Animal-Genome cDNA 20110601C-008422


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-008422
         (1693 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_001029559.1| nuclear pore complex protein Nup85 [Bos taur...   977   0.0  

>ref|NP_001029559.1| nuclear pore complex protein Nup85 [Bos taurus].
          Length = 656

 Score =  977 bits (2526), Expect(2) = 0.0
 Identities = 476/516 (92%), Positives = 492/516 (95%)
 Frame = +3

Query: 87   MEELDGEPTVTLIPGVNSQKKQMCFDWGPGEMLVCETSFNKKEKSEMVPGCPYIHIIRKD 266
            MEE DGEPTVT IPGVNSQKKQMCFDWGPGEMLVCETSFNKKEKSEMV GCP+IHIIRKD
Sbjct: 1    MEEFDGEPTVTWIPGVNSQKKQMCFDWGPGEMLVCETSFNKKEKSEMVAGCPFIHIIRKD 60

Query: 267  IDVYCKILRKLFNESHGIFVGLQRIEEEFTGKSRKAQLVRVSKNYRSVIRACMEEMHQLA 446
            IDVY KILRKLFNESHGIFVGLQRIEEE TGKSRKAQLVRVSKNYRSVIRACMEEMHQ A
Sbjct: 61   IDVYSKILRKLFNESHGIFVGLQRIEEELTGKSRKAQLVRVSKNYRSVIRACMEEMHQFA 120

Query: 447  IAAKDPASGGQFSSQISILSAMELIWNLCEILFIEVAPAGPXXXXXXDWVRLHVCEVDSL 626
            +A KD A G QFSSQ+SILSA+ELIWNLCEILFIEVAPAGP      DWVRLHVCEVDSL
Sbjct: 121  VADKDSAIGRQFSSQVSILSAVELIWNLCEILFIEVAPAGPLLLYLLDWVRLHVCEVDSL 180

Query: 627  SADVLGSENPSKHQDFWKLVTILVLQGRLDEARQMLSKEADASPTSAGMCRVLGDLMRTM 806
            SADVLGSENPSKH+ FW LVT LVLQGRLDEARQMLSKEAD++PTSAGMCRVLGDLMRTM
Sbjct: 181  SADVLGSENPSKHESFWNLVTTLVLQGRLDEARQMLSKEADSNPTSAGMCRVLGDLMRTM 240

Query: 807  PVLSPGNTQTLTELELKWQHWHEECERHLQDGTFASSPHLESLCKIMLGDEAALLEQKEL 986
            P+LSPGNTQTLTELEL+WQHWHEECERHLQDGTFAS+PHLESLCK++LGD+AALLE KEL
Sbjct: 241  PILSPGNTQTLTELELRWQHWHEECERHLQDGTFASNPHLESLCKVLLGDDAALLEHKEL 300

Query: 987  LSNWYHFLVTRLLYSCPTVKPMDLHCYAQSSLDLFLGGESSAEPLDNILLAAFEFDIHQV 1166
            LSNWYHFLVTRLLYS PTVKPMDLH YAQSSLDLFLGGESS EPLDNIL+AAFEFDIHQV
Sbjct: 301  LSNWYHFLVTRLLYSQPTVKPMDLHLYAQSSLDLFLGGESSPEPLDNILMAAFEFDIHQV 360

Query: 1167 IKECSIALSNWWFVAHLTDLLDHCKLLQSHNLYFGSNMREFLLLEYASGLFAHHSLWQLG 1346
            IKECSIALSNWWFVAHLTDLLDHCKLLQSHNLYFGSNMREFLLLEYASGLFAHHSLWQLG
Sbjct: 361  IKECSIALSNWWFVAHLTDLLDHCKLLQSHNLYFGSNMREFLLLEYASGLFAHHSLWQLG 420

Query: 1347 VDYFDHCPELGRVSLELHIERIPLSTEQKALKVLRVCEQRQMTEQVRSICKILAMKAVRN 1526
            VDY DHCPELGRVSLELHIERIPL+TEQKALKVLRVCEQRQMTEQVRSICK+LAMKAVRN
Sbjct: 421  VDYCDHCPELGRVSLELHIERIPLTTEQKALKVLRVCEQRQMTEQVRSICKVLAMKAVRN 480

Query: 1527 NRLGSALSWSIRAKDAAFATLVSDRFLRDYCERGCF 1634
            NRLGSALSWSIRAKDAAFATLVSDRFLRDYCERGCF
Sbjct: 481  NRLGSALSWSIRAKDAAFATLVSDRFLRDYCERGCF 516



 Score = 29.6 bits (65), Expect(2) = 0.0
 Identities = 13/13 (100%), Positives = 13/13 (100%)
 Frame = +2

Query: 1655 NLGPAMMLSDRLT 1693
            NLGPAMMLSDRLT
Sbjct: 524  NLGPAMMLSDRLT 536


  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: 68,786,659
Number of extensions: 1931538
Number of successful extensions: 7748
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 7725
Number of HSP's successfully gapped: 2
Length of query: 564
Length of database: 17,681,374
Length adjustment: 107
Effective length of query: 457
Effective length of database: 14,140,958
Effective search space: 6462417806
Effective search space used: 6462417806
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-008422
         (1693 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_533121.2| PREDICTED: similar to pericentrin 1 isoform 1 [...   980   0.0  
Alignment   gi|XP_859218.1| PREDICTED: similar to pericentrin 1 isoform 2 [...   674   0.0  

>ref|XP_533121.2| PREDICTED: similar to pericentrin 1 isoform 1 [Canis familiaris].
          Length = 655

 Score =  980 bits (2534), Expect(2) = 0.0
 Identities = 479/516 (92%), Positives = 496/516 (96%)
 Frame = +3

Query: 87   MEELDGEPTVTLIPGVNSQKKQMCFDWGPGEMLVCETSFNKKEKSEMVPGCPYIHIIRKD 266
            MEELDGEPTVTLIPGVNS+ KQMCFDWGPGEMLVCETSFNK EKSE  PGCP+I+IIRKD
Sbjct: 1    MEELDGEPTVTLIPGVNSKMKQMCFDWGPGEMLVCETSFNKNEKSETEPGCPFIYIIRKD 60

Query: 267  IDVYCKILRKLFNESHGIFVGLQRIEEEFTGKSRKAQLVRVSKNYRSVIRACMEEMHQLA 446
            IDVY +ILRKLFNESHGIFVGLQRIEEE TGKSRKAQLVRVSKNYRSVIRACMEEMHQ+A
Sbjct: 61   IDVYSQILRKLFNESHGIFVGLQRIEEELTGKSRKAQLVRVSKNYRSVIRACMEEMHQVA 120

Query: 447  IAAKDPASGGQFSSQISILSAMELIWNLCEILFIEVAPAGPXXXXXXDWVRLHVCEVDSL 626
            IAAKDPASG QFSSQ+SILSAMELIWNLCEILFIEVAPAGP      DWVRLHVCEVDSL
Sbjct: 121  IAAKDPASGRQFSSQVSILSAMELIWNLCEILFIEVAPAGPLLLHLLDWVRLHVCEVDSL 180

Query: 627  SADVLGSENPSKHQDFWKLVTILVLQGRLDEARQMLSKEADASPTSAGMCRVLGDLMRTM 806
             ADVLGSENPSKH+ FW LVTILVLQGRLDEARQMLSKEADA+P+SAGMCR+LGDLMRTM
Sbjct: 181  LADVLGSENPSKHESFWNLVTILVLQGRLDEARQMLSKEADANPSSAGMCRILGDLMRTM 240

Query: 807  PVLSPGNTQTLTELELKWQHWHEECERHLQDGTFASSPHLESLCKIMLGDEAALLEQKEL 986
            PVLSPGNTQTLTELELKWQHWHEECERHLQD TFA+SPHLESLCKI+LGDEAALLEQKEL
Sbjct: 241  PVLSPGNTQTLTELELKWQHWHEECERHLQDSTFAASPHLESLCKILLGDEAALLEQKEL 300

Query: 987  LSNWYHFLVTRLLYSCPTVKPMDLHCYAQSSLDLFLGGESSAEPLDNILLAAFEFDIHQV 1166
            L+NWYHFLVTRLLYS PTVKP+DLH YAQSSLDLFLGGESS EPLDNILLAAFEFDIHQV
Sbjct: 301  LNNWYHFLVTRLLYSHPTVKPIDLHLYAQSSLDLFLGGESSPEPLDNILLAAFEFDIHQV 360

Query: 1167 IKECSIALSNWWFVAHLTDLLDHCKLLQSHNLYFGSNMREFLLLEYASGLFAHHSLWQLG 1346
            IKECSIALSNWWFVAHLTDLLDHCKLLQSHNLYFGSNMREFLLLEYASGLFAHHSLWQLG
Sbjct: 361  IKECSIALSNWWFVAHLTDLLDHCKLLQSHNLYFGSNMREFLLLEYASGLFAHHSLWQLG 420

Query: 1347 VDYFDHCPELGRVSLELHIERIPLSTEQKALKVLRVCEQRQMTEQVRSICKILAMKAVRN 1526
            VDYFD+CPELGRVSLELHIERIPLSTEQKALKVLR+CEQRQMTEQVRSICKILAMKAVRN
Sbjct: 421  VDYFDYCPELGRVSLELHIERIPLSTEQKALKVLRICEQRQMTEQVRSICKILAMKAVRN 480

Query: 1527 NRLGSALSWSIRAKDAAFATLVSDRFLRDYCERGCF 1634
            NRLGSALSWSIRAKDAAFATLVSDRFL+DYCERGCF
Sbjct: 481  NRLGSALSWSIRAKDAAFATLVSDRFLKDYCERGCF 516



 Score = 29.6 bits (65), Expect(2) = 0.0
 Identities = 13/13 (100%), Positives = 13/13 (100%)
 Frame = +2

Query: 1655 NLGPAMMLSDRLT 1693
            NLGPAMMLSDRLT
Sbjct: 524  NLGPAMMLSDRLT 536


>ref|XP_859218.1| PREDICTED: similar to pericentrin 1 isoform 2 [Canis familiaris].
          Length = 378

 Score =  674 bits (1740), Expect = 0.0
 Identities = 330/364 (90%), Positives = 344/364 (94%)
 Frame = +3

Query: 87   MEELDGEPTVTLIPGVNSQKKQMCFDWGPGEMLVCETSFNKKEKSEMVPGCPYIHIIRKD 266
            MEELDGEPTVTLIPGVNS+ KQMCFDWGPGEMLVCETSFNK EKSE  PGCP+I+IIRKD
Sbjct: 1    MEELDGEPTVTLIPGVNSKMKQMCFDWGPGEMLVCETSFNKNEKSETEPGCPFIYIIRKD 60

Query: 267  IDVYCKILRKLFNESHGIFVGLQRIEEEFTGKSRKAQLVRVSKNYRSVIRACMEEMHQLA 446
            IDVY +ILRKLFNESHGIFVGLQRIEEE TGKSRKAQLVRVSKNYRSVIRACMEEMHQ+A
Sbjct: 61   IDVYSQILRKLFNESHGIFVGLQRIEEELTGKSRKAQLVRVSKNYRSVIRACMEEMHQVA 120

Query: 447  IAAKDPASGGQFSSQISILSAMELIWNLCEILFIEVAPAGPXXXXXXDWVRLHVCEVDSL 626
            IAAKDPASG QFSSQ+SILSAMELIWNLCEILFIEVAPAGP      DWVRLHVCEVDSL
Sbjct: 121  IAAKDPASGRQFSSQVSILSAMELIWNLCEILFIEVAPAGPLLLHLLDWVRLHVCEVDSL 180

Query: 627  SADVLGSENPSKHQDFWKLVTILVLQGRLDEARQMLSKEADASPTSAGMCRVLGDLMRTM 806
             ADVLGSENPSKH+ FW LVTILVLQGRLDEARQMLSKEADA+P+SAGMCR+LGDLMRTM
Sbjct: 181  LADVLGSENPSKHESFWNLVTILVLQGRLDEARQMLSKEADANPSSAGMCRILGDLMRTM 240

Query: 807  PVLSPGNTQTLTELELKWQHWHEECERHLQDGTFASSPHLESLCKIMLGDEAALLEQKEL 986
            PVLSPGNTQTLTELELKWQHWHEECERHLQD TFA+SPHLESLCKI+LGDEAALLEQKEL
Sbjct: 241  PVLSPGNTQTLTELELKWQHWHEECERHLQDSTFAASPHLESLCKILLGDEAALLEQKEL 300

Query: 987  LSNWYHFLVTRLLYSCPTVKPMDLHCYAQSSLDLFLGGESSAEPLDNILLAAFEFDIHQV 1166
            L+NWYHFLVTRLLYS PTVKP+DLH YAQSSLDLFLGGESS EPLDNILLAAFEFDIHQV
Sbjct: 301  LNNWYHFLVTRLLYSHPTVKPIDLHLYAQSSLDLFLGGESSPEPLDNILLAAFEFDIHQV 360

Query: 1167 IKEC 1178
            IKEC
Sbjct: 361  IKEC 364


  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: 71,625,741
Number of extensions: 1980651
Number of successful extensions: 7868
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 7848
Number of HSP's successfully gapped: 3
Length of query: 564
Length of database: 18,874,504
Length adjustment: 108
Effective length of query: 456
Effective length of database: 15,274,216
Effective search space: 6965042496
Effective search space used: 6965042496
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-008422
         (1693 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_003131259.1| PREDICTED: nuclear pore complex protein Nup8...  1039   0.0  

>ref|XP_003131259.1| PREDICTED: nuclear pore complex protein Nup85-like [Sus scrofa].
          Length = 656

 Score = 1039 bits (2687), Expect(2) = 0.0
 Identities = 510/516 (98%), Positives = 510/516 (98%)
 Frame = +3

Query: 87   MEELDGEPTVTLIPGVNSQKKQMCFDWGPGEMLVCETSFNKKEKSEMVPGCPYIHIIRKD 266
            MEELDGEPTVTLIPGVNSQKKQMCFDWGPGEMLVCETSFNKKEKSEMVPGCPYIHIIRKD
Sbjct: 1    MEELDGEPTVTLIPGVNSQKKQMCFDWGPGEMLVCETSFNKKEKSEMVPGCPYIHIIRKD 60

Query: 267  IDVYCKILRKLFNESHGIFVGLQRIEEEFTGKSRKAQLVRVSKNYRSVIRACMEEMHQLA 446
            IDVYCKILRKLFNESHGIFVGLQRIEEEFTGKSRKAQLVRVSKNYRSVIRACMEEMHQLA
Sbjct: 61   IDVYCKILRKLFNESHGIFVGLQRIEEEFTGKSRKAQLVRVSKNYRSVIRACMEEMHQLA 120

Query: 447  IAAKDPASGGQFSSQISILSAMELIWNLCEILFIEVAPAGPXXXXXXDWVRLHVCEVDSL 626
            IAAKDPASGGQFSSQISILSAMELIWNLCEILFIEVAPAGP      DWVRLHVCEVDSL
Sbjct: 121  IAAKDPASGGQFSSQISILSAMELIWNLCEILFIEVAPAGPLLLHLLDWVRLHVCEVDSL 180

Query: 627  SADVLGSENPSKHQDFWKLVTILVLQGRLDEARQMLSKEADASPTSAGMCRVLGDLMRTM 806
            SADVLGSENPSKHQDFWKLVTILVLQGRLDEARQMLSKEADASPTSAGMCRVLGDLMRTM
Sbjct: 181  SADVLGSENPSKHQDFWKLVTILVLQGRLDEARQMLSKEADASPTSAGMCRVLGDLMRTM 240

Query: 807  PVLSPGNTQTLTELELKWQHWHEECERHLQDGTFASSPHLESLCKIMLGDEAALLEQKEL 986
            PVLSPGNTQTLTELELKWQHWHEECERHLQDGTFASSPHLESLCKIMLGDEAALLEQKEL
Sbjct: 241  PVLSPGNTQTLTELELKWQHWHEECERHLQDGTFASSPHLESLCKIMLGDEAALLEQKEL 300

Query: 987  LSNWYHFLVTRLLYSCPTVKPMDLHCYAQSSLDLFLGGESSAEPLDNILLAAFEFDIHQV 1166
            LSNWYHFLVTRLLYSCPTVKPMDLHCYAQSSLDLFLGGESSAEPLDNILLAAFEFDIHQV
Sbjct: 301  LSNWYHFLVTRLLYSCPTVKPMDLHCYAQSSLDLFLGGESSAEPLDNILLAAFEFDIHQV 360

Query: 1167 IKECSIALSNWWFVAHLTDLLDHCKLLQSHNLYFGSNMREFLLLEYASGLFAHHSLWQLG 1346
            IKECSIALSNWWFVAHLTDLLDHCKLLQSHNLYFGSNMREFLLLEYASGLFAHHSLWQLG
Sbjct: 361  IKECSIALSNWWFVAHLTDLLDHCKLLQSHNLYFGSNMREFLLLEYASGLFAHHSLWQLG 420

Query: 1347 VDYFDHCPELGRVSLELHIERIPLSTEQKALKVLRVCEQRQMTEQVRSICKILAMKAVRN 1526
            VDYFDHCPELGRVSLELHIERIPLSTEQKALKVLRVCEQRQMTEQVRSICKILAMKAVRN
Sbjct: 421  VDYFDHCPELGRVSLELHIERIPLSTEQKALKVLRVCEQRQMTEQVRSICKILAMKAVRN 480

Query: 1527 NRLGSALSWSIRAKDAAFATLVSDRFLRDYCERGCF 1634
            NRLGSALSWSIRAKDAAFATLVSDRFLRDYCERGCF
Sbjct: 481  NRLGSALSWSIRAKDAAFATLVSDRFLRDYCERGCF 516



 Score = 29.6 bits (65), Expect(2) = 0.0
 Identities = 13/13 (100%), Positives = 13/13 (100%)
 Frame = +2

Query: 1655 NLGPAMMLSDRLT 1693
            NLGPAMMLSDRLT
Sbjct: 524  NLGPAMMLSDRLT 536


  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: 44,328,370
Number of extensions: 1244864
Number of successful extensions: 5199
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 5183
Number of HSP's successfully gapped: 2
Length of query: 564
Length of database: 11,343,932
Length adjustment: 104
Effective length of query: 460
Effective length of database: 8,754,644
Effective search space: 4027136240
Effective search space used: 4027136240
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-008422
         (1693 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_001002929.3| nuclear pore complex protein Nup85 [Mus musc...   953   0.0  

>ref|NP_001002929.3| nuclear pore complex protein Nup85 [Mus musculus].
          Length = 656

 Score =  953 bits (2463), Expect(2) = 0.0
 Identities = 462/516 (89%), Positives = 491/516 (95%)
 Frame = +3

Query: 87   MEELDGEPTVTLIPGVNSQKKQMCFDWGPGEMLVCETSFNKKEKSEMVPGCPYIHIIRKD 266
            MEELD EP VT IPGVNS+KKQMCFDWGPGEML+CETSFN+  KSE VP CP+I+IIRKD
Sbjct: 1    MEELDCEPAVTWIPGVNSKKKQMCFDWGPGEMLLCETSFNQTGKSEKVPSCPFIYIIRKD 60

Query: 267  IDVYCKILRKLFNESHGIFVGLQRIEEEFTGKSRKAQLVRVSKNYRSVIRACMEEMHQLA 446
            +DVY +ILRKLFNESHGIFVGLQ+IEEE +GKSRKAQLVRVSKNYRSVIRACMEEMHQ+A
Sbjct: 61   VDVYSQILRKLFNESHGIFVGLQKIEEELSGKSRKAQLVRVSKNYRSVIRACMEEMHQVA 120

Query: 447  IAAKDPASGGQFSSQISILSAMELIWNLCEILFIEVAPAGPXXXXXXDWVRLHVCEVDSL 626
            IAAKDPASG QFSSQ+SILSAMELIWNLCEILFIEVAPAGP      DWVRLHVCEVDSL
Sbjct: 121  IAAKDPASGRQFSSQVSILSAMELIWNLCEILFIEVAPAGPLLLHLLDWVRLHVCEVDSL 180

Query: 627  SADVLGSENPSKHQDFWKLVTILVLQGRLDEARQMLSKEADASPTSAGMCRVLGDLMRTM 806
            SADVLG +NPSKH++FW LVT+LVLQGRLDEARQML+KEADA+P+ AGMCRVLGDLMRTM
Sbjct: 181  SADVLGGDNPSKHENFWDLVTVLVLQGRLDEARQMLAKEADANPSCAGMCRVLGDLMRTM 240

Query: 807  PVLSPGNTQTLTELELKWQHWHEECERHLQDGTFASSPHLESLCKIMLGDEAALLEQKEL 986
            P+LSPGNTQTLTELELKWQHW EECERHLQD TFA++P LESLCKIMLGDEAALLEQKEL
Sbjct: 241  PILSPGNTQTLTELELKWQHWREECERHLQDNTFAANPRLESLCKIMLGDEAALLEQKEL 300

Query: 987  LSNWYHFLVTRLLYSCPTVKPMDLHCYAQSSLDLFLGGESSAEPLDNILLAAFEFDIHQV 1166
            LSNWYHFLVTRLLYS PTVKP+DLH YAQSSLD+FLGGESS EPLDNIL+AAFEFDIHQV
Sbjct: 301  LSNWYHFLVTRLLYSNPTVKPIDLHFYAQSSLDMFLGGESSPEPLDNILMAAFEFDIHQV 360

Query: 1167 IKECSIALSNWWFVAHLTDLLDHCKLLQSHNLYFGSNMREFLLLEYASGLFAHHSLWQLG 1346
            IKECSIALSNWWFVAHLTDLLDHC+LLQSHNLYFGSNMREFLLLEYASGLFAHHSLWQLG
Sbjct: 361  IKECSIALSNWWFVAHLTDLLDHCRLLQSHNLYFGSNMREFLLLEYASGLFAHHSLWQLG 420

Query: 1347 VDYFDHCPELGRVSLELHIERIPLSTEQKALKVLRVCEQRQMTEQVRSICKILAMKAVRN 1526
            VDYFD+CPELGRVSLELHIERIPL+TEQKALKVLR+CEQRQMTEQV+SICKILAMKAVRN
Sbjct: 421  VDYFDYCPELGRVSLELHIERIPLNTEQKALKVLRICEQRQMTEQVKSICKILAMKAVRN 480

Query: 1527 NRLGSALSWSIRAKDAAFATLVSDRFLRDYCERGCF 1634
            NRLGSALSWSIRAKDAAFATLVSDRFLRDYCERGCF
Sbjct: 481  NRLGSALSWSIRAKDAAFATLVSDRFLRDYCERGCF 516



 Score = 26.6 bits (57), Expect(2) = 0.0
 Identities = 12/13 (92%), Positives = 12/13 (92%)
 Frame = +2

Query: 1655 NLGPAMMLSDRLT 1693
            NLG AMMLSDRLT
Sbjct: 524  NLGSAMMLSDRLT 536


  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: 59,495,693
Number of extensions: 1628418
Number of successful extensions: 6373
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 6305
Number of HSP's successfully gapped: 2
Length of query: 564
Length of database: 15,617,559
Length adjustment: 107
Effective length of query: 457
Effective length of database: 12,403,707
Effective search space: 5668494099
Effective search space used: 5668494099
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-008422
         (1693 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_079120.1| nuclear pore complex protein Nup85 [Homo sapien...   967   0.0  

>ref|NP_079120.1| nuclear pore complex protein Nup85 [Homo sapiens].
          Length = 656

 Score =  967 bits (2500), Expect(2) = 0.0
 Identities = 473/516 (91%), Positives = 494/516 (95%)
 Frame = +3

Query: 87   MEELDGEPTVTLIPGVNSQKKQMCFDWGPGEMLVCETSFNKKEKSEMVPGCPYIHIIRKD 266
            MEELDGEPTVTLIPGVNS+K QM FDWGPGEMLVCETSFNKKEKSEMVP CP+I+IIRKD
Sbjct: 1    MEELDGEPTVTLIPGVNSKKNQMYFDWGPGEMLVCETSFNKKEKSEMVPSCPFIYIIRKD 60

Query: 267  IDVYCKILRKLFNESHGIFVGLQRIEEEFTGKSRKAQLVRVSKNYRSVIRACMEEMHQLA 446
            +DVY +ILRKLFNESHGIF+GLQRI+EE TGKSRK+QLVRVSKNYRSVIRACMEEMHQ+A
Sbjct: 61   VDVYSQILRKLFNESHGIFLGLQRIDEELTGKSRKSQLVRVSKNYRSVIRACMEEMHQVA 120

Query: 447  IAAKDPASGGQFSSQISILSAMELIWNLCEILFIEVAPAGPXXXXXXDWVRLHVCEVDSL 626
            IAAKDPA+G QFSSQ+SILSAMELIWNLCEILFIEVAPAGP      DWVRLHVCEVDSL
Sbjct: 121  IAAKDPANGRQFSSQVSILSAMELIWNLCEILFIEVAPAGPLLLHLLDWVRLHVCEVDSL 180

Query: 627  SADVLGSENPSKHQDFWKLVTILVLQGRLDEARQMLSKEADASPTSAGMCRVLGDLMRTM 806
            SADVLGSENPSKH  FW LVTILVLQGRLDEARQMLSKEADASP SAG+CR++GDLMRTM
Sbjct: 181  SADVLGSENPSKHDSFWNLVTILVLQGRLDEARQMLSKEADASPASAGICRIMGDLMRTM 240

Query: 807  PVLSPGNTQTLTELELKWQHWHEECERHLQDGTFASSPHLESLCKIMLGDEAALLEQKEL 986
            P+LSPGNTQTLTELELKWQHWHEECER+LQD TFA+SPHLESL KIMLGDEAALLEQKEL
Sbjct: 241  PILSPGNTQTLTELELKWQHWHEECERYLQDSTFATSPHLESLLKIMLGDEAALLEQKEL 300

Query: 987  LSNWYHFLVTRLLYSCPTVKPMDLHCYAQSSLDLFLGGESSAEPLDNILLAAFEFDIHQV 1166
            LSNWYHFLVTRLLYS PTVKP+DLH YAQSSLDLFLGGESS EPLDNILLAAFEFDIHQV
Sbjct: 301  LSNWYHFLVTRLLYSNPTVKPIDLHYYAQSSLDLFLGGESSPEPLDNILLAAFEFDIHQV 360

Query: 1167 IKECSIALSNWWFVAHLTDLLDHCKLLQSHNLYFGSNMREFLLLEYASGLFAHHSLWQLG 1346
            IKECSIALSNWWFVAHLTDLLDHCKLLQSHNLYFGSNMREFLLLEYASGLFAH SLWQLG
Sbjct: 361  IKECSIALSNWWFVAHLTDLLDHCKLLQSHNLYFGSNMREFLLLEYASGLFAHPSLWQLG 420

Query: 1347 VDYFDHCPELGRVSLELHIERIPLSTEQKALKVLRVCEQRQMTEQVRSICKILAMKAVRN 1526
            VDYFD+CPELGRVSLELHIERIPL+TEQKALKVLR+CEQRQMTEQVRSICKILAMKAVRN
Sbjct: 421  VDYFDYCPELGRVSLELHIERIPLNTEQKALKVLRICEQRQMTEQVRSICKILAMKAVRN 480

Query: 1527 NRLGSALSWSIRAKDAAFATLVSDRFLRDYCERGCF 1634
            NRLGSALSWSIRAKDAAFATLVSDRFLRDYCERGCF
Sbjct: 481  NRLGSALSWSIRAKDAAFATLVSDRFLRDYCERGCF 516



 Score = 29.6 bits (65), Expect(2) = 0.0
 Identities = 13/13 (100%), Positives = 13/13 (100%)
 Frame = +2

Query: 1655 NLGPAMMLSDRLT 1693
            NLGPAMMLSDRLT
Sbjct: 524  NLGPAMMLSDRLT 536


  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: 70,344,582
Number of extensions: 1945751
Number of successful extensions: 7539
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 7514
Number of HSP's successfully gapped: 2
Length of query: 564
Length of database: 18,297,164
Length adjustment: 108
Effective length of query: 456
Effective length of database: 14,737,052
Effective search space: 6720095712
Effective search space used: 6720095712
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-008422
         (1693 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_Chr12                                                         313   2e-82

>Sscrofa_Chr12 
||          Length = 63588571

 Score =  313 bits (158), Expect = 2e-82
 Identities = 158/158 (100%)
 Strand = Plus / Minus

                                                                           
Query: 219     tcagagatggtgcctggttgcccctatatccatattatccggaaagatatagatgtttat 278
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6060248 tcagagatggtgcctggttgcccctatatccatattatccggaaagatatagatgtttat 6060189

                                                                           
Query: 279     tgtaaaatcctaagaaaactcttcaacgagtcccatggaatctttgtgggccttcagaga 338
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6060188 tgtaaaatcctaagaaaactcttcaacgagtcccatggaatctttgtgggccttcagaga 6060129

                                                     
Query: 339     attgaagaagagtttactggaaaatccagaaaagctca 376
               ||||||||||||||||||||||||||||||||||||||
Sbjct: 6060128 attgaagaagagtttactggaaaatccagaaaagctca 6060091



 Score =  307 bits (155), Expect = 1e-80
 Identities = 155/155 (100%)
 Strand = Plus / Minus

                                                                           
Query: 1328    cagcctgtggcagctgggggtggattactttgaccactgccctgagctgggccgagtttc 1387
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6040046 cagcctgtggcagctgggggtggattactttgaccactgccctgagctgggccgagtttc 6039987

                                                                           
Query: 1388    gttggagctgcatatcgagcggatcccgctgagcacggagcagaaagccctcaaggtgct 1447
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6039986 gttggagctgcatatcgagcggatcccgctgagcacggagcagaaagccctcaaggtgct 6039927

                                                  
Query: 1448    gcgggtttgcgagcagcggcagatgacggagcaag 1482
               |||||||||||||||||||||||||||||||||||
Sbjct: 6039926 gcgggtttgcgagcagcggcagatgacggagcaag 6039892



 Score =  270 bits (136), Expect = 2e-69
 Identities = 136/136 (100%)
 Strand = Plus / Minus

                                                                           
Query: 683     ggtgaccatcctggtgctgcagggccggctggacgaggcccggcagatgctctccaagga 742
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6048588 ggtgaccatcctggtgctgcagggccggctggacgaggcccggcagatgctctccaagga 6048529

                                                                           
Query: 743     agccgacgccagccccacctctgcaggcatgtgccgcgtcctgggggacctgatgaggac 802
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6048528 agccgacgccagccccacctctgcaggcatgtgccgcgtcctgggggacctgatgaggac 6048469

                               
Query: 803     aatgcccgttctcagc 818
               ||||||||||||||||
Sbjct: 6048468 aatgcccgttctcagc 6048453



 Score =  266 bits (134), Expect = 4e-68
 Identities = 134/134 (100%)
 Strand = Plus / Minus

                                                                           
Query: 940     agatcatgctgggagacgaagctgccctgttggagcaaaaggagcttctgagtaactggt 999
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6048018 agatcatgctgggagacgaagctgccctgttggagcaaaaggagcttctgagtaactggt 6047959

                                                                           
Query: 1000    accatttcctagtgacccggctcctgtactcttgtcccacagtgaaacccatggacctgc 1059
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6047958 accatttcctagtgacccggctcctgtactcttgtcccacagtgaaacccatggacctgc 6047899

                             
Query: 1060    actgctatgcccag 1073
               ||||||||||||||
Sbjct: 6047898 actgctatgcccag 6047885



 Score =  256 bits (129), Expect = 3e-65
 Identities = 129/129 (100%)
 Strand = Plus / Minus

                                                                           
Query: 557     cccagccggccccctcctccttcacctccttgactgggtccgattgcacgtgtgtgaggt 616
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6051410 cccagccggccccctcctccttcacctccttgactgggtccgattgcacgtgtgtgaggt 6051351

                                                                           
Query: 617     ggacagtttgtcggcagatgttctgggcagtgagaatccaagcaaacaccaggacttctg 676
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6051350 ggacagtttgtcggcagatgttctgggcagtgagaatccaagcaaacaccaggacttctg 6051291

                        
Query: 677     gaagctggt 685
               |||||||||
Sbjct: 6051290 gaagctggt 6051282



 Score =  244 bits (123), Expect = 1e-61
 Identities = 123/123 (100%)
 Strand = Plus / Minus

                                                                           
Query: 1480    aagttcgcagcatttgtaagatcttagccatgaaagctgtccgcaacaatcgcctgggct 1539
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6039128 aagttcgcagcatttgtaagatcttagccatgaaagctgtccgcaacaatcgcctgggct 6039069

                                                                           
Query: 1540    ccgccctctcttggagcattcgagccaaagatgctgcctttgccacgctggtgtcagaca 1599
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6039068 ccgccctctcttggagcattcgagccaaagatgctgcctttgccacgctggtgtcagaca 6039009

                  
Query: 1600    ggt 1602
               |||
Sbjct: 6039008 ggt 6039006



 Score =  244 bits (123), Expect = 1e-61
 Identities = 123/123 (100%)
 Strand = Plus / Minus

                                                                           
Query: 819     cctggtaacactcagacgttgaccgagctggagctgaagtggcagcactggcacgaggag 878
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6048349 cctggtaacactcagacgttgaccgagctggagctgaagtggcagcactggcacgaggag 6048290

                                                                           
Query: 879     tgcgagcggcacctccaagatggcacattcgcctccagtcctcacctcgagtctctttgc 938
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6048289 tgcgagcggcacctccaagatggcacattcgcctccagtcctcacctcgagtctctttgc 6048230

                  
Query: 939     aag 941
               |||
Sbjct: 6048229 aag 6048227



 Score =  232 bits (117), Expect = 5e-58
 Identities = 117/117 (100%)
 Strand = Plus / Minus

                                                                           
Query: 3       tttctcgcagcgggttctgagcgggaggcccgagccgcgaacatttgcggccctgagaga 62
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6066161 tttctcgcagcgggttctgagcgggaggcccgagccgcgaacatttgcggccctgagaga 6066102

                                                                        
Query: 63      tccaggcggctgtggtgcggcgcaatggaggagctcgatggggagccgacagtcact 119
               |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6066101 tccaggcggctgtggtgcggcgcaatggaggagctcgatggggagccgacagtcact 6066045



 Score =  218 bits (110), Expect = 8e-54
 Identities = 110/110 (100%)
 Strand = Plus / Minus

                                                                           
Query: 1071    cagtccagcctggacctgtttctgggaggtgagagcagcgcagaacccttggacaacatc 1130
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6047637 cagtccagcctggacctgtttctgggaggtgagagcagcgcagaacccttggacaacatc 6047578

                                                                 
Query: 1131    ttgttggcagccttcgagttcgacatccaccaagtgataaaggagtgcag 1180
               ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6047577 ttgttggcagccttcgagttcgacatccaccaagtgataaaggagtgcag 6047528



 Score =  176 bits (89), Expect = 3e-41
 Identities = 96/97 (98%), Gaps = 1/97 (1%)
 Strand = Plus / Minus

                                                                           
Query: 1598    caggttcctcagggattactgtgagcgaggctgcttt-ccgacctcgatctcattgacaa 1656
               ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Sbjct: 6038902 caggttcctcagggattactgtgagcgaggctgcttttccgacctcgatctcattgacaa 6038843

                                                    
Query: 1657    cctggggccagccatgatgctcagtgatcgactgacg 1693
               |||||||||||||||||||||||||||||||||||||
Sbjct: 6038842 cctggggccagccatgatgctcagtgatcgactgacg 6038806



 Score =  172 bits (87), Expect = 4e-40
 Identities = 87/87 (100%)
 Strand = Plus / Minus

                                                                           
Query: 120     ttgattccaggagtgaattcccagaagaagcaaatgtgttttgactggggtccaggggag 179
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6064077 ttgattccaggagtgaattcccagaagaagcaaatgtgttttgactggggtccaggggag 6064018

                                          
Query: 180     atgctggtatgtgaaacctctttcaac 206
               |||||||||||||||||||||||||||
Sbjct: 6064017 atgctggtatgtgaaacctctttcaac 6063991



 Score =  170 bits (86), Expect = 2e-39
 Identities = 86/86 (100%)
 Strand = Plus / Minus

                                                                           
Query: 1179    agcattgccctcagcaactggtggtttgtggcccacctgacagacctgctggatcactgc 1238
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6040552 agcattgccctcagcaactggtggtttgtggcccacctgacagacctgctggatcactgc 6040493

                                         
Query: 1239    aaactcctccagtctcacaacctcta 1264
               ||||||||||||||||||||||||||
Sbjct: 6040492 aaactcctccagtctcacaacctcta 6040467



 Score =  141 bits (71), Expect = 1e-30
 Identities = 71/71 (100%)
 Strand = Plus / Minus

                                                                           
Query: 377     attggttcgagtgagtaaaaactaccgatcagtcataagagcgtgcatggaggaaatgca 436
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6057512 attggttcgagtgagtaaaaactaccgatcagtcataagagcgtgcatggaggaaatgca 6057453

                          
Query: 437     ccagcttgcaa 447
               |||||||||||
Sbjct: 6057452 ccagcttgcaa 6057442



 Score =  135 bits (68), Expect = 9e-29
 Identities = 71/72 (98%)
 Strand = Plus / Minus

                                                                           
Query: 490     agatctccattttgtcagccatggagctcatttggaacctttgtgagattctttttattg 549
               |||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||
Sbjct: 6054281 agatctccattttgtcagccatggagctaatttggaacctttgtgagattctttttattg 6054222

                           
Query: 550     aagtggccccag 561
               ||||||||||||
Sbjct: 6054221 aagtggccccag 6054210



 Score =  131 bits (66), Expect = 1e-27
 Identities = 66/66 (100%)
 Strand = Plus / Minus

                                                                           
Query: 1265    cttcgggtccaacatgagagagttcctcctgctggaatatgcctcaggcctgtttgccca 1324
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6040316 cttcgggtccaacatgagagagttcctcctgctggaatatgcctcaggcctgtttgccca 6040257

                     
Query: 1325    tcacag 1330
               ||||||
Sbjct: 6040256 tcacag 6040251



 Score = 87.7 bits (44), Expect = 2e-14
 Identities = 44/44 (100%)
 Strand = Plus / Minus

                                                           
Query: 448     ttgctgctaaagatccagccagtggcggccagtttagcagccag 491
               ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6055817 ttgctgctaaagatccagccagtggcggccagtttagcagccag 6055774


  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: 45,173,795
Number of extensions: 263
Number of successful extensions: 263
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 262
Number of HSP's successfully gapped: 16
Length of query: 1693
Length of database: 2,808,509,378
Length adjustment: 22
Effective length of query: 1671
Effective length of database: 2,808,408,574
Effective search space: 4692850727154
Effective search space used: 4692850727154
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)