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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctttgctgcaaatttgtttaacctatgctttagagaagtcaggtcaaccttcatgagaataagctaattacaatactttttattttctctttgtgcagCCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGG

Basic information

species Glycine max
transcript GLYMA13G09260.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G09260.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g15090.t01 (Vitis vinifera), 3'ss of exon 3
ctctttgctgcaaatttgtttaacctatgctttagagaagtcaggtcaaccttcatgagaataa--gctaattacaatactttttat--tttctctttgtgcagCCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGG
  | || ||  | ||        ||| ||  |  |||| || ||   ||   |    | || |   | |||| |   || | | |||  || |||||  |||||| |||||||| || ||||||||||||||||||||||| |||||||||||||| ||  |||| ||||
--ccttccttaagatgcagccttcctttgtct--gagatgttagaaaaattgtgggaaaaacagatgttaataatggtaatctctatacttcctcttcatgcagCTGGACAGGAGAGATTTAGAACACTTACTAGTTCATACTACAGAGGAGCTCAGGGCGTAATAATGG

upper sequence: GLYMA13G09260.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ14579 (Selaginella moellendorffii), 3'ss of exon 2
ctctttgctgcaaatttgtttaacctatgctttagagaagtcaggtcaaccttcatgagaataagctaattacaatactttttattttctctttgtgcagCCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGG
                                  |  |  | ||  || |  ||    | || || |  | | | |  ||||| | ||    | | | ||| || |||||||| ||||||||||| || |||||||| ||  |||||||||||||  | ||| | |
----------------------------------gtaacttgagcacagctatctcttgtatgagttt-tgagagttttttttttcttgatctcgcgtagCTGGGCAGGAAAGATTTAGAACACTCACGAGTTCATACTATCGAGGAGCTCAAGGCGTCATTCTTG
















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|12691494|gb|BG157830.1|BG157830
EST:     ATATGTTACAATGGGAGGGAAAAAGTTGAAACTTGCTATTTGGGACACTG                         CCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTC
genomic: ATATGTTACAATGGGAGGGAAAAAGTTGAAACTTGCTATTTGGGACACTGgtaatgtgca ... ctttgtgcagCCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTC
EST: gi|163928959|gb|EH038663.1|EH038663
EST:     ATATGTTACAATGGGAGGGAAAAAGTTGAAACTTGCTATTTGGGACACTG                         CCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTC
genomic: ATATGTTACAATGGGAGGGAAAAAGTTGAAACTTGCTATTTGGGACACTGgtaatgtgca ... ctttgtgcagCCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTC
EST: gi|298187162|gb|HO034311.1|HO034311
EST:     ATATGTTACAATGGGAGGGAAAAAGTTGAAACTTGCTATTTGGGACACTG                         CCGGACAGGAAAGGTTTAGAACACTTACTA
genomic: ATATGTTACAATGGGAGGGAAAAAGTTGAAACTTGCTATTTGGGACACTGgtaatgtgca ... ctttgtgcagCCGGACAGGAAAGGTTTAGAACACTTACTA
EST: gi|151394671|gb|EV264542.1|EV264542
EST:     ATATGTTACAATGGGAGGGAAAAAGTCGAAACTTGCTATTTGGGACACTG                         CCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTC
genomic: ATATGTTACAATGGGAGGGAAAAAGTTGAAACTTGCTATTTGGGACACTGgtaatgtgca ... ctttgtgcagCCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTC
EST: gi|254322261|gb|GR837675.1|GR837675
EST:     ATATGTTACAATGGGAGGGAAAAAGTTGAAACTTGCTATTTGGGACACTG                         CCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTC
genomic: ATATGTTACAATGGGAGGGAAAAAGTTGAAACTTGCTATTTGGGACACTGgtaatgtgca ... ctttgtgcagCCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTC
EST: gi|207783131|gb|GD757152.1|GD757152
EST:     ATATGTTACAATGGGAGGGAAAAAGTTGAAACTTGCTATTTGGGACACTG                         CCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTC
genomic: ATATGTTACAATGGGAGGGAAAAAGTTGAAACTTGCTATTTGGGACACTGgtaatgtgca ... ctttgtgcagCCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTC
EST: gi|298179524|gb|HO027995.1|HO027995
EST:     ATATGTTACAATGGGAGGGAAAAAGTTGAAACTTGCTATTTGGGACACTG                         CCGGACAGGAAAGGTTTAGAACACTTACT
genomic: ATATGTTACAATGGGAGGGAAAAAGTTGAAACTTGCTATTTGGGACACTGgtaatgtgca ... ctttgtgcagCCGGACAGGAAAGGTTTAGAACACTTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaccttcatgagaataagctaattacaatactttttattttctctttgtgcagCCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGG
                  agctaat  putative branch site (score: 3)
                              tactttttattttctc  putative PPT
              aataagctaattacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctttgctgcaaatttgtttaacctatgctttagagaagtcaggtcaaccttcatgagaataagctaattacaatactttttattttctctttgtgcagCCGGACAGGAAAGGTTTAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - ttgctgc
- - - - - - - - - - - -cctatgc
- - - - - - - - - - - - - - - - - - - - - - gtcaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - tcatgag