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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattttttatatattgcttagctgcgagccactgatcaacaaatagtatgtaatccaattttatttttttttctgttttcttggctttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTTCAACATCCTTTCTTCCAG

Basic information

species Glycine max
transcript GLYMA09G34610.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G34610.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 10
----------------------------------------------------------------------------------------------gtaagtattttttatatattgcttagctgcgag--ccactgatcaacaaatagtatgtaatccaattttatt--tttttttctgttttcttggctttaa---tgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTTCAACATCCTTTCTTCCAG
                                                                                              || | | | || | | | | |||  |  || ||  |  |  |        || | |||  |    | ||| |   |||| | | |||| |    |||||   || |||||||||| || |||||||||||||||||||||||||| |  ||||||||||| |||||||||||||||
gtaagcatcagtaactctgtttccttcatcctttttttcctcacatattttccaaacttatttctgtttcactcttaactataaactgatgctggttattgtgttgtgtgtgt-gctggggggcaagggctgcaaaagggagtgtattgtgtgctgtgttattagtagcttttatttattttttgttttttaaacatgcagTCACTTTGTTCATGGGATCCCTGCAAGAGGCCAACAGCCTTGGAGGCTCTTCAGCATCCTTTCTTCCAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|21637546|gb|BM107701.1|BM107701
EST:     TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
EST: gi|22521888|gb|BU080699.1|BU080699
EST:     TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTCCTGGGATCCCTGCAAGAGGNCAACAGCTTCAGAGGCTCTT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
EST: gi|120533910|gb|EH262043.1|EH262043
EST:     TTTATGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
EST: gi|308098976|gb|HO760817.1|HO760817
EST:     TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
EST: gi|26048713|gb|CA785166.1|CA785166
EST:     TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
EST: gi|15662868|gb|BI700239.1|BI700239
EST:     TTTCTGCTTTAATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACGGCTTCAGAGGCACTT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
EST: gi|151399948|gb|EV269819.1|EV269819
EST:     TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTCCTGGGATCCCTACAAGAGGCCAACAGCTTCAGAGGCTCTT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
EST: gi|120533985|gb|EH262118.1|EH262118
EST:     TTTATGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
EST: gi|192325797|gb|FK018019.1|FK018019
EST:     TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
EST: gi|13311347|gb|BG404998.1|BG404998
EST:     TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
EST: gi|9565983|gb|BE475492.1|BE475492
EST:     TTTCTGCTTTGATTCCGTCTGCTACTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTTCCTGG-ATCCCTGCAAGAAGCCAACAGCTTCAGAAGCTCT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCT-CCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCT
EST: gi|207750556|gb|GD724397.1|GD724397
EST:     TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
EST: gi|18732820|gb|BM527268.1|BM527268
EST:     TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
EST: gi|193451674|gb|FK419830.1|FK419830
EST:     TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
EST: gi|21600601|gb|BQ610932.1|BQ610932
EST:     TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACA                         TCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT
genomic: TTTCTGCTTTGATTCCGTCTGCTAGTGATGATGCAATCAGCCTTATTACAgtaagtattt ... tttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatagtatgtaatccaattttatttttttttctgttttcttggctttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTTCAACATCCTTTCTTCCAG
                                            ctttaat  putative branch site (score: 4)
                  ttttatttttttttct  CT-rich tract
          taatccaattttattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattttttatatattgcttagctgcgagccactgatcaacaaatagtatgtaatccaattttatttttttttctgttttcttggctttaatgtagTCACTTTGCTCCTGGGATCCCTGCAAGAGGCCAACAGCTTCAGAGGCTCTTCAACATCCTTTCTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG