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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaccttagttttgtaaaattcatacttccttattttaatagtaacaaatgggatttttctgtgtacagattcctaaaatatactctttttgtattgcagACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGGACAATGGTAGCAGGAGGTGGTGCAAGTGTAATTTATGCTGATACG

Basic information

species Glycine max
transcript GLYMA03G38810.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38810.3 (Glycine max), 3'ss of exon 7
lower sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
-----------------------------gtacc-ttagttttgtaaaattcatacttcc-ttattttaatagtaacaaatgggatttttctgtgtacagattcctaaaatatactctttttgta-ttgcagACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGGACAATGGTAGCAGGAGGTGGTGCAAGTGTAATTTATGCTGATACG
                               ||    |  ||  |  | | || ||||     ||   |||   |    | | |||  ||   | |||||  || |||    || | ||| |||   |||||||  |||| ||  ||||||| || ||| |||||||||| || ||||| ||||||||||| || ||||||||||| ||||| ||||| |||||||| 
gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttc-tatacagggtcttaag---tagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
















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|193548970|gb|FK505377.1|FK505377
EST:     AGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATAAG                         ACAAGTGCATCATTGAAATTTACTATATTGAATCCAAAAGGACGCATATGG
genomic: AGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATAAGgtattttttt ... tgtattgcagACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG
EST: gi|58024571|gb|CX711312.1|CX711312
EST:     TACAGAAAGCTTCATTCATTCCTTGGATGATAAG                         ACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG
genomic: TACAGAAAGCTTCATTCATTCCTTGGATGATAAGgtattttttt ... tgtattgcagACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG
EST: gi|6228216|gb|AW156815.1|AW156815
EST:     GAAGAATTCTGAGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATAAG                         ACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG
genomic: GAAGAATTCTGAGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATAAGgtattttttt ... tgtattgcagACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG
EST: gi|151402134|gb|EV271947.1|EV271947
EST:     GAAGAATTCTGAGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATAAG                         ACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG
genomic: GAAGAATTCTGAGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATAAGgtattttttt ... tgtattgcagACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG
EST: gi|58021506|gb|CX708247.1|CX708247
EST:     TGAGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATAAG                         ACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG
genomic: TGAGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATAAGgtattttttt ... tgtattgcagACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG
EST: gi|58018692|gb|CX705434.1|CX705434
EST:     GAAGAATTCTGAGCCNTACAGAAAGCTTCATTCATTCNTTGGATGATAAG                         ACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG
genomic: GAAGAATTCTGAGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATAAGgtattttttt ... tgtattgcagACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG
EST: gi|37997687|gb|CF809276.1|CF809276
EST:     GAAGAATTCTGAGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATAAG                         ACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG
genomic: GAAGAATTCTGAGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATAAGgtattttttt ... tgtattgcagACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG
EST: gi|151407958|gb|EV277773.1|EV277773
EST:     GAAGAATTCTGAGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATA-G                         ACA-GTGCATCATTGAAATTTACTATAT-GAATC
genomic: GAAGAATTCTGAGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATAAGgtattttttt ... tgtattgcagACAAGTGCATCATTGAAATTTACTATATTGAATC
EST: gi|15202616|gb|BI425495.1|BI425495
EST:     GAAGAATTCTGAGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATAAG                         ACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG
genomic: GAAGAATTCTGAGCCCTACAGAAAGCTTCATTCATTCCTTGGATGATAAGgtattttttt ... tgtattgcagACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatgggatttttctgtgtacagattcctaaaatatactctttttgtattgcagACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGGACAATGGTAGCAGGAGGTGGTGCAAGTGTAATTTATGCTGATACG
                          tcctaaa  putative branch site (score: 2)
                                    tactcttttt  putative PPT
                             taaaatatactctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccttagttttgtaaaattcatacttccttattttaatagtaacaaatgggatttttctgtgtacagattcctaaaatatactctttttgtattgcagACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGGACAATGGTAGCAGGAGGTGGTGCAAGTGTAATTTATGCTGATACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT