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-001319
(1774 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_001039504.1| U1 small nuclear ribonucleoprotein A [Bos ta... 365 e-101
Alignment gi|NP_001179481.1| U2 small nuclear ribonucleoprotein B'' [Bos ... 160 3e-39
Alignment gi|XP_002683786.1| PREDICTED: small nuclear ribonucleoprotein p... 160 3e-39
Alignment gi|NP_001070585.1| RNA-binding protein 40 [Bos taurus]. 50 8e-06
>ref|NP_001039504.1| U1 small nuclear ribonucleoprotein A [Bos taurus].
Length = 282
Score = 365 bits (938), Expect = e-101
Identities = 199/282 (70%), Positives = 200/282 (70%)
Frame = +3
Query: 81 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 260
MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK
Sbjct: 1 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 60
Query: 261 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVXXXXXXXXXXXXSQETPA 440
EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV SQETPA
Sbjct: 61 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPA 120
Query: 441 SKKXXXXXXXXXXXXXXXXXXXXXXXXTQTPRIMHHXXXXXXXXXXXXXXXXXXXXXXXX 620
+KK TQ PRIMHH
Sbjct: 121 AKKAVQGGAAAPVVGTVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQL 180
Query: 621 XXXXXXXXXXXXXXXXXXXXXSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV 800
SENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV
Sbjct: 181 PPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV 240
Query: 801 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 926
PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK
Sbjct: 241 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282
>ref|NP_001179481.1| U2 small nuclear ribonucleoprotein B'' [Bos taurus].
Length = 218
Score = 160 bits (406), Expect = 3e-39
Identities = 73/97 (75%), Positives = 90/97 (92%)
Frame = +3
Query: 93 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 272
+ RPNHTIYINN+N+KIKK+ELK+SLYA+FSQFG ++DI+ +++KMRGQAFVIFKE+ S
Sbjct: 2 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 61
Query: 273 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 383
+TNALR +QGFPFY KPMRIQYAKTDSDII+KM+GTF
Sbjct: 62 STNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTF 98
Score = 140 bits (354), Expect = 3e-33
Identities = 67/78 (85%), Positives = 75/78 (96%)
Frame = +3
Query: 693 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDAL 872
PPN+ILFL NLPEETNE+MLSMLFNQFPGFKEVRLVPGRHDIAFVEF+N+ QAGAARDAL
Sbjct: 141 PPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDAL 200
Query: 873 QGFKITQNNAMKISFAKK 926
QGFKIT ++AMKI++AKK
Sbjct: 201 QGFKITPSHAMKITYAKK 218
>ref|XP_002683786.1| PREDICTED: small nuclear ribonucleoprotein polypeptide B'' [Bos
taurus].
Length = 218
Score = 160 bits (406), Expect = 3e-39
Identities = 73/97 (75%), Positives = 90/97 (92%)
Frame = +3
Query: 93 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 272
+ RPNHTIYINN+N+KIKK+ELK+SLYA+FSQFG ++DI+ +++KMRGQAFVIFKE+ S
Sbjct: 2 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 61
Query: 273 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 383
+TNALR +QGFPFY KPMRIQYAKTDSDII+KM+GTF
Sbjct: 62 STNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTF 98
Score = 140 bits (354), Expect = 3e-33
Identities = 67/78 (85%), Positives = 75/78 (96%)
Frame = +3
Query: 693 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDAL 872
PPN+ILFL NLPEETNE+MLSMLFNQFPGFKEVRLVPGRHDIAFVEF+N+ QAGAARDAL
Sbjct: 141 PPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDAL 200
Query: 873 QGFKITQNNAMKISFAKK 926
QGFKIT ++AMKI++AKK
Sbjct: 201 QGFKITPSHAMKITYAKK 218
>ref|NP_001070585.1| RNA-binding protein 40 [Bos taurus].
Length = 516
Score = 49.7 bits (117), Expect = 8e-06
Identities = 28/86 (32%), Positives = 48/86 (55%), Gaps = 4/86 (4%)
Frame = +3
Query: 102 PNHTIYINNLNEKIKKDELKKSL--YAIFSQFGQ--ILDILVSRSLKMRGQAFVIFKEVS 269
PN IY+ NL + +++ +LK Y FS Q + DI + + +M+GQAF+
Sbjct: 417 PNCRIYVKNLAKHVQEKDLKFIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEK 476
Query: 270 SATNALRSMQGFPFYDKPMRIQYAKT 347
+A AL+ G+ + KPM +Q+A++
Sbjct: 477 AAAKALKEANGYVLFGKPMVVQFARS 502
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: 52,524,478
Number of extensions: 1738923
Number of successful extensions: 8015
Number of sequences better than 1.0e-05: 4
Number of HSP's gapped: 7875
Number of HSP's successfully gapped: 7
Length of query: 591
Length of database: 17,681,374
Length adjustment: 108
Effective length of query: 483
Effective length of database: 14,107,870
Effective search space: 6814101210
Effective search space used: 6814101210
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-001319
(1774 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_533663.2| PREDICTED: similar to U1 small nuclear ribonucl... 365 e-101
Alignment gi|XP_547687.2| PREDICTED: similar to U1 small nuclear ribonucl... 190 4e-48
Alignment gi|XP_860797.1| PREDICTED: similar to U1 small nuclear ribonucl... 190 4e-48
Alignment gi|XP_850163.1| PREDICTED: similar to small nuclear ribonucleop... 188 1e-47
Alignment gi|XP_850387.1| PREDICTED: similar to small nuclear ribonucleop... 162 7e-40
Alignment gi|XP_534338.2| PREDICTED: similar to U2 small nuclear ribonucl... 160 3e-39
Alignment gi|XP_857793.1| PREDICTED: similar to U2 small nuclear ribonucl... 160 3e-39
Alignment gi|XP_857753.1| PREDICTED: similar to U2 small nuclear ribonucl... 160 3e-39
Alignment gi|XP_857709.1| PREDICTED: similar to U2 small nuclear ribonucl... 160 3e-39
Alignment gi|XP_857667.1| PREDICTED: similar to U2 small nuclear ribonucl... 160 3e-39
>ref|XP_533663.2| PREDICTED: similar to U1 small nuclear ribonucleoprotein A (U1
snRNP protein A) (U1A protein) (U1-A) [Canis
familiaris].
Length = 282
Score = 365 bits (938), Expect = e-101
Identities = 199/282 (70%), Positives = 200/282 (70%)
Frame = +3
Query: 81 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 260
MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK
Sbjct: 1 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 60
Query: 261 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVXXXXXXXXXXXXSQETPA 440
EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV SQETPA
Sbjct: 61 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPA 120
Query: 441 SKKXXXXXXXXXXXXXXXXXXXXXXXXTQTPRIMHHXXXXXXXXXXXXXXXXXXXXXXXX 620
+KK TQ PRIMHH
Sbjct: 121 AKKAVQGGAAAPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQI 180
Query: 621 XXXXXXXXXXXXXXXXXXXXXSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV 800
SENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV
Sbjct: 181 PPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV 240
Query: 801 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 926
PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK
Sbjct: 241 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282
>ref|XP_547687.2| PREDICTED: similar to U1 small nuclear ribonucleoprotein A (U1
snRNP protein A) (U1-A) (Sex determination protein snf)
isoform 1 [Canis familiaris].
Length = 215
Score = 190 bits (482), Expect = 4e-48
Identities = 97/102 (95%), Positives = 98/102 (96%)
Frame = +3
Query: 81 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 260
MAVPET PNHTIYIN+LNEKIKKDELKKSLYAIFSQFGQIL ILVSRSLKMRGQAFVIFK
Sbjct: 1 MAVPETCPNHTIYINSLNEKIKKDELKKSLYAIFSQFGQILHILVSRSLKMRGQAFVIFK 60
Query: 261 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 386
EVS ATNALRSMQGFPFYDKPM IQYAKTDSDIIAKMKGTFV
Sbjct: 61 EVSRATNALRSMQGFPFYDKPMSIQYAKTDSDIIAKMKGTFV 102
Score = 150 bits (380), Expect = 3e-36
Identities = 75/81 (92%), Positives = 76/81 (93%)
Frame = +3
Query: 684 SENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAR 863
SENPPNH LFLTNLPEETNELMLSMLFNQFPGFKEVRL PG HDIAFVEFDNEVQA AR
Sbjct: 135 SENPPNHFLFLTNLPEETNELMLSMLFNQFPGFKEVRLDPGWHDIAFVEFDNEVQAEDAR 194
Query: 864 DALQGFKITQNNAMKISFAKK 926
+ALQGFKITQNNAMKISFAKK
Sbjct: 195 NALQGFKITQNNAMKISFAKK 215
>ref|XP_860797.1| PREDICTED: similar to U1 small nuclear ribonucleoprotein A (U1
snRNP protein A) (U1-A) (Sex determination protein snf)
isoform 3 [Canis familiaris].
Length = 229
Score = 190 bits (482), Expect = 4e-48
Identities = 97/102 (95%), Positives = 98/102 (96%)
Frame = +3
Query: 81 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 260
MAVPET PNHTIYIN+LNEKIKKDELKKSLYAIFSQFGQIL ILVSRSLKMRGQAFVIFK
Sbjct: 1 MAVPETCPNHTIYINSLNEKIKKDELKKSLYAIFSQFGQILHILVSRSLKMRGQAFVIFK 60
Query: 261 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 386
EVS ATNALRSMQGFPFYDKPM IQYAKTDSDIIAKMKGTFV
Sbjct: 61 EVSRATNALRSMQGFPFYDKPMSIQYAKTDSDIIAKMKGTFV 102
Score = 150 bits (380), Expect = 3e-36
Identities = 75/81 (92%), Positives = 76/81 (93%)
Frame = +3
Query: 684 SENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAR 863
SENPPNH LFLTNLPEETNELMLSMLFNQFPGFKEVRL PG HDIAFVEFDNEVQA AR
Sbjct: 149 SENPPNHFLFLTNLPEETNELMLSMLFNQFPGFKEVRLDPGWHDIAFVEFDNEVQAEDAR 208
Query: 864 DALQGFKITQNNAMKISFAKK 926
+ALQGFKITQNNAMKISFAKK
Sbjct: 209 NALQGFKITQNNAMKISFAKK 229
>ref|XP_850163.1| PREDICTED: similar to small nuclear ribonucleoprotein polypeptide A
isoform 2 [Canis familiaris].
Length = 217
Score = 188 bits (478), Expect = 1e-47
Identities = 96/101 (95%), Positives = 97/101 (96%)
Frame = +3
Query: 81 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 260
MAVPET PNHTIYIN+LNEKIKKDELKKSLYAIFSQFGQIL ILVSRSLKMRGQAFVIFK
Sbjct: 1 MAVPETCPNHTIYINSLNEKIKKDELKKSLYAIFSQFGQILHILVSRSLKMRGQAFVIFK 60
Query: 261 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 383
EVS ATNALRSMQGFPFYDKPM IQYAKTDSDIIAKMKGTF
Sbjct: 61 EVSRATNALRSMQGFPFYDKPMSIQYAKTDSDIIAKMKGTF 101
Score = 150 bits (380), Expect = 3e-36
Identities = 75/81 (92%), Positives = 76/81 (93%)
Frame = +3
Query: 684 SENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAR 863
SENPPNH LFLTNLPEETNELMLSMLFNQFPGFKEVRL PG HDIAFVEFDNEVQA AR
Sbjct: 137 SENPPNHFLFLTNLPEETNELMLSMLFNQFPGFKEVRLDPGWHDIAFVEFDNEVQAEDAR 196
Query: 864 DALQGFKITQNNAMKISFAKK 926
+ALQGFKITQNNAMKISFAKK
Sbjct: 197 NALQGFKITQNNAMKISFAKK 217
>ref|XP_850387.1| PREDICTED: similar to small nuclear ribonucleoprotein polypeptide A
(predicted) [Canis familiaris].
Length = 233
Score = 162 bits (411), Expect = 7e-40
Identities = 80/81 (98%), Positives = 80/81 (98%)
Frame = +3
Query: 684 SENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAR 863
SENPPNHILFLTNLPEETNELM SMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAR
Sbjct: 153 SENPPNHILFLTNLPEETNELMPSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAR 212
Query: 864 DALQGFKITQNNAMKISFAKK 926
DALQGFKITQNNAMKISFAKK
Sbjct: 213 DALQGFKITQNNAMKISFAKK 233
Score = 162 bits (409), Expect = 1e-39
Identities = 90/123 (73%), Positives = 92/123 (74%)
Frame = +3
Query: 81 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 260
MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK
Sbjct: 1 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 60
Query: 261 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVXXXXXXXXXXXXSQETPA 440
E SSATN YAKTDSDIIAK+KGTFV SQETPA
Sbjct: 61 EASSATN------------------YAKTDSDIIAKIKGTFVERDRKREKRKPKSQETPA 102
Query: 441 SKK 449
+KK
Sbjct: 103 AKK 105
>ref|XP_534338.2| PREDICTED: similar to U2 small nuclear ribonucleoprotein B isoform
1 [Canis familiaris].
Length = 260
Score = 160 bits (406), Expect = 3e-39
Identities = 73/97 (75%), Positives = 90/97 (92%)
Frame = +3
Query: 93 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 272
+ RPNHTIYINN+N+KIKK+ELK+SLYA+FSQFG ++DI+ +++KMRGQAFVIFKE+ S
Sbjct: 37 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 96
Query: 273 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 383
+TNALR +QGFPFY KPMRIQYAKTDSDII+KM+GTF
Sbjct: 97 STNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTF 133
Score = 140 bits (354), Expect = 3e-33
Identities = 67/78 (85%), Positives = 75/78 (96%)
Frame = +3
Query: 693 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDAL 872
PPN+ILFL NLPEETNE+MLSMLFNQFPGFKEVRLVPGRHDIAFVEF+N+ QAGAARDAL
Sbjct: 183 PPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDAL 242
Query: 873 QGFKITQNNAMKISFAKK 926
QGFKIT ++AMKI++AKK
Sbjct: 243 QGFKITPSHAMKITYAKK 260
>ref|XP_857793.1| PREDICTED: similar to U2 small nuclear ribonucleoprotein B isoform
9 [Canis familiaris].
Length = 253
Score = 160 bits (406), Expect = 3e-39
Identities = 73/97 (75%), Positives = 90/97 (92%)
Frame = +3
Query: 93 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 272
+ RPNHTIYINN+N+KIKK+ELK+SLYA+FSQFG ++DI+ +++KMRGQAFVIFKE+ S
Sbjct: 37 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 96
Query: 273 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 383
+TNALR +QGFPFY KPMRIQYAKTDSDII+KM+GTF
Sbjct: 97 STNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTF 133
Score = 140 bits (354), Expect = 3e-33
Identities = 67/78 (85%), Positives = 75/78 (96%)
Frame = +3
Query: 693 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDAL 872
PPN+ILFL NLPEETNE+MLSMLFNQFPGFKEVRLVPGRHDIAFVEF+N+ QAGAARDAL
Sbjct: 176 PPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDAL 235
Query: 873 QGFKITQNNAMKISFAKK 926
QGFKIT ++AMKI++AKK
Sbjct: 236 QGFKITPSHAMKITYAKK 253
>ref|XP_857753.1| PREDICTED: similar to U2 small nuclear ribonucleoprotein B isoform
8 [Canis familiaris].
Length = 250
Score = 160 bits (406), Expect = 3e-39
Identities = 73/97 (75%), Positives = 90/97 (92%)
Frame = +3
Query: 93 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 272
+ RPNHTIYINN+N+KIKK+ELK+SLYA+FSQFG ++DI+ +++KMRGQAFVIFKE+ S
Sbjct: 37 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 96
Query: 273 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 383
+TNALR +QGFPFY KPMRIQYAKTDSDII+KM+GTF
Sbjct: 97 STNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTF 133
Score = 140 bits (354), Expect = 3e-33
Identities = 67/78 (85%), Positives = 75/78 (96%)
Frame = +3
Query: 693 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDAL 872
PPN+ILFL NLPEETNE+MLSMLFNQFPGFKEVRLVPGRHDIAFVEF+N+ QAGAARDAL
Sbjct: 173 PPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDAL 232
Query: 873 QGFKITQNNAMKISFAKK 926
QGFKIT ++AMKI++AKK
Sbjct: 233 QGFKITPSHAMKITYAKK 250
>ref|XP_857709.1| PREDICTED: similar to U2 small nuclear ribonucleoprotein B isoform
7 [Canis familiaris].
Length = 262
Score = 160 bits (406), Expect = 3e-39
Identities = 73/97 (75%), Positives = 90/97 (92%)
Frame = +3
Query: 93 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 272
+ RPNHTIYINN+N+KIKK+ELK+SLYA+FSQFG ++DI+ +++KMRGQAFVIFKE+ S
Sbjct: 37 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 96
Query: 273 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 383
+TNALR +QGFPFY KPMRIQYAKTDSDII+KM+GTF
Sbjct: 97 STNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTF 133
Score = 140 bits (354), Expect = 3e-33
Identities = 67/78 (85%), Positives = 75/78 (96%)
Frame = +3
Query: 693 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDAL 872
PPN+ILFL NLPEETNE+MLSMLFNQFPGFKEVRLVPGRHDIAFVEF+N+ QAGAARDAL
Sbjct: 185 PPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDAL 244
Query: 873 QGFKITQNNAMKISFAKK 926
QGFKIT ++AMKI++AKK
Sbjct: 245 QGFKITPSHAMKITYAKK 262
>ref|XP_857667.1| PREDICTED: similar to U2 small nuclear ribonucleoprotein B isoform
6 [Canis familiaris].
Length = 297
Score = 160 bits (406), Expect = 3e-39
Identities = 73/97 (75%), Positives = 90/97 (92%)
Frame = +3
Query: 93 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 272
+ RPNHTIYINN+N+KIKK+ELK+SLYA+FSQFG ++DI+ +++KMRGQAFVIFKE+ S
Sbjct: 37 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 96
Query: 273 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 383
+TNALR +QGFPFY KPMRIQYAKTDSDII+KM+GTF
Sbjct: 97 STNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTF 133
Score = 140 bits (354), Expect = 3e-33
Identities = 67/78 (85%), Positives = 75/78 (96%)
Frame = +3
Query: 693 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDAL 872
PPN+ILFL NLPEETNE+MLSMLFNQFPGFKEVRLVPGRHDIAFVEF+N+ QAGAARDAL
Sbjct: 220 PPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDAL 279
Query: 873 QGFKITQNNAMKISFAKK 926
QGFKIT ++AMKI++AKK
Sbjct: 280 QGFKITPSHAMKITYAKK 297
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: 53,818,269
Number of extensions: 1551418
Number of successful extensions: 8517
Number of sequences better than 1.0e-05: 15
Number of HSP's gapped: 8362
Number of HSP's successfully gapped: 30
Length of query: 591
Length of database: 18,874,504
Length adjustment: 108
Effective length of query: 483
Effective length of database: 15,274,216
Effective search space: 7377446328
Effective search space used: 7377446328
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-001319
(1774 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_004587.1| U1 small nuclear ribonucleoprotein A [Homo sapi... 365 e-101
Alignment gi|NP_003083.1| U2 small nuclear ribonucleoprotein B'' [Homo sa... 160 3e-39
Alignment gi|NP_937863.1| U2 small nuclear ribonucleoprotein B'' [Homo sa... 160 3e-39
Alignment gi|NP_060089.1| RNA-binding protein 40 [Homo sapiens]. 50 7e-06
>ref|NP_004587.1| U1 small nuclear ribonucleoprotein A [Homo sapiens].
Length = 282
Score = 365 bits (938), Expect = e-101
Identities = 199/282 (70%), Positives = 200/282 (70%)
Frame = +3
Query: 81 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 260
MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK
Sbjct: 1 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 60
Query: 261 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVXXXXXXXXXXXXSQETPA 440
EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV SQETPA
Sbjct: 61 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPA 120
Query: 441 SKKXXXXXXXXXXXXXXXXXXXXXXXXTQTPRIMHHXXXXXXXXXXXXXXXXXXXXXXXX 620
+KK TQ PRIMHH
Sbjct: 121 TKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQI 180
Query: 621 XXXXXXXXXXXXXXXXXXXXXSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV 800
SENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV
Sbjct: 181 PPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV 240
Query: 801 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 926
PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK
Sbjct: 241 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282
>ref|NP_003083.1| U2 small nuclear ribonucleoprotein B'' [Homo sapiens].
Length = 225
Score = 160 bits (406), Expect = 3e-39
Identities = 73/97 (75%), Positives = 90/97 (92%)
Frame = +3
Query: 93 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 272
+ RPNHTIYINN+N+KIKK+ELK+SLYA+FSQFG ++DI+ +++KMRGQAFVIFKE+ S
Sbjct: 2 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 61
Query: 273 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 383
+TNALR +QGFPFY KPMRIQYAKTDSDII+KM+GTF
Sbjct: 62 STNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTF 98
Score = 140 bits (354), Expect = 3e-33
Identities = 67/78 (85%), Positives = 75/78 (96%)
Frame = +3
Query: 693 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDAL 872
PPN+ILFL NLPEETNE+MLSMLFNQFPGFKEVRLVPGRHDIAFVEF+N+ QAGAARDAL
Sbjct: 148 PPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDAL 207
Query: 873 QGFKITQNNAMKISFAKK 926
QGFKIT ++AMKI++AKK
Sbjct: 208 QGFKITPSHAMKITYAKK 225
>ref|NP_937863.1| U2 small nuclear ribonucleoprotein B'' [Homo sapiens].
Length = 225
Score = 160 bits (406), Expect = 3e-39
Identities = 73/97 (75%), Positives = 90/97 (92%)
Frame = +3
Query: 93 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 272
+ RPNHTIYINN+N+KIKK+ELK+SLYA+FSQFG ++DI+ +++KMRGQAFVIFKE+ S
Sbjct: 2 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 61
Query: 273 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 383
+TNALR +QGFPFY KPMRIQYAKTDSDII+KM+GTF
Sbjct: 62 STNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTF 98
Score = 140 bits (354), Expect = 3e-33
Identities = 67/78 (85%), Positives = 75/78 (96%)
Frame = +3
Query: 693 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDAL 872
PPN+ILFL NLPEETNE+MLSMLFNQFPGFKEVRLVPGRHDIAFVEF+N+ QAGAARDAL
Sbjct: 148 PPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDAL 207
Query: 873 QGFKITQNNAMKISFAKK 926
QGFKIT ++AMKI++AKK
Sbjct: 208 QGFKITPSHAMKITYAKK 225
>ref|NP_060089.1| RNA-binding protein 40 [Homo sapiens].
Length = 517
Score = 50.1 bits (118), Expect = 7e-06
Identities = 28/86 (32%), Positives = 48/86 (55%), Gaps = 4/86 (4%)
Frame = +3
Query: 102 PNHTIYINNLNEKIKKDELKKSL--YAIFSQFGQ--ILDILVSRSLKMRGQAFVIFKEVS 269
PN IY+ NL + +++ +LK Y FS Q + DI + + +M+GQAF+
Sbjct: 418 PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEK 477
Query: 270 SATNALRSMQGFPFYDKPMRIQYAKT 347
+A AL+ G+ + KPM +Q+A++
Sbjct: 478 AAAKALKEANGYVLFGKPMVVQFARS 503
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: 52,020,649
Number of extensions: 1459393
Number of successful extensions: 7685
Number of sequences better than 1.0e-05: 4
Number of HSP's gapped: 7514
Number of HSP's successfully gapped: 7
Length of query: 591
Length of database: 18,297,164
Length adjustment: 108
Effective length of query: 483
Effective length of database: 14,737,052
Effective search space: 7117996116
Effective search space used: 7117996116
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 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-001319
(1774 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_001040102.1| U1 small nuclear ribonucleoprotein A [Mus mu... 349 5e-96
Alignment gi|NP_056597.3| U1 small nuclear ribonucleoprotein A [Mus muscu... 349 5e-96
Alignment gi|XP_003086803.1| PREDICTED: u1 small nuclear ribonucleoprotei... 338 6e-93
Alignment gi|XP_356179.3| PREDICTED: u1 small nuclear ribonucleoprotein A... 333 3e-91
Alignment gi|XP_995150.2| PREDICTED: u1 small nuclear ribonucleoprotein A... 319 4e-87
Alignment gi|NP_067310.1| U2 small nuclear ribonucleoprotein B'' [Mus mus... 160 2e-39
Alignment gi|NP_001033785.1| RNA-binding protein 40 [Mus musculus]. 50 7e-06
Alignment gi|NP_080319.2| RNA-binding protein 40 [Mus musculus]. 50 7e-06
>ref|NP_001040102.1| U1 small nuclear ribonucleoprotein A [Mus musculus].
Length = 287
Score = 349 bits (895), Expect = 5e-96
Identities = 192/283 (67%), Positives = 197/283 (69%)
Frame = +3
Query: 78 SMAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIF 257
+M VPETR NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR +KMRGQAFVIF
Sbjct: 6 TMPVPETRANHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIF 65
Query: 258 KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVXXXXXXXXXXXXSQETP 437
KEV+SATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGT+V SQETP
Sbjct: 66 KEVTSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTYVERDRKREKRKPKSQETP 125
Query: 438 ASKKXXXXXXXXXXXXXXXXXXXXXXXXTQTPRIMHHXXXXXXXXXXXXXXXXXXXXXXX 617
A+KK Q PRIMHH
Sbjct: 126 AAKK-AVQGGAAAPVVGAVQPVPGMPPMPQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQ 184
Query: 618 XXXXXXXXXXXXXXXXXXXXXXSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL 797
SENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL
Sbjct: 185 IPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL 244
Query: 798 VPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 926
VPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK
Sbjct: 245 VPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 287
>ref|NP_056597.3| U1 small nuclear ribonucleoprotein A [Mus musculus].
Length = 287
Score = 349 bits (895), Expect = 5e-96
Identities = 192/283 (67%), Positives = 197/283 (69%)
Frame = +3
Query: 78 SMAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIF 257
+M VPETR NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR +KMRGQAFVIF
Sbjct: 6 TMPVPETRANHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIF 65
Query: 258 KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVXXXXXXXXXXXXSQETP 437
KEV+SATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGT+V SQETP
Sbjct: 66 KEVTSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTYVERDRKREKRKPKSQETP 125
Query: 438 ASKKXXXXXXXXXXXXXXXXXXXXXXXXTQTPRIMHHXXXXXXXXXXXXXXXXXXXXXXX 617
A+KK Q PRIMHH
Sbjct: 126 AAKK-AVQGGAAAPVVGAVQPVPGMPPMPQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQ 184
Query: 618 XXXXXXXXXXXXXXXXXXXXXXSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL 797
SENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL
Sbjct: 185 IPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL 244
Query: 798 VPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 926
VPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK
Sbjct: 245 VPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 287
>ref|XP_003086803.1| PREDICTED: u1 small nuclear ribonucleoprotein A-like [Mus
musculus].
Length = 282
Score = 338 bits (868), Expect = 6e-93
Identities = 185/282 (65%), Positives = 190/282 (67%)
Frame = +3
Query: 81 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 260
MAVPETRPNHTIYIN+LNEKIKKDELKKS YAIFSQFGQILDILVS+SLKMRGQ+FVIFK
Sbjct: 1 MAVPETRPNHTIYINSLNEKIKKDELKKSPYAIFSQFGQILDILVSQSLKMRGQSFVIFK 60
Query: 261 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVXXXXXXXXXXXXSQETPA 440
EVSS NALRSMQGFPFY KPM IQYAKTDSDIIAKMKGTFV SQE PA
Sbjct: 61 EVSSTINALRSMQGFPFYGKPMHIQYAKTDSDIIAKMKGTFVERDHKREKRKPKSQEKPA 120
Query: 441 SKKXXXXXXXXXXXXXXXXXXXXXXXXTQTPRIMHHXXXXXXXXXXXXXXXXXXXXXXXX 620
+KK Q PR+MHH
Sbjct: 121 AKKAVQGGAAAPVVGAVQPPVPGMPPMPQAPRVMHHMPGQPPYMRPPGMILPPGLPPGQI 180
Query: 621 XXXXXXXXXXXXXXXXXXXXXSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV 800
SENPPNHILFLTNLPEETNELMLSMLF QFPGFKEVRLV
Sbjct: 181 PSRAMPPQQLIPGQMPHAQPLSENPPNHILFLTNLPEETNELMLSMLFTQFPGFKEVRLV 240
Query: 801 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 926
PGRHDI FVEFDNEVQAGAARD LQGFKITQNNAMKISFAKK
Sbjct: 241 PGRHDIDFVEFDNEVQAGAARDVLQGFKITQNNAMKISFAKK 282
>ref|XP_356179.3| PREDICTED: u1 small nuclear ribonucleoprotein A-like isoform 1 [Mus
musculus].
Length = 281
Score = 333 bits (854), Expect = 3e-91
Identities = 185/282 (65%), Positives = 189/282 (67%)
Frame = +3
Query: 81 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 260
MAVPETRPNHTIYIN+LNEKIKKDELKKS YAIFSQFGQILDILVS+SLKMRGQ+FVIFK
Sbjct: 1 MAVPETRPNHTIYINSLNEKIKKDELKKSPYAIFSQFGQILDILVSQSLKMRGQSFVIFK 60
Query: 261 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVXXXXXXXXXXXXSQETPA 440
EVSS NALRSMQGFPFY KPM IQYAKTDSDIIAKMKGTFV SQE PA
Sbjct: 61 EVSSTINALRSMQGFPFYGKPMHIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQEKPA 120
Query: 441 SKKXXXXXXXXXXXXXXXXXXXXXXXXTQTPRIMHHXXXXXXXXXXXXXXXXXXXXXXXX 620
KK Q PR+MHH
Sbjct: 121 VKK-GCSGWGSAPVVGAVQPVPGMPPMPQAPRVMHHMPGQPPYMRPPGMILPPGLPPGQI 179
Query: 621 XXXXXXXXXXXXXXXXXXXXXSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV 800
SENPPNHILFLTNLPEETNELMLSMLF QFPGFKEVRLV
Sbjct: 180 PSRAMPPQQLIPGQMPHAQPLSENPPNHILFLTNLPEETNELMLSMLFTQFPGFKEVRLV 239
Query: 801 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 926
PGRHDI FVEFDNEVQAGAARD LQGFKITQNNAMKISFAKK
Sbjct: 240 PGRHDIDFVEFDNEVQAGAARDVLQGFKITQNNAMKISFAKK 281
>ref|XP_995150.2| PREDICTED: u1 small nuclear ribonucleoprotein A-like [Mus
musculus].
Length = 309
Score = 319 bits (818), Expect = 4e-87
Identities = 180/283 (63%), Positives = 185/283 (65%)
Frame = +3
Query: 78 SMAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIF 257
+M V ETR NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS+SLKMRGQ FVIF
Sbjct: 3 TMPVLETRSNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSQSLKMRGQVFVIF 62
Query: 258 KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVXXXXXXXXXXXXSQETP 437
KEV+ ATNAL SM GFPFYDKPMRIQY KT+SD IAKMKGTFV SQETP
Sbjct: 63 KEVTIATNALWSMLGFPFYDKPMRIQYTKTESDNIAKMKGTFVERDHKGEKRKPKSQETP 122
Query: 438 ASKKXXXXXXXXXXXXXXXXXXXXXXXXTQTPRIMHHXXXXXXXXXXXXXXXXXXXXXXX 617
A+KK Q PRIMHH
Sbjct: 123 AAKK-AVQGGAAAPVVGAVQPVPGMPPMPQAPRIMHHVPGQPPYMPPAGMIPPTGLAPGQ 181
Query: 618 XXXXXXXXXXXXXXXXXXXXXXSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL 797
SENPPNHILFLTNLPEETNELMLSMLF QFPGFKE L
Sbjct: 182 IPPGAMPPQQLMPGQMPPAPPLSENPPNHILFLTNLPEETNELMLSMLFTQFPGFKEAHL 241
Query: 798 VPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 926
VPG HDIAFVEFDNEVQAGAA DALQGFKITQNNAMKISF KK
Sbjct: 242 VPGCHDIAFVEFDNEVQAGAALDALQGFKITQNNAMKISFVKK 284
>ref|NP_067310.1| U2 small nuclear ribonucleoprotein B'' [Mus musculus].
Length = 225
Score = 160 bits (406), Expect = 2e-39
Identities = 73/97 (75%), Positives = 90/97 (92%)
Frame = +3
Query: 93 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 272
+ RPNHTIYINN+N+KIKK+ELK+SLYA+FSQFG ++DI+ +++KMRGQAFVIFKE+ S
Sbjct: 2 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 61
Query: 273 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 383
+TNALR +QGFPFY KPMRIQYAKTDSDII+KM+GTF
Sbjct: 62 STNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTF 98
Score = 140 bits (354), Expect = 2e-33
Identities = 67/78 (85%), Positives = 75/78 (96%)
Frame = +3
Query: 693 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDAL 872
PPN+ILFL NLPEETNE+MLSMLFNQFPGFKEVRLVPGRHDIAFVEF+N+ QAGAARDAL
Sbjct: 148 PPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDAL 207
Query: 873 QGFKITQNNAMKISFAKK 926
QGFKIT ++AMKI++AKK
Sbjct: 208 QGFKITPSHAMKITYAKK 225
>ref|NP_001033785.1| RNA-binding protein 40 [Mus musculus].
Length = 514
Score = 49.7 bits (117), Expect = 7e-06
Identities = 29/86 (33%), Positives = 47/86 (54%), Gaps = 4/86 (4%)
Frame = +3
Query: 102 PNHTIYINNLNEKIKKDELKKSL--YAIFSQFGQ--ILDILVSRSLKMRGQAFVIFKEVS 269
PN IY+ NL +++ +LK Y FS Q + DI + + +M+GQAFV
Sbjct: 416 PNCRIYVKNLARHVQEKDLKFIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFVGLPNEK 475
Query: 270 SATNALRSMQGFPFYDKPMRIQYAKT 347
+A AL+ G+ + KPM +Q+A++
Sbjct: 476 AAAKALKEANGYVLFGKPMVVQFARS 501
>ref|NP_080319.2| RNA-binding protein 40 [Mus musculus].
Length = 514
Score = 49.7 bits (117), Expect = 7e-06
Identities = 29/86 (33%), Positives = 47/86 (54%), Gaps = 4/86 (4%)
Frame = +3
Query: 102 PNHTIYINNLNEKIKKDELKKSL--YAIFSQFGQ--ILDILVSRSLKMRGQAFVIFKEVS 269
PN IY+ NL +++ +LK Y FS Q + DI + + +M+GQAFV
Sbjct: 416 PNCRIYVKNLARHVQEKDLKFIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFVGLPNEK 475
Query: 270 SATNALRSMQGFPFYDKPMRIQYAKT 347
+A AL+ G+ + KPM +Q+A++
Sbjct: 476 AAAKALKEANGYVLFGKPMVVQFARS 501
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: 43,381,753
Number of extensions: 1196533
Number of successful extensions: 5954
Number of sequences better than 1.0e-05: 8
Number of HSP's gapped: 5769
Number of HSP's successfully gapped: 14
Length of query: 591
Length of database: 15,617,559
Length adjustment: 107
Effective length of query: 484
Effective length of database: 12,403,707
Effective search space: 6003394188
Effective search space used: 6003394188
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-001319
(1774 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|NP_001070690.1| U1 small nuclear ribonucleoprotein A [Sus sc... 369 e-102
Alignment gi|NP_001070696.1| hypothetical protein LOC768116 [Sus scrofa]. 160 2e-39
Alignment gi|XP_003125932.2| PREDICTED: RNA-binding protein 40-like [Sus ... 50 5e-06
Alignment gi|XP_003125931.1| PREDICTED: RNA-binding protein 40-like [Sus ... 50 5e-06
>ref|NP_001070690.1| U1 small nuclear ribonucleoprotein A [Sus scrofa].
Length = 282
Score = 369 bits (946), Expect = e-102
Identities = 201/282 (71%), Positives = 201/282 (71%)
Frame = +3
Query: 81 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 260
MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK
Sbjct: 1 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 60
Query: 261 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVXXXXXXXXXXXXSQETPA 440
EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV SQETPA
Sbjct: 61 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPA 120
Query: 441 SKKXXXXXXXXXXXXXXXXXXXXXXXXTQTPRIMHHXXXXXXXXXXXXXXXXXXXXXXXX 620
SKK TQTPRIMHH
Sbjct: 121 SKKAVQGGAAAPVVGAVQGPVPGMPPMTQTPRIMHHMPGQPPYMPPPGMIPPPGLAPGQI 180
Query: 621 XXXXXXXXXXXXXXXXXXXXXSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV 800
SENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV
Sbjct: 181 PPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV 240
Query: 801 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 926
PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK
Sbjct: 241 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282
>ref|NP_001070696.1| hypothetical protein LOC768116 [Sus scrofa].
Length = 225
Score = 160 bits (406), Expect = 2e-39
Identities = 73/97 (75%), Positives = 90/97 (92%)
Frame = +3
Query: 93 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 272
+ RPNHTIYINN+N+KIKK+ELK+SLYA+FSQFG ++DI+ +++KMRGQAFVIFKE+ S
Sbjct: 2 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 61
Query: 273 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 383
+TNALR +QGFPFY KPMRIQYAKTDSDII+KM+GTF
Sbjct: 62 STNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTF 98
Score = 140 bits (354), Expect = 2e-33
Identities = 67/78 (85%), Positives = 75/78 (96%)
Frame = +3
Query: 693 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDAL 872
PPN+ILFL NLPEETNE+MLSMLFNQFPGFKEVRLVPGRHDIAFVEF+N+ QAGAARDAL
Sbjct: 148 PPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDAL 207
Query: 873 QGFKITQNNAMKISFAKK 926
QGFKIT ++AMKI++AKK
Sbjct: 208 QGFKITPSHAMKITYAKK 225
>ref|XP_003125932.2| PREDICTED: RNA-binding protein 40-like [Sus scrofa].
Length = 669
Score = 49.7 bits (117), Expect = 5e-06
Identities = 28/86 (32%), Positives = 48/86 (55%), Gaps = 4/86 (4%)
Frame = +3
Query: 102 PNHTIYINNLNEKIKKDELKKSL--YAIFSQFGQ--ILDILVSRSLKMRGQAFVIFKEVS 269
PN IY+ NL + +++ +LK Y FS Q + DI + + +M+GQAF+
Sbjct: 570 PNCRIYVKNLAKHVQEKDLKFIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEK 629
Query: 270 SATNALRSMQGFPFYDKPMRIQYAKT 347
+A AL+ G+ + KPM +Q+A++
Sbjct: 630 AAAKALKEANGYVLFGKPMVVQFARS 655
>ref|XP_003125931.1| PREDICTED: RNA-binding protein 40-like [Sus scrofa].
Length = 515
Score = 49.7 bits (117), Expect = 5e-06
Identities = 28/86 (32%), Positives = 48/86 (55%), Gaps = 4/86 (4%)
Frame = +3
Query: 102 PNHTIYINNLNEKIKKDELKKSL--YAIFSQFGQ--ILDILVSRSLKMRGQAFVIFKEVS 269
PN IY+ NL + +++ +LK Y FS Q + DI + + +M+GQAF+
Sbjct: 416 PNCRIYVKNLAKHVQEKDLKFIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEK 475
Query: 270 SATNALRSMQGFPFYDKPMRIQYAKT 347
+A AL+ G+ + KPM +Q+A++
Sbjct: 476 AAAKALKEANGYVLFGKPMVVQFARS 501
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: 36,506,965
Number of extensions: 1506798
Number of successful extensions: 5186
Number of sequences better than 1.0e-05: 4
Number of HSP's gapped: 5091
Number of HSP's successfully gapped: 6
Length of query: 591
Length of database: 11,343,932
Length adjustment: 105
Effective length of query: 486
Effective length of database: 8,729,747
Effective search space: 4242657042
Effective search space used: 4242657042
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 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-001319
(1774 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_Chr06 361 9e-97
>Sscrofa_Chr06
|| Length = 157765593
Score = 361 bits (182), Expect = 9e-97
Identities = 182/182 (100%)
Strand = Plus / Plus
Query: 326 gcgcatccagtacgccaagaccgactcggatatcatcgccaagatgaagggcaccttcgt 385
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 44662621 gcgcatccagtacgccaagaccgactcggatatcatcgccaagatgaagggcaccttcgt 44662680
Query: 386 ggagcgggaccgcaagcgggagaagaggaagcccaagagccaagagaccccggcctccaa 445
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 44662681 ggagcgggaccgcaagcgggagaagaggaagcccaagagccaagagaccccggcctccaa 44662740
Query: 446 gaaggccgtgcagggcggggcagccgcccccgtggtgggcgccgttcagggtcctgtccc 505
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 44662741 gaaggccgtgcagggcggggcagccgcccccgtggtgggcgccgttcagggtcctgtccc 44662800
Query: 506 gg 507
||
Sbjct: 44662801 gg 44662802
Score = 345 bits (174), Expect = 5e-92
Identities = 174/174 (100%)
Strand = Plus / Plus
Query: 153 gagctgaagaagtccctgtacgccatcttctcccagtttggccagatcctggatatcctg 212
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 44660030 gagctgaagaagtccctgtacgccatcttctcccagtttggccagatcctggatatcctg 44660089
Query: 213 gtctcacgaagcctgaagatgaggggccaggcctttgtcatcttcaaggaggtcagcagc 272
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 44660090 gtctcacgaagcctgaagatgaggggccaggcctttgtcatcttcaaggaggtcagcagc 44660149
Query: 273 gccaccaatgccctgcgctccatgcagggtttccccttctacgacaagcccatg 326
||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 44660150 gccaccaatgccctgcgctccatgcagggtttccccttctacgacaagcccatg 44660203
Score = 319 bits (161), Expect = 3e-84
Identities = 161/161 (100%)
Strand = Plus / Plus
Query: 770 gttccctggcttcaaggaggtccggctggtccctgggcggcacgacatcgcctttgtgga 829
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 44666845 gttccctggcttcaaggaggtccggctggtccctgggcggcacgacatcgcctttgtgga 44666904
Query: 830 gtttgacaacgaggtgcaggcgggggccgctcgcgatgccctgcagggcttcaagatcac 889
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 44666905 gtttgacaacgaggtgcaggcgggggccgctcgcgatgccctgcagggcttcaagatcac 44666964
Query: 890 ccagaacaacgccatgaagatctccttcgccaagaagtagc 930
|||||||||||||||||||||||||||||||||||||||||
Sbjct: 44666965 ccagaacaacgccatgaagatctccttcgccaagaagtagc 44667005
Score = 305 bits (154), Expect = 4e-80
Identities = 168/175 (96%)
Strand = Plus / Plus
Query: 506 gggcatgccgccgatgactcagacaccccgcatcatgcaccacatgccgggccagcctcc 565
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 44664772 gggcatgccgccgatgactcagacaccccgcatcatgcaccacatgccgggccagcctcc 44664831
Query: 566 ctacatgccgccccctggcatgatcccgcctccaggcctcgcgcccggccagatcccgcc 625
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 44664832 ctacatgccgccccctggcatgatcccgcctccaggcctcgcgcccggccagatcccgcc 44664891
Query: 626 cggggccatgnnnnnnnagcagcttatgcctgggcagatgccacctgcccagcct 680
|||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct: 44664892 cggggccatgcccccccagcagcttatgcctgggcagatgccacctgcccagcct 44664946
Score = 190 bits (96), Expect = 2e-45
Identities = 96/96 (100%)
Strand = Plus / Plus
Query: 58 gctctgtctcagcaactccttccatggcagttcccgagacccgtcccaatcacactattt 117
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 44656470 gctctgtctcagcaactccttccatggcagttcccgagacccgtcccaatcacactattt 44656529
Query: 118 atatcaacaatctcaacgagaagatcaagaaggatg 153
||||||||||||||||||||||||||||||||||||
Sbjct: 44656530 atatcaacaatctcaacgagaagatcaagaaggatg 44656565
Score = 180 bits (91), Expect = 2e-42
Identities = 91/91 (100%)
Strand = Plus / Plus
Query: 681 ctttcagaaaacccaccaaatcacatcttgttcctcaccaacctgccggaggagaccaac 740
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 44665349 ctttcagaaaacccaccaaatcacatcttgttcctcaccaacctgccggaggagaccaac 44665408
Query: 741 gagctcatgctttccatgcttttcaaccagt 771
|||||||||||||||||||||||||||||||
Sbjct: 44665409 gagctcatgctttccatgcttttcaaccagt 44665439
Score = 109 bits (55), Expect = 5e-21
Identities = 55/55 (100%)
Strand = Plus / Plus
Query: 4 tttgtggtcggcgcacagcaacgcagaaggtgccgcttgcgggagctgcgacttg 58
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 44655948 tttgtggtcggcgcacagcaacgcagaaggtgccgcttgcgggagctgcgacttg 44656002
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: 29,058,976
Number of extensions: 312
Number of successful extensions: 312
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 311
Number of HSP's successfully gapped: 7
Length of query: 1774
Length of database: 2,808,509,378
Length adjustment: 22
Effective length of query: 1752
Effective length of database: 2,808,408,574
Effective search space: 4920331821648
Effective search space used: 4920331821648
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)