctttgacttctcccgctccctgagtgccttgcgc 1364
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106415887 ggctgcagcgagctcatcagctccatctttgacttctcccgctccctgagtgccttgcgc 106415946
Query: 1365 ttttccgaggacgagattgcactctacacagccctcgtcctcatcaatgcca 1416
||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106415947 ttttccgaggacgagattgcactctacacagccctcgtcctcatcaatgcca 106415998
Score = 218 bits (110), Expect = 8e-54
Identities = 110/110 (100%)
Strand = Plus / Plus
Query: 1417 accggccaggactccaagagaaaaggaaagtagaacagctgcagtacaatctggagctgg 1476
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106417172 accggccaggactccaagagaaaaggaaagtagaacagctgcagtacaatctggagctgg 106417231
Query: 1477 cctttcatcatcatctctgcaagacccatcgccaaggcatcctggccaag 1526
||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106417232 cctttcatcatcatctctgcaagacccatcgccaaggcatcctggccaag 106417281
Score = 172 bits (87), Expect = 4e-40
Identities = 87/87 (100%)
Strand = Plus / Plus
Query: 202 cacaaattgaagtgatcccctgcaaaatctgtggggacaagtcgtctgggatccactacg 261
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106411679 cacaaattgaagtgatcccctgcaaaatctgtggggacaagtcgtctgggatccactacg 106411738
Query: 262 gggttatcacctgtgaggggtgcaagg 288
|||||||||||||||||||||||||||
Sbjct: 106411739 gggttatcacctgtgaggggtgcaagg 106411765
>Sscrofa_Chr08
|| Length = 148491826
Score = 133 bits (67), Expect = 4e-28
Identities = 70/71 (98%)
Strand = Plus / Minus
Query: 1128 gagttcgctaagaggctctcgggctttatggagctctgccagaacgaccagatcgtgcta 1187
|||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||
Sbjct: 70985918 gagttcgctaagaggctctcgggctttatggagctctgccagaatgaccagatcgtgcta 70985859
Query: 1188 ctcaaagcagg 1198
|||||||||||
Sbjct: 70985858 ctcaaagcagg 70985848
>Sscrofa_Chr01
|| Length = 315321322
Score = 77.8 bits (39), Expect = 2e-11
Identities = 75/87 (86%)
Strand = Plus / Plus
Query: 202 cacaaattgaagtgatcccctgcaaaatctgtggggacaagtcgtctgggatccactacg 261
|||||||||||||||| || |||||||| ||||| || || || ||||||||||||||||
Sbjct: 254616177 cacaaattgaagtgataccatgcaaaatttgtggcgataaatcctctgggatccactacg 254616236
Query: 262 gggttatcacctgtgaggggtgcaagg 288
| || ||||| ||||| || |||||||
Sbjct: 254616237 gagtcatcacatgtgaaggctgcaagg 254616263
Score = 67.9 bits (34), Expect = 2e-08
Identities = 55/62 (88%)
Strand = Plus / Plus
Query: 429 gctgtcaagtttggccgcatgtccaagaagcaaagggacagcctgcatgctgaggtgcag 488
||||| |||||||| | |||||||||||||||||||||||||| |||| |||||||||
Sbjct: 254628166 gctgtgaagtttgggaggatgtccaagaagcaaagggacagcctctatgccgaggtgcag 254628225
Query: 489 aa 490
||
Sbjct: 254628226 aa 254628227
Database: Sscrofa_10.2.fasta
Posted date: Nov 16, 2011 10:34 AM
Number of letters in database: 2,808,509,378
Number of sequences in database: 4582
Lambda K H
1.37 0.711 1.31
Gapped
Lambda K H
1.37 0.711 1.31
Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 4582
Number of Hits to DB: 47,306,062
Number of extensions: 363
Number of successful extensions: 363
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 363
Number of HSP's successfully gapped: 14
Length of query: 1757
Length of database: 2,808,509,378
Length adjustment: 22
Effective length of query: 1735
Effective length of database: 2,808,408,574
Effective search space: 4872588875890
Effective search space used: 4872588875890
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 50 (99.1 bits)
S1: 18 (36.2 bits)
S2: 30 (60.0 bits)