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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcatctttcttatatcatggtgtttagtggcaaaatagaaaattttctatttaaccaagacttatatgtctcctaacacggatatgttctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGCATTGATCAG

Basic information

species Glycine max
transcript GLYMA19G36130.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36130.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g03130.t01 (Vitis vinifera), 3'ss of exon 3
---tatcatctttcttatatcatggtgtttagtggcaaaatagaaaattttctatttaaccaagacttatatgtctcctaacacggatatgttctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGCATTGATCAG
          |  |    ||| |       | |  |||   | |   |||  | ||| ||    | | ||   | |  || || || | |  | ||   |||||||| ||||||||||||||| |||||||| || || ||||||||||| ||||||||||||
gtagggagattggccggcatcctctgag--actatcaatggaaagtgtttcatttttgacagcaattcat-catttaatatcatggttctaatttgttgacagGATAGAATGGATGCATCTGGGGTGGCACTAGTTTTAATTGGACCTGGTAGCATTGATCAG
















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|9258245|gb|BE346392.1|BE346392
EST:     GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAG                         GATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
genomic: GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAGgtaaagtttt ... ctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
EST: gi|151403056|gb|EV272866.1|EV272866
EST:     GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAG                         GATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
genomic: GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAGgtaaagtttt ... ctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
EST: gi|9258744|gb|BE346891.1|BE346891
EST:     GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAG                         GATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGNGAGC
genomic: GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAGgtaaagtttt ... ctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
EST: gi|192297273|gb|FG990621.1|FG990621
EST:     GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAG                         GATATAGTGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
genomic: GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAGgtaaagtttt ... ctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
EST: gi|15287410|gb|BI471301.1|BI471301
EST:     GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAG                         GATATAATGGATGCATCTGGTGTGGCACTTGTATTGATT
genomic: GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAGgtaaagtttt ... ctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATT
EST: gi|15202597|gb|BI425484.1|BI425484
EST:     GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAG                         GATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGNGAGC
genomic: GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAGgtaaagtttt ... ctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
EST: gi|15284825|gb|BI468716.1|BI468716
EST:     GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAG                         GATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
genomic: GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAGgtaaagtttt ... ctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
EST: gi|120496088|gb|EH224255.1|EH224255
EST:     GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAG                         GATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
genomic: GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAGgtaaagtttt ... ctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
EST: gi|9902843|gb|BE611811.1|BE611811
EST:     GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAG                         GATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
genomic: GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAGgtaaagtttt ... ctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
EST: gi|27425152|gb|CA936672.1|CA936672
EST:     GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAG                         GATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
genomic: GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAGgtaaagtttt ... ctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
EST: gi|117557702|gb|EG702087.1|EG702087
EST:     GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAG                         GATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
genomic: GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAGgtaaagtttt ... ctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
EST: gi|27809251|gb|CB063673.1|CB063673
EST:     GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAG                         GATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
genomic: GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAGgtaaagtttt ... ctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
EST: gi|31473394|gb|CD415407.1|CD415407
EST:     GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAG                         GATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC
genomic: GTGCGTGTTGTGCCGCAAAAGGGCTGATTATCTTTCATCCAAGAAGgtaaagtttt ... ctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctatttaaccaagacttatatgtctcctaacacggatatgttctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGCATTGATCAG
                           tcctaac  putative branch site (score: 1)
                                           ttctgcc  putative PPT
                acttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcatctttcttatatcatggtgtttagtggcaaaatagaaaattttctatttaaccaagacttatatgtctcctaacacggatatgttctgccaacagGATATAATGGATGCATCTGGTGTGGCACTTGTATTGATTGGACCTGGGAGCATTGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - -catggtg
- - - - - - - - - - - - - - - - - -aatagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaagac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctaaca