Animal-Genome cDNA 20110601C-000025


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-000025
         (1033 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_001014847.1| RNA-binding protein Raly [Bos taurus].            276   3e-74
Alignment   gi|NP_001071400.1| RNA-binding Raly-like protein [Bos taurus].       174   1e-43
Alignment   gi|NP_001029567.1| heterogeneous nuclear ribonucleoprotein C [B...   156   3e-38
Alignment   gi|NP_001030349.1| serine/arginine-rich splicing factor 6 [Bos ...    54   2e-07
Alignment   gi|NP_001014901.1| RNA-binding protein 14 [Bos taurus].               54   3e-07
Alignment   gi|NP_001092399.1| splicing factor, arginine/serine-rich 5 [Bos...    49   9e-06

>ref|NP_001014847.1| RNA-binding protein Raly [Bos taurus].
          Length = 283

 Score =  276 bits (705), Expect = 3e-74
 Identities = 155/212 (73%), Positives = 157/212 (74%)
 Frame = +3

Query: 396  MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
            MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV
Sbjct: 1    MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 60

Query: 576  QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIXXXXXXXXXXXX 755
            QYANERHARAAV+GENGRVLAGQTLDINMAGEPKPNRPKGLKR ASAI            
Sbjct: 61   QYANERHARAAVVGENGRVLAGQTLDINMAGEPKPNRPKGLKRAASAI------------ 108

Query: 756  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTIPVKLFARSTAITTGSAKI 935
                                                    TIPVKLFARSTAITTG+AKI
Sbjct: 109  ----YRLFDYRGRLSPVPVPRAVPVKRPRVTVPLVRRVKTTIPVKLFARSTAITTGTAKI 164

Query: 936  KLKSSELQAIKTELTQIKSNIDALLGRLEPIA 1031
            KLKSSELQ IKTELTQIKSNIDALLGRLE IA
Sbjct: 165  KLKSSELQTIKTELTQIKSNIDALLGRLEQIA 196


>ref|NP_001071400.1| RNA-binding Raly-like protein [Bos taurus].
          Length = 293

 Score =  174 bits (441), Expect = 1e-43
 Identities = 86/109 (78%), Positives = 95/109 (87%), Gaps = 1/109 (0%)
 Frame = +3

Query: 396 MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
           M+ K QTSNVTNKNDPKSINSRVFIGNLNTA+VKK D+E IFSKYG++ GCSVHKGYAFV
Sbjct: 1   MTGKTQTSNVTNKNDPKSINSRVFIGNLNTAIVKKVDIEAIFSKYGKIVGCSVHKGYAFV 60

Query: 576 QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTASAI 719
           QY +ERHARAAV GEN R++AGQ LDINMAGEPKP RPK G KR  SA+
Sbjct: 61  QYMSERHARAAVAGENARIIAGQPLDINMAGEPKPYRPKPGNKRPISAL 109



 Score = 50.4 bits (119), Expect = 2e-06
 Identities = 27/44 (61%), Positives = 32/44 (72%)
 Frame = +3

Query: 897  ARSTAITTGSAKIKLKSSELQAIKTELTQIKSNIDALLGRLEPI 1028
            +RS    + S+  KLKS ELQ IK ELTQIK+ ID+LLGRLE I
Sbjct: 179  SRSAVSGSSSSGSKLKSDELQTIKKELTQIKTKIDSLLGRLEKI 222


>ref|NP_001029567.1| heterogeneous nuclear ribonucleoprotein C [Bos taurus].
          Length = 294

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|NP_001030349.1| serine/arginine-rich splicing factor 6 [Bos taurus].
          Length = 345

 Score = 53.9 bits (128), Expect = 2e-07
 Identities = 29/76 (38%), Positives = 45/76 (59%)
 Frame = +3

Query: 459 RVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERHARAAVLGENGRVLA 638
           RV+IG L+  V +K D++  FS YGR+ G  +  GY FV++ + R A  AV   NG+ L 
Sbjct: 3   RVYIGRLSYNVREK-DIQRFFSGYGRLLGIDLKNGYGFVEFEDSRDADDAVYELNGKELC 61

Query: 639 GQTLDINMAGEPKPNR 686
           G+ + +  A  P+ +R
Sbjct: 62  GERVIVEHARGPRRDR 77


>ref|NP_001014901.1| RNA-binding protein 14 [Bos taurus].
          Length = 669

 Score = 53.5 bits (127), Expect = 3e-07
 Identities = 26/90 (28%), Positives = 53/90 (58%), Gaps = 1/90 (1%)
 Frame = +3

Query: 423 VTNKNDPKSINS-RVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERHA 599
           V   + P+ +N+ ++F+GN++ A   + ++ ++F + GRV  C V K YAFV    E  A
Sbjct: 67  VVEMSRPRPLNTWKIFVGNVSAACTSQ-ELRSLFERRGRVIECDVVKDYAFVHMEKEADA 125

Query: 600 RAAVLGENGRVLAGQTLDINMAGEPKPNRP 689
           +AA+   NG+ + G+ +++ ++ + +   P
Sbjct: 126 KAAIAQLNGKEVKGKRINVELSTKGQKKGP 155


>ref|NP_001092399.1| splicing factor, arginine/serine-rich 5 [Bos taurus].
          Length = 272

 Score = 48.5 bits (114), Expect = 9e-06
 Identities = 27/69 (39%), Positives = 39/69 (56%)
 Frame = +3

Query: 459 RVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERHARAAVLGENGRVLA 638
           RVFIG LN A  +K DVE  F  YGR+    + +G+ FV++ + R A  AV   +G+ L 
Sbjct: 5   RVFIGRLNPAAREK-DVERFFKGYGRIRDIDLKRGFGFVEFEDPRDADDAVYELDGKELC 63

Query: 639 GQTLDINMA 665
            + + I  A
Sbjct: 64  SERVTIEHA 72


  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: 32,744,660
Number of extensions: 835105
Number of successful extensions: 3661
Number of sequences better than 1.0e-05: 6
Number of HSP's gapped: 3631
Number of HSP's successfully gapped: 8
Length of query: 344
Length of database: 17,681,374
Length adjustment: 103
Effective length of query: 241
Effective length of database: 14,273,310
Effective search space: 3439867710
Effective search space used: 3439867710
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: 34 (17.7 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-000025
         (1033 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_542969.2| PREDICTED: similar to RNA-binding protein Raly ...   279   4e-75
Alignment   gi|XP_544154.2| PREDICTED: similar to autoantigenic hnRNP-assoc...   174   1e-43
Alignment   gi|XP_863713.1| PREDICTED: similar to Heterogeneous nuclear rib...   166   4e-41
Alignment   gi|XP_532622.1| PREDICTED: similar to heterogeneous nuclear rib...   156   3e-38
Alignment   gi|XP_863957.1| PREDICTED: similar to heterogeneous nuclear rib...   156   3e-38
Alignment   gi|XP_863937.1| PREDICTED: similar to heterogeneous nuclear rib...   156   3e-38
Alignment   gi|XP_863916.1| PREDICTED: similar to heterogeneous nuclear rib...   156   3e-38
Alignment   gi|XP_863897.1| PREDICTED: similar to heterogeneous nuclear rib...   156   3e-38
Alignment   gi|XP_863871.1| PREDICTED: similar to heterogeneous nuclear rib...   156   3e-38
Alignment   gi|XP_863848.1| PREDICTED: similar to Heterogeneous nuclear rib...   156   3e-38

>ref|XP_542969.2| PREDICTED: similar to RNA-binding protein Raly (hnRNP associated with
            lethal yellow protein) (Maternally expressed hnRNP
            C-related protein) [Canis familiaris].
          Length = 293

 Score =  279 bits (713), Expect = 4e-75
 Identities = 155/212 (73%), Positives = 155/212 (73%)
 Frame = +3

Query: 396  MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
            MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV
Sbjct: 1    MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 60

Query: 576  QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIXXXXXXXXXXXX 755
            QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKR AS I            
Sbjct: 61   QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRAASVIYSGYSFDYDYYR 120

Query: 756  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTIPVKLFARSTAITTGSAKI 935
                                                    TIPVKLFARSTAIT GSAKI
Sbjct: 121  DDFYDRLFDYRGRLSPVPVPRAVPVKRPRVTVPLVRRVKTTIPVKLFARSTAITAGSAKI 180

Query: 936  KLKSSELQAIKTELTQIKSNIDALLGRLEPIA 1031
            KLKSSELQ IKTELTQIKSNIDALLGRLE IA
Sbjct: 181  KLKSSELQTIKTELTQIKSNIDALLGRLEQIA 212


>ref|XP_544154.2| PREDICTED: similar to autoantigenic hnRNP-associated with lethal
           yellow isoform 1 [Canis familiaris].
          Length = 293

 Score =  174 bits (441), Expect = 1e-43
 Identities = 86/109 (78%), Positives = 95/109 (87%), Gaps = 1/109 (0%)
 Frame = +3

Query: 396 MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
           M+ K QTSNVTNKNDPKSINSRVFIGNLNTA+VKK D+E IFSKYG++ GCSVHKGYAFV
Sbjct: 1   MTGKTQTSNVTNKNDPKSINSRVFIGNLNTAIVKKVDIEAIFSKYGKIVGCSVHKGYAFV 60

Query: 576 QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTASAI 719
           QY +ERHARAAV GEN R++AGQ LDINMAGEPKP RPK G KR  SA+
Sbjct: 61  QYMSERHARAAVAGENARIIAGQPLDINMAGEPKPYRPKPGNKRPLSAL 109



 Score = 52.4 bits (124), Expect = 7e-07
 Identities = 28/44 (63%), Positives = 33/44 (75%)
 Frame = +3

Query: 897  ARSTAITTGSAKIKLKSSELQAIKTELTQIKSNIDALLGRLEPI 1028
            +RST   + S+  KLKS ELQ IK ELTQIK+ ID+LLGRLE I
Sbjct: 179  SRSTVSGSSSSGSKLKSDELQTIKKELTQIKTKIDSLLGRLEKI 222


>ref|XP_863713.1| PREDICTED: similar to Heterogeneous nuclear ribonucleoproteins C1/C2
            (hnRNP C1 / hnRNP C2) isoform 17 [Canis familiaris].
          Length = 296

 Score =  166 bits (419), Expect = 4e-41
 Identities = 98/205 (47%), Positives = 118/205 (57%), Gaps = 1/205 (0%)
 Frame = +3

Query: 417  SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
            SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3    SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597  ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTASAIXXXXXXXXXXXXXXXXXX 773
            ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+ +                  
Sbjct: 63   ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAAEMYGSSFDLDYDFQRDYYDR 122

Query: 774  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTIPVKLFARSTAITTGSAKIKLKSSE 953
                                                  K   R ++  +G    KLK  +
Sbjct: 123  YVKARVPPPPPIARAVVPSKRQRVSGNTSRRGKSGFNSKSGQRGSSSKSG----KLKGDD 178

Query: 954  LQAIKTELTQIKSNIDALLGRLEPI 1028
            LQ IK ELTQIK  +D+LL  LE I
Sbjct: 179  LQTIKKELTQIKQKVDSLLESLEKI 203


>ref|XP_532622.1| PREDICTED: similar to heterogeneous nuclear ribonucleoprotein C
           isoform b isoform 1 [Canis familiaris].
          Length = 294

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|XP_863957.1| PREDICTED: similar to heterogeneous nuclear ribonucleoprotein C
           isoform b isoform 27 [Canis familiaris].
          Length = 294

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|XP_863937.1| PREDICTED: similar to heterogeneous nuclear ribonucleoprotein C
           isoform b isoform 26 [Canis familiaris].
          Length = 294

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|XP_863916.1| PREDICTED: similar to heterogeneous nuclear ribonucleoprotein C
           isoform b isoform 25 [Canis familiaris].
          Length = 294

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|XP_863897.1| PREDICTED: similar to heterogeneous nuclear ribonucleoprotein C
           isoform b isoform 24 [Canis familiaris].
          Length = 294

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|XP_863871.1| PREDICTED: similar to heterogeneous nuclear ribonucleoprotein C
           isoform b isoform 23 [Canis familiaris].
          Length = 294

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|XP_863848.1| PREDICTED: similar to Heterogeneous nuclear ribonucleoproteins
           C1/C2 (hnRNP C1 / hnRNP C2) isoform 22 [Canis
           familiaris].
          Length = 307

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


  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: 34,059,893
Number of extensions: 853794
Number of successful extensions: 3724
Number of sequences better than 1.0e-05: 33
Number of HSP's gapped: 3692
Number of HSP's successfully gapped: 35
Length of query: 344
Length of database: 18,874,504
Length adjustment: 104
Effective length of query: 240
Effective length of database: 15,407,560
Effective search space: 3697814400
Effective search space used: 3697814400
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 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-000025
         (1033 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_057951.1| RNA-binding protein Raly isoform 1 [Homo sapien...   270   2e-72
Alignment   gi|NP_031393.2| RNA-binding protein Raly isoform 2 [Homo sapien...   265   4e-71
Alignment   gi|NP_001093863.1| RNA-binding Raly-like protein isoform 2 [Hom...   174   9e-44
Alignment   gi|NP_001093862.1| RNA-binding Raly-like protein isoform 2 [Hom...   174   9e-44
Alignment   gi|NP_001093861.1| RNA-binding Raly-like protein isoform 1 [Hom...   174   9e-44
Alignment   gi|NP_776247.3| RNA-binding Raly-like protein isoform 2 [Homo s...   174   9e-44
Alignment   gi|NP_001070911.1| heterogeneous nuclear ribonucleoproteins C1/...   156   3e-38
Alignment   gi|NP_001070910.1| heterogeneous nuclear ribonucleoproteins C1/...   156   3e-38
Alignment   gi|NP_004491.2| heterogeneous nuclear ribonucleoproteins C1/C2 ...   156   3e-38
Alignment   gi|NP_112604.2| heterogeneous nuclear ribonucleoproteins C1/C2 ...   156   3e-38

>ref|NP_057951.1| RNA-binding protein Raly isoform 1 [Homo sapiens].
          Length = 306

 Score =  270 bits (689), Expect = 2e-72
 Identities = 148/212 (69%), Positives = 154/212 (72%)
 Frame = +3

Query: 396  MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
            MSLK+Q SNVTNKNDPKSINSRVFIGNLNTA+VKKSDVETIFSKYGRVAGCSVHKGYAFV
Sbjct: 1    MSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFV 60

Query: 576  QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIXXXXXXXXXXXX 755
            QY+NERHARAAVLGENGRVLAGQTLDINMAGEPKP+RPKGLKR ASAI            
Sbjct: 61   QYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRPKGLKRAASAIYSGYIFDYDYYR 120

Query: 756  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTIPVKLFARSTAITTGSAKI 935
                                                     +PVKLFARSTA+TT SAKI
Sbjct: 121  DDFYDRLFDYRGRLSPVPVPRAVPVKRPRVTVPLVRRVKTNVPVKLFARSTAVTTSSAKI 180

Query: 936  KLKSSELQAIKTELTQIKSNIDALLGRLEPIA 1031
            KLKSSELQAIKTELTQIKSNIDALL RLE IA
Sbjct: 181  KLKSSELQAIKTELTQIKSNIDALLSRLEQIA 212


>ref|NP_031393.2| RNA-binding protein Raly isoform 2 [Homo sapiens].
          Length = 290

 Score =  265 bits (678), Expect = 4e-71
 Identities = 148/212 (69%), Positives = 154/212 (72%)
 Frame = +3

Query: 396  MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
            MSLK+Q SNVTNKNDPKSINSRVFIGNLNTA+VKKSDVETIFSKYGRVAGCSVHKGYAFV
Sbjct: 1    MSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFV 60

Query: 576  QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIXXXXXXXXXXXX 755
            QY+NERHARAAVLGENGRVLAGQTLDINMAGEPKP+RPKGLKR ASAI            
Sbjct: 61   QYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRPKGLKRAASAI------------ 108

Query: 756  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTIPVKLFARSTAITTGSAKI 935
                                                     +PVKLFARSTA+TT SAKI
Sbjct: 109  ----YRLFDYRGRLSPVPVPRAVPVKRPRVTVPLVRRVKTNVPVKLFARSTAVTTSSAKI 164

Query: 936  KLKSSELQAIKTELTQIKSNIDALLGRLEPIA 1031
            KLKSSELQAIKTELTQIKSNIDALL RLE IA
Sbjct: 165  KLKSSELQAIKTELTQIKSNIDALLSRLEQIA 196


>ref|NP_001093863.1| RNA-binding Raly-like protein isoform 2 [Homo sapiens].
          Length = 291

 Score =  174 bits (442), Expect = 9e-44
 Identities = 87/109 (79%), Positives = 95/109 (87%), Gaps = 1/109 (0%)
 Frame = +3

Query: 396 MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
           M+ K QTSNVTNKNDPKSINSRVFIGNLNTA+VKK D+E IFSKYG++ GCSVHKGYAFV
Sbjct: 1   MTGKTQTSNVTNKNDPKSINSRVFIGNLNTAIVKKVDIEAIFSKYGKIVGCSVHKGYAFV 60

Query: 576 QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTASAI 719
           QY +ERHARAAV GEN RV+AGQ LDINMAGEPKP RPK G KR  SA+
Sbjct: 61  QYMSERHARAAVAGENARVIAGQPLDINMAGEPKPYRPKPGNKRPLSAL 109



 Score = 52.4 bits (124), Expect = 7e-07
 Identities = 30/44 (68%), Positives = 34/44 (77%)
 Frame = +3

Query: 897  ARSTAITTGSAKIKLKSSELQAIKTELTQIKSNIDALLGRLEPI 1028
            +RSTA  +GS   KLKS ELQ IK ELTQIK+ ID+LLGRLE I
Sbjct: 179  SRSTA--SGSTGSKLKSDELQTIKKELTQIKTKIDSLLGRLEKI 220


>ref|NP_001093862.1| RNA-binding Raly-like protein isoform 2 [Homo sapiens].
          Length = 291

 Score =  174 bits (442), Expect = 9e-44
 Identities = 87/109 (79%), Positives = 95/109 (87%), Gaps = 1/109 (0%)
 Frame = +3

Query: 396 MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
           M+ K QTSNVTNKNDPKSINSRVFIGNLNTA+VKK D+E IFSKYG++ GCSVHKGYAFV
Sbjct: 1   MTGKTQTSNVTNKNDPKSINSRVFIGNLNTAIVKKVDIEAIFSKYGKIVGCSVHKGYAFV 60

Query: 576 QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTASAI 719
           QY +ERHARAAV GEN RV+AGQ LDINMAGEPKP RPK G KR  SA+
Sbjct: 61  QYMSERHARAAVAGENARVIAGQPLDINMAGEPKPYRPKPGNKRPLSAL 109



 Score = 52.4 bits (124), Expect = 7e-07
 Identities = 30/44 (68%), Positives = 34/44 (77%)
 Frame = +3

Query: 897  ARSTAITTGSAKIKLKSSELQAIKTELTQIKSNIDALLGRLEPI 1028
            +RSTA  +GS   KLKS ELQ IK ELTQIK+ ID+LLGRLE I
Sbjct: 179  SRSTA--SGSTGSKLKSDELQTIKKELTQIKTKIDSLLGRLEKI 220


>ref|NP_001093861.1| RNA-binding Raly-like protein isoform 1 [Homo sapiens].
          Length = 304

 Score =  174 bits (442), Expect = 9e-44
 Identities = 87/109 (79%), Positives = 95/109 (87%), Gaps = 1/109 (0%)
 Frame = +3

Query: 396 MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
           M+ K QTSNVTNKNDPKSINSRVFIGNLNTA+VKK D+E IFSKYG++ GCSVHKGYAFV
Sbjct: 14  MTGKTQTSNVTNKNDPKSINSRVFIGNLNTAIVKKVDIEAIFSKYGKIVGCSVHKGYAFV 73

Query: 576 QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTASAI 719
           QY +ERHARAAV GEN RV+AGQ LDINMAGEPKP RPK G KR  SA+
Sbjct: 74  QYMSERHARAAVAGENARVIAGQPLDINMAGEPKPYRPKPGNKRPLSAL 122



 Score = 52.4 bits (124), Expect = 7e-07
 Identities = 30/44 (68%), Positives = 34/44 (77%)
 Frame = +3

Query: 897  ARSTAITTGSAKIKLKSSELQAIKTELTQIKSNIDALLGRLEPI 1028
            +RSTA  +GS   KLKS ELQ IK ELTQIK+ ID+LLGRLE I
Sbjct: 192  SRSTA--SGSTGSKLKSDELQTIKKELTQIKTKIDSLLGRLEKI 233


>ref|NP_776247.3| RNA-binding Raly-like protein isoform 2 [Homo sapiens].
          Length = 291

 Score =  174 bits (442), Expect = 9e-44
 Identities = 87/109 (79%), Positives = 95/109 (87%), Gaps = 1/109 (0%)
 Frame = +3

Query: 396 MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
           M+ K QTSNVTNKNDPKSINSRVFIGNLNTA+VKK D+E IFSKYG++ GCSVHKGYAFV
Sbjct: 1   MTGKTQTSNVTNKNDPKSINSRVFIGNLNTAIVKKVDIEAIFSKYGKIVGCSVHKGYAFV 60

Query: 576 QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTASAI 719
           QY +ERHARAAV GEN RV+AGQ LDINMAGEPKP RPK G KR  SA+
Sbjct: 61  QYMSERHARAAVAGENARVIAGQPLDINMAGEPKPYRPKPGNKRPLSAL 109



 Score = 52.4 bits (124), Expect = 7e-07
 Identities = 30/44 (68%), Positives = 34/44 (77%)
 Frame = +3

Query: 897  ARSTAITTGSAKIKLKSSELQAIKTELTQIKSNIDALLGRLEPI 1028
            +RSTA  +GS   KLKS ELQ IK ELTQIK+ ID+LLGRLE I
Sbjct: 179  SRSTA--SGSTGSKLKSDELQTIKKELTQIKTKIDSLLGRLEKI 220


>ref|NP_001070911.1| heterogeneous nuclear ribonucleoproteins C1/C2 isoform b [Homo
           sapiens].
          Length = 293

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|NP_001070910.1| heterogeneous nuclear ribonucleoproteins C1/C2 isoform a [Homo
           sapiens].
          Length = 306

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|NP_004491.2| heterogeneous nuclear ribonucleoproteins C1/C2 isoform b [Homo
           sapiens].
          Length = 293

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|NP_112604.2| heterogeneous nuclear ribonucleoproteins C1/C2 isoform a [Homo
           sapiens].
          Length = 306

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


  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: 33,481,741
Number of extensions: 842157
Number of successful extensions: 3574
Number of sequences better than 1.0e-05: 18
Number of HSP's gapped: 3552
Number of HSP's successfully gapped: 24
Length of query: 344
Length of database: 18,297,164
Length adjustment: 103
Effective length of query: 241
Effective length of database: 14,901,872
Effective search space: 3591351152
Effective search space used: 3591351152
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: 34 (17.7 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-000025
         (1033 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_001132985.1| RNA-binding protein Raly long isoform [Mus m...   281   8e-76
Alignment   gi|NP_075619.2| RNA-binding protein Raly short isoform [Mus mus...   276   1e-74
Alignment   gi|NP_001132984.1| RNA-binding protein Raly short isoform [Mus ...   276   1e-74
Alignment   gi|NP_001132983.1| RNA-binding protein Raly short isoform [Mus ...   276   1e-74
Alignment   gi|NP_001156800.1| RNA-binding Raly-like protein isoform a [Mus...   174   8e-44
Alignment   gi|NP_848746.1| RNA-binding Raly-like protein isoform a [Mus mu...   174   8e-44
Alignment   gi|NP_001164454.1| heterogeneous nuclear ribonucleoproteins C1/...   156   3e-38
Alignment   gi|NP_058580.1| heterogeneous nuclear ribonucleoproteins C1/C2 ...   156   3e-38
Alignment   gi|NP_001164453.1| heterogeneous nuclear ribonucleoproteins C1/...   156   3e-38
Alignment   gi|NP_001164455.1| heterogeneous nuclear ribonucleoproteins C1/...   156   3e-38

>ref|NP_001132985.1| RNA-binding protein Raly long isoform [Mus musculus].
          Length = 312

 Score =  281 bits (718), Expect = 8e-76
 Identities = 155/212 (73%), Positives = 157/212 (74%)
 Frame = +3

Query: 396  MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
            MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV
Sbjct: 1    MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 60

Query: 576  QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIXXXXXXXXXXXX 755
            QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKR A+AI            
Sbjct: 61   QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRAATAIYSGYSFDYDYYQ 120

Query: 756  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTIPVKLFARSTAITTGSAKI 935
                                                    TIPVKLFARSTA+TTGSAKI
Sbjct: 121  DYFCARLFDYRGRLSPVPVPRAVPVKRPRVTVPLVRRVKTTIPVKLFARSTAVTTGSAKI 180

Query: 936  KLKSSELQAIKTELTQIKSNIDALLGRLEPIA 1031
            KLKSSELQ IKTELTQIKSNIDALLGRLE IA
Sbjct: 181  KLKSSELQTIKTELTQIKSNIDALLGRLEQIA 212


>ref|NP_075619.2| RNA-binding protein Raly short isoform [Mus musculus].
          Length = 296

 Score =  276 bits (707), Expect = 1e-74
 Identities = 155/212 (73%), Positives = 157/212 (74%)
 Frame = +3

Query: 396  MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
            MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV
Sbjct: 1    MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 60

Query: 576  QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIXXXXXXXXXXXX 755
            QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKR A+AI            
Sbjct: 61   QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRAATAI------------ 108

Query: 756  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTIPVKLFARSTAITTGSAKI 935
                                                    TIPVKLFARSTA+TTGSAKI
Sbjct: 109  ----YRLFDYRGRLSPVPVPRAVPVKRPRVTVPLVRRVKTTIPVKLFARSTAVTTGSAKI 164

Query: 936  KLKSSELQAIKTELTQIKSNIDALLGRLEPIA 1031
            KLKSSELQ IKTELTQIKSNIDALLGRLE IA
Sbjct: 165  KLKSSELQTIKTELTQIKSNIDALLGRLEQIA 196


>ref|NP_001132984.1| RNA-binding protein Raly short isoform [Mus musculus].
          Length = 296

 Score =  276 bits (707), Expect = 1e-74
 Identities = 155/212 (73%), Positives = 157/212 (74%)
 Frame = +3

Query: 396  MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
            MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV
Sbjct: 1    MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 60

Query: 576  QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIXXXXXXXXXXXX 755
            QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKR A+AI            
Sbjct: 61   QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRAATAI------------ 108

Query: 756  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTIPVKLFARSTAITTGSAKI 935
                                                    TIPVKLFARSTA+TTGSAKI
Sbjct: 109  ----YRLFDYRGRLSPVPVPRAVPVKRPRVTVPLVRRVKTTIPVKLFARSTAVTTGSAKI 164

Query: 936  KLKSSELQAIKTELTQIKSNIDALLGRLEPIA 1031
            KLKSSELQ IKTELTQIKSNIDALLGRLE IA
Sbjct: 165  KLKSSELQTIKTELTQIKSNIDALLGRLEQIA 196


>ref|NP_001132983.1| RNA-binding protein Raly short isoform [Mus musculus].
          Length = 296

 Score =  276 bits (707), Expect = 1e-74
 Identities = 155/212 (73%), Positives = 157/212 (74%)
 Frame = +3

Query: 396  MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
            MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV
Sbjct: 1    MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 60

Query: 576  QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIXXXXXXXXXXXX 755
            QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKR A+AI            
Sbjct: 61   QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRAATAI------------ 108

Query: 756  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTIPVKLFARSTAITTGSAKI 935
                                                    TIPVKLFARSTA+TTGSAKI
Sbjct: 109  ----YRLFDYRGRLSPVPVPRAVPVKRPRVTVPLVRRVKTTIPVKLFARSTAVTTGSAKI 164

Query: 936  KLKSSELQAIKTELTQIKSNIDALLGRLEPIA 1031
            KLKSSELQ IKTELTQIKSNIDALLGRLE IA
Sbjct: 165  KLKSSELQTIKTELTQIKSNIDALLGRLEQIA 196


>ref|NP_001156800.1| RNA-binding Raly-like protein isoform a [Mus musculus].
          Length = 293

 Score =  174 bits (442), Expect = 8e-44
 Identities = 86/109 (78%), Positives = 95/109 (87%), Gaps = 1/109 (0%)
 Frame = +3

Query: 396 MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
           M+ K QTSN+TNKNDPKSINSRVFIGNLNTA+VKK D+E IFSKYG++ GCSVHKGYAFV
Sbjct: 1   MTGKTQTSNITNKNDPKSINSRVFIGNLNTAIVKKVDIEAIFSKYGKIVGCSVHKGYAFV 60

Query: 576 QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTASAI 719
           QY +ERHARAAV GEN RV+AGQ LDINMAGEPKP RPK G KR  SA+
Sbjct: 61  QYMSERHARAAVAGENARVIAGQPLDINMAGEPKPYRPKPGSKRPLSAL 109



 Score = 51.6 bits (122), Expect = 1e-06
 Identities = 28/44 (63%), Positives = 33/44 (75%)
 Frame = +3

Query: 897  ARSTAITTGSAKIKLKSSELQAIKTELTQIKSNIDALLGRLEPI 1028
            +RST   + S+  KLKS ELQ IK ELTQIK+ ID+LLGRLE I
Sbjct: 179  SRSTVGGSSSSGSKLKSDELQTIKKELTQIKTKIDSLLGRLEKI 222


>ref|NP_848746.1| RNA-binding Raly-like protein isoform a [Mus musculus].
          Length = 293

 Score =  174 bits (442), Expect = 8e-44
 Identities = 86/109 (78%), Positives = 95/109 (87%), Gaps = 1/109 (0%)
 Frame = +3

Query: 396 MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
           M+ K QTSN+TNKNDPKSINSRVFIGNLNTA+VKK D+E IFSKYG++ GCSVHKGYAFV
Sbjct: 1   MTGKTQTSNITNKNDPKSINSRVFIGNLNTAIVKKVDIEAIFSKYGKIVGCSVHKGYAFV 60

Query: 576 QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTASAI 719
           QY +ERHARAAV GEN RV+AGQ LDINMAGEPKP RPK G KR  SA+
Sbjct: 61  QYMSERHARAAVAGENARVIAGQPLDINMAGEPKPYRPKPGSKRPLSAL 109



 Score = 51.6 bits (122), Expect = 1e-06
 Identities = 28/44 (63%), Positives = 33/44 (75%)
 Frame = +3

Query: 897  ARSTAITTGSAKIKLKSSELQAIKTELTQIKSNIDALLGRLEPI 1028
            +RST   + S+  KLKS ELQ IK ELTQIK+ ID+LLGRLE I
Sbjct: 179  SRSTVGGSSSSGSKLKSDELQTIKKELTQIKTKIDSLLGRLEKI 222


>ref|NP_001164454.1| heterogeneous nuclear ribonucleoproteins C1/C2 isoform 3 [Mus
           musculus].
          Length = 293

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|NP_058580.1| heterogeneous nuclear ribonucleoproteins C1/C2 isoform 1 [Mus
           musculus].
          Length = 313

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|NP_001164453.1| heterogeneous nuclear ribonucleoproteins C1/C2 isoform 2 [Mus
           musculus].
          Length = 300

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|NP_001164455.1| heterogeneous nuclear ribonucleoproteins C1/C2 isoform 4 [Mus
           musculus].
          Length = 292

 Score =  156 bits (394), Expect = 3e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


  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: 28,354,027
Number of extensions: 707528
Number of successful extensions: 3205
Number of sequences better than 1.0e-05: 19
Number of HSP's gapped: 3163
Number of HSP's successfully gapped: 25
Length of query: 344
Length of database: 15,617,559
Length adjustment: 102
Effective length of query: 242
Effective length of database: 12,553,887
Effective search space: 3038040654
Effective search space used: 3038040654
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: 34 (17.7 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-000025
         (1033 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_003134445.2| PREDICTED: RNA-binding protein Raly-like iso...   286   2e-77
Alignment   gi|XP_003359995.1| PREDICTED: RNA-binding protein Raly [Sus scr...   286   2e-77
Alignment   gi|XP_001929139.2| PREDICTED: RNA-binding protein Raly isoform ...   286   2e-77
Alignment   gi|XP_003134451.1| PREDICTED: RNA-binding protein Raly isoform ...   281   3e-76
Alignment   gi|NP_001230622.1| heterogeneous nuclear ribonucleoprotein C (C...   156   2e-38
Alignment   gi|NP_001230623.1| heterogeneous nuclear ribonucleoprotein C (C...   156   2e-38
Alignment   gi|XP_003125632.1| PREDICTED: RNA-binding Raly-like protein-lik...   146   2e-35
Alignment   gi|NP_001070685.1| serine/arginine-rich splicing factor 6 [Sus ...    51   1e-06
Alignment   gi|XP_003360793.1| PREDICTED: serine/arginine-rich splicing fac...    49   6e-06
Alignment   gi|XP_001927469.2| PREDICTED: serine/arginine-rich splicing fac...    49   6e-06

>ref|XP_003134445.2| PREDICTED: RNA-binding protein Raly-like isoform 1 [Sus scrofa].
          Length = 327

 Score =  286 bits (731), Expect = 2e-77
 Identities = 159/212 (75%), Positives = 159/212 (75%)
 Frame = +3

Query: 396  MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
            MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV
Sbjct: 1    MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 60

Query: 576  QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIXXXXXXXXXXXX 755
            QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAI            
Sbjct: 61   QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIYSGYSFDYDYYR 120

Query: 756  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTIPVKLFARSTAITTGSAKI 935
                                                    TIPVKLFARSTAITTGSAKI
Sbjct: 121  DDFYDRLFDYRGRLSPVPVPRAVPVKRPRVTVPLVRRVKTTIPVKLFARSTAITTGSAKI 180

Query: 936  KLKSSELQAIKTELTQIKSNIDALLGRLEPIA 1031
            KLKSSELQAIKTELTQIKSNIDALLGRLE IA
Sbjct: 181  KLKSSELQAIKTELTQIKSNIDALLGRLEQIA 212


>ref|XP_003359995.1| PREDICTED: RNA-binding protein Raly [Sus scrofa].
          Length = 327

 Score =  286 bits (731), Expect = 2e-77
 Identities = 159/212 (75%), Positives = 159/212 (75%)
 Frame = +3

Query: 396  MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
            MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV
Sbjct: 1    MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 60

Query: 576  QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIXXXXXXXXXXXX 755
            QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAI            
Sbjct: 61   QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIYSGYSFDYDYYR 120

Query: 756  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTIPVKLFARSTAITTGSAKI 935
                                                    TIPVKLFARSTAITTGSAKI
Sbjct: 121  DDFYDRLFDYRGRLSPVPVPRAVPVKRPRVTVPLVRRVKTTIPVKLFARSTAITTGSAKI 180

Query: 936  KLKSSELQAIKTELTQIKSNIDALLGRLEPIA 1031
            KLKSSELQAIKTELTQIKSNIDALLGRLE IA
Sbjct: 181  KLKSSELQAIKTELTQIKSNIDALLGRLEQIA 212


>ref|XP_001929139.2| PREDICTED: RNA-binding protein Raly isoform 1 [Sus scrofa].
          Length = 327

 Score =  286 bits (731), Expect = 2e-77
 Identities = 159/212 (75%), Positives = 159/212 (75%)
 Frame = +3

Query: 396  MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
            MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV
Sbjct: 1    MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 60

Query: 576  QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIXXXXXXXXXXXX 755
            QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAI            
Sbjct: 61   QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIYSGYSFDYDYYR 120

Query: 756  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTIPVKLFARSTAITTGSAKI 935
                                                    TIPVKLFARSTAITTGSAKI
Sbjct: 121  DDFYDRLFDYRGRLSPVPVPRAVPVKRPRVTVPLVRRVKTTIPVKLFARSTAITTGSAKI 180

Query: 936  KLKSSELQAIKTELTQIKSNIDALLGRLEPIA 1031
            KLKSSELQAIKTELTQIKSNIDALLGRLE IA
Sbjct: 181  KLKSSELQAIKTELTQIKSNIDALLGRLEQIA 212


>ref|XP_003134451.1| PREDICTED: RNA-binding protein Raly isoform 2 [Sus scrofa].
          Length = 311

 Score =  281 bits (720), Expect = 3e-76
 Identities = 159/212 (75%), Positives = 159/212 (75%)
 Frame = +3

Query: 396  MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
            MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV
Sbjct: 1    MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 60

Query: 576  QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAIXXXXXXXXXXXX 755
            QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAI            
Sbjct: 61   QYANERHARAAVLGENGRVLAGQTLDINMAGEPKPNRPKGLKRTASAI------------ 108

Query: 756  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTIPVKLFARSTAITTGSAKI 935
                                                    TIPVKLFARSTAITTGSAKI
Sbjct: 109  ----YRLFDYRGRLSPVPVPRAVPVKRPRVTVPLVRRVKTTIPVKLFARSTAITTGSAKI 164

Query: 936  KLKSSELQAIKTELTQIKSNIDALLGRLEPIA 1031
            KLKSSELQAIKTELTQIKSNIDALLGRLE IA
Sbjct: 165  KLKSSELQAIKTELTQIKSNIDALLGRLEQIA 196


>ref|NP_001230622.1| heterogeneous nuclear ribonucleoprotein C (C1/C2) 1 [Sus scrofa].
          Length = 313

 Score =  156 bits (394), Expect = 2e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|NP_001230623.1| heterogeneous nuclear ribonucleoprotein C (C1/C2) 2 [Sus scrofa].
          Length = 294

 Score =  156 bits (394), Expect = 2e-38
 Identities = 76/100 (76%), Positives = 89/100 (89%), Gaps = 1/100 (1%)
 Frame = +3

Query: 417 SNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERH 596
           SNVTNK DP+S+NSRVFIGNLNT VVKKSDVE IFSKYG++ GCSVHKG+AFVQY NER+
Sbjct: 3   SNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN 62

Query: 597 ARAAVLGENGRVLAGQTLDINMAGEPKPNRPK-GLKRTAS 713
           ARAAV GE+GR++AGQ LDIN+A EPK NR K G+KR+A+
Sbjct: 63  ARAAVAGEDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAA 102


>ref|XP_003125632.1| PREDICTED: RNA-binding Raly-like protein-like [Sus scrofa].
          Length = 88

 Score =  146 bits (368), Expect = 2e-35
 Identities = 69/86 (80%), Positives = 77/86 (89%)
 Frame = +3

Query: 396 MSLKIQTSNVTNKNDPKSINSRVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFV 575
           M+ K QTSNVTNKNDPKSINSRVFIGNLNTA+VKK D+E IFSKYG++ GCSVHKGYAFV
Sbjct: 1   MTGKTQTSNVTNKNDPKSINSRVFIGNLNTAIVKKVDIEAIFSKYGKIVGCSVHKGYAFV 60

Query: 576 QYANERHARAAVLGENGRVLAGQTLD 653
           QY +ERHARAAV GEN R++AGQ LD
Sbjct: 61  QYMSERHARAAVAGENARIIAGQPLD 86


>ref|NP_001070685.1| serine/arginine-rich splicing factor 6 [Sus scrofa].
          Length = 345

 Score = 50.8 bits (120), Expect = 1e-06
 Identities = 28/76 (36%), Positives = 44/76 (57%)
 Frame = +3

Query: 459 RVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERHARAAVLGENGRVLA 638
           RV+IG L+  V +K D++  FS YGR+    +  GY FV++ + R A  AV   NG+ L 
Sbjct: 3   RVYIGRLSYNVREK-DIQRFFSGYGRLLEIDLKNGYGFVEFEDSRDADDAVYELNGKELC 61

Query: 639 GQTLDINMAGEPKPNR 686
           G+ + +  A  P+ +R
Sbjct: 62  GERVIVEHARGPRRDR 77


>ref|XP_003360793.1| PREDICTED: serine/arginine-rich splicing factor 5-like [Sus
           scrofa].
          Length = 221

 Score = 48.5 bits (114), Expect = 6e-06
 Identities = 27/69 (39%), Positives = 39/69 (56%)
 Frame = +3

Query: 459 RVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERHARAAVLGENGRVLA 638
           RVFIG LN A  +K DVE  F  YGR+    + +G+ FV++ + R A  AV   +G+ L 
Sbjct: 5   RVFIGRLNPAAREK-DVERFFKGYGRIRDIDLKRGFGFVEFEDPRDADDAVYELDGKELC 63

Query: 639 GQTLDINMA 665
            + + I  A
Sbjct: 64  SERVTIEHA 72


>ref|XP_001927469.2| PREDICTED: serine/arginine-rich splicing factor 5 isoform 2 [Sus
           scrofa].
          Length = 272

 Score = 48.5 bits (114), Expect = 6e-06
 Identities = 27/69 (39%), Positives = 39/69 (56%)
 Frame = +3

Query: 459 RVFIGNLNTAVVKKSDVETIFSKYGRVAGCSVHKGYAFVQYANERHARAAVLGENGRVLA 638
           RVFIG LN A  +K DVE  F  YGR+    + +G+ FV++ + R A  AV   +G+ L 
Sbjct: 5   RVFIGRLNPAAREK-DVERFFKGYGRIRDIDLKRGFGFVEFEDPRDADDAVYELDGKELC 63

Query: 639 GQTLDINMA 665
            + + I  A
Sbjct: 64  SERVTIEHA 72


  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: 21,102,626
Number of extensions: 536953
Number of successful extensions: 2375
Number of sequences better than 1.0e-05: 14
Number of HSP's gapped: 2356
Number of HSP's successfully gapped: 18
Length of query: 344
Length of database: 11,343,932
Length adjustment: 100
Effective length of query: 244
Effective length of database: 8,854,232
Effective search space: 2160432608
Effective search space used: 2160432608
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: 34 (17.7 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-000025
         (1033 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_Chr17                                                         527   e-147
Sscrofa_Chr01                                                          80   3e-12
Sscrofa_Chr04                                                          68   1e-08

>Sscrofa_Chr17 
||          Length = 69701581

 Score =  527 bits (266), Expect = e-147
 Identities = 266/266 (100%)
 Strand = Plus / Minus

                                                                            
Query: 386      ggtggctaccatgtccttaaagatccagacaagcaacgtaaccaacaagaatgaccccaa 445
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42879590 ggtggctaccatgtccttaaagatccagacaagcaacgtaaccaacaagaatgaccccaa 42879531

                                                                            
Query: 446      gtctatcaactctagggtcttcattggaaacctcaacacagccgtggtgaagaaatctga 505
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42879530 gtctatcaactctagggtcttcattggaaacctcaacacagccgtggtgaagaaatctga 42879471

                                                                            
Query: 506      tgtggagactatcttctccaagtatggccgtgtggccggctgttctgtgcacaagggcta 565
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42879470 tgtggagactatcttctccaagtatggccgtgtggccggctgttctgtgcacaagggcta 42879411

                                                                            
Query: 566      tgcctttgtgcagtatgccaacgagcgccatgcccgggcagctgtgctgggagagaatgg 625
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42879410 tgcctttgtgcagtatgccaacgagcgccatgcccgggcagctgtgctgggagagaatgg 42879351

                                          
Query: 626      gcgagtgctggccgggcagaccctgg 651
                ||||||||||||||||||||||||||
Sbjct: 42879350 gcgagtgctggccgggcagaccctgg 42879325



 Score =  420 bits (212), Expect = e-115
 Identities = 212/212 (100%)
 Strand = Plus / Minus

                                                                            
Query: 1        gtgcggcggggcgcgcgagcagcgcggctgcggggtgggctgagcagagagaagctgagg 60
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42965518 gtgcggcggggcgcgcgagcagcgcggctgcggggtgggctgagcagagagaagctgagg 42965459

                                                                            
Query: 61       gggcggtagcggcagcggcgattcgcgtgcctgtgctcagctcctcacgccgcggccggg 120
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42965458 gggcggtagcggcagcggcgattcgcgtgcctgtgctcagctcctcacgccgcggccggg 42965399

                                                                            
Query: 121      gccgccttctccctccttccttcccgcccccgagtgcggcggtaccgcctccttcagcgc 180
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42965398 gccgccttctccctccttccttcccgcccccgagtgcggcggtaccgcctccttcagcgc 42965339

                                                
Query: 181      cgcgcggcttcctccagacctccgtgcgcggg 212
                ||||||||||||||||||||||||||||||||
Sbjct: 42965338 cgcgcggcttcctccagacctccgtgcgcggg 42965307



 Score =  339 bits (171), Expect = 2e-90
 Identities = 171/171 (100%)
 Strand = Plus / Minus

                                                                            
Query: 769      acaggctcttcgactatcggggccgcctgtcaccagtgccagtgcccagggcggtccctg 828
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42875295 acaggctcttcgactatcggggccgcctgtcaccagtgccagtgcccagggcggtccctg 42875236

                                                                            
Query: 829      tgaagcgaccccgggtcacagtccccttggtccggcgtgtcaaaaccaccatacctgtca 888
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42875235 tgaagcgaccccgggtcacagtccccttggtccggcgtgtcaaaaccaccatacctgtca 42875176

                                                                   
Query: 889      agctctttgcccgctccacagctatcaccaccggctcagccaagatcaagt 939
                |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42875175 agctctttgcccgctccacagctatcaccaccggctcagccaagatcaagt 42875125



 Score =  178 bits (90), Expect = 4e-42
 Identities = 97/98 (98%), Gaps = 1/98 (1%)
 Strand = Plus / Minus

                                                                            
Query: 211      gggccatcccttagccttctacacactgaactgaaactcaagccctctccttggaactct 270
                ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42943055 gggccatcccttagc-ttctacacactgaactgaaactcaagccctctccttggaactct 42942997

                                                      
Query: 271      tcaaagactggaggaaattccttaaaaccagtggtgag 308
                ||||||||||||||||||||||||||||||||||||||
Sbjct: 42942996 tcaaagactggaggaaattccttaaaaccagtggtgag 42942959



 Score =  170 bits (86), Expect = 1e-39
 Identities = 86/86 (100%)
 Strand = Plus / Minus

                                                                            
Query: 303      ggtgagctctgttctcagaggcatttggtgctgatcctgtaacccaaaagaggaaattgc 362
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42925743 ggtgagctctgttctcagaggcatttggtgctgatcctgtaacccaaaagaggaaattgc 42925684

                                          
Query: 363      tgcctgagatcagccttggtactggt 388
                ||||||||||||||||||||||||||
Sbjct: 42925683 tgcctgagatcagccttggtactggt 42925658



 Score =  163 bits (82), Expect = 2e-37
 Identities = 91/94 (96%)
 Strand = Plus / Minus

                                                                            
Query: 940      taaagagcagtgaactgcaggccatcaagacagagctgacccaaatcaagtccaacatcg 999
                ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct: 42874407 taaagagcagtgaactgcaggccatcaagacagagctgacccagatcaagtccaacatcg 42874348

                                                  
Query: 1000     atgccctgctgggtcgcttggagccaattgctga 1033
                ||||||||||||||||||||||||  ||||||||
Sbjct: 42874347 atgccctgctgggtcgcttggagcagattgctga 42874314



 Score =  147 bits (74), Expect = 1e-32
 Identities = 74/74 (100%)
 Strand = Plus / Minus

                                                                            
Query: 651      gacatcaacatggctggagagcccaagcccaacagacccaaggggctaaaaagaacagca 710
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42877894 gacatcaacatggctggagagcccaagcccaacagacccaaggggctaaaaagaacagca 42877835

                              
Query: 711      tctgccatatacag 724
                ||||||||||||||
Sbjct: 42877834 tctgccatatacag 42877821



 Score =  103 bits (52), Expect = 2e-19
 Identities = 52/52 (100%)
 Strand = Plus / Minus

                                                                    
Query: 722      cagtggctacagctttgactatgattactaccgggacgacttctacgacagg 773
                ||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42877631 cagtggctacagctttgactatgattactaccgggacgacttctacgacagg 42877580


>Sscrofa_Chr01 
||          Length = 315321322

 Score = 79.8 bits (40), Expect = 3e-12
 Identities = 58/64 (90%)
 Strand = Plus / Plus

                                                                             
Query: 316       ctcagaggcatttggtgctgatcctgtaacccaaaagaggaaattgctgcctgagatcag 375
                 |||||||||| ||||| |||||||||||||| |||| |||||||||||| ||||| ||||
Sbjct: 218275488 ctcagaggcagttggtactgatcctgtaaccaaaaataggaaattgctggctgagctcag 218275547

                     
Query: 376       cctt 379
                 ||||
Sbjct: 218275548 cctt 218275551


>Sscrofa_Chr04 
||          Length = 143465943

 Score = 67.9 bits (34), Expect = 1e-08
 Identities = 67/78 (85%)
 Strand = Plus / Minus

                                                                            
Query: 411      cagacaagcaacgtaaccaacaagaatgaccccaagtctatcaactctagggtcttcatt 470
                ||||| ||||| || ||||| ||||||||||||||||| ||||||||| | || ||||||
Sbjct: 57539553 cagaccagcaatgtcaccaataagaatgaccccaagtccatcaactctcgagttttcatt 57539494

                                  
Query: 471      ggaaacctcaacacagcc 488
                ||||| || || ||||||
Sbjct: 57539493 ggaaatctaaatacagcc 57539476


  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: 26,131,447
Number of extensions: 410
Number of successful extensions: 410
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 410
Number of HSP's successfully gapped: 10
Length of query: 1033
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1012
Effective length of database: 2,808,413,156
Effective search space: 2842114113872
Effective search space used: 2842114113872
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 50 (99.1 bits)
S1: 18 (36.2 bits)
S2: 29 (58.0 bits)