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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcaagatgctgcggattttgatgacagtaggactggagaacttctttttctaaatgataatcagataataacagtttttatattcttgtttgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGACAAAGACCCACCGTAAGCAAGTCTGACCTTGATGTTCATGAGAGATTCA

Basic information

species Glycine max
transcript GLYMA11G19120.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------gtattcaagatgctgcggattttgatgacagtaggactggagaacttctt----tttctaaatgataatcagataataacagtttttatattctt-----gtttgctgta-cagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGACAAAGACCCACCGTAAGCAAGTCTGACCTTGATGTTCATGAGAGATTCA
                      |||     | | |  | ||||  |        |   |  | | | | |      ||  | ||||  ||     || |     || | ||||         |    || | |||||  | ||||| || ||  | ||||||||||| || || |||||||| |||||||| || || || |||||||||||||||||||| || ||||||||||
gtacgcatctaaactttgaatatatcatttaggttttgtatttcaagcttctctgatttctaaatcctttcaatccttacatatgacgatttctaaagactgaattgtgtatttcatgtgaataaattgcaacagATTATTCCACCACCAATCACCAGAACAGATTTCGAGAAGGTACTTGCAAGACAAAGGCCAACAGTGAGCAAGTCTGACCTTGATGTCCACGAGAGATTCA

upper sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 7
gtattcaagatgctgcggattttgatgacagtaggactggagaacttctttt-tctaaatgataatcagataataacagtttttatattcttgtttgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGACAAAGACCCACCGTAAGCAAGTCTGACCTTGATGTTCATGAGAGATTCA
     ||  ||| || | | | |      | ||    |  | ||  |  ||  || |  ||  |   |   ||||   |||  |  ||| ||     |  | |||||||| ||||| || ||  | |  |  |||||||| || ||||| || |||||||| || ||||| ||||| ||||||||||| || || ||||||||||
----acataatgatgagaactgtttgtttattatatatatataatgtgattagtccacctgcaagctaataaatatttgttgctg-atttttaacacccatgcagATCCTTCCACCCCCCATCACAAAGAATGATTTTGATAAGGTACTGGCAAGACAAAGGCCGACCGTGAGCAAATCTGACCTTGAGGTGCACGAGAGATTCA
















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|207826145|gb|GD798976.1|GD798976
EST:     CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAG                         ATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
genomic: CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAGgtattcaaga ... tgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
EST: gi|254326206|gb|GR840798.1|GR840798
EST:     CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAG                         ATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
genomic: CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAGgtattcaaga ... tgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
EST: gi|207770928|gb|GD743803.1|GD743803
EST:     CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAG                         ATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
genomic: CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAGgtattcaaga ... tgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
EST: gi|308098773|gb|HO760514.1|HO760514
EST:     CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAG                         ATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGT
genomic: CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAGgtattcaaga ... tgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGT
EST: gi|22525915|gb|BU084726.1|BU084726
EST:     CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAG                         ATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
genomic: CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAGgtattcaaga ... tgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
EST: gi|12489948|gb|BG043469.1|BG043469
EST:     CAGTGCAAACTACAATGCATGATATTGCTGCGAAACGACTCGCTTCTAAG                         ATCCTCGCACCTCCTATATCGAGAACAGATGTTGACAAAGTACTTGCTAGA
genomic: CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAGgtattcaaga ... tgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
EST: gi|23730472|gb|BU763325.1|BU763325
EST:     CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAG                         ATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
genomic: CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAGgtattcaaga ... tgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
EST: gi|193393622|gb|FK360664.1|FK360664
EST:     CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAG                         ATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
genomic: CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAGgtattcaaga ... tgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
EST: gi|193488655|gb|FK454476.1|FK454476
EST:     CAGTACAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAG                         ATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
genomic: CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAGgtattcaaga ... tgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
EST: gi|23730696|gb|BU763444.1|BU763444
EST:     CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAG                         ATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
genomic: CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAGgtattcaaga ... tgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
EST: gi|22928118|gb|BU545257.1|BU545257
EST:     CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAG                         ATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
genomic: CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAGgtattcaaga ... tgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
EST: gi|208266914|gb|GE060979.1|GE060979
EST:     CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAG                         ATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA
genomic: CAGTGCAAACTACAATGCAGGATATTGCTGCGAAAGGACTTGCTTCTAAGgtattcaaga ... tgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctaaatgataatcagataataacagtttttatattcttgtttgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGACAAAGACCCACCGTAAGCAAGTCTGACCTTGATGTTCATGAGAGATTCA
                    taataac  putative branch site (score: 1)
                                     ttcttgttt  putative PPT
     taaatgataatcagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcaagatgctgcggattttgatgacagtaggactggagaacttctttttctaaatgataatcagataataacagtttttatattcttgtttgctgtacagATCCTCCCACCTCCTATATCGAGAACAGATTTTGACAAAGTACTTGCTAGACAAAGACCCACCGTAAGCAAGTCTGACCTTGATGTTCATGAGAGATTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG