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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtgctctttctctgatctacttgcatactaaaaatagaaacttggtcttggttctaactttttgattaactgaacccccagtggctttgtgattgcagTTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGTTAAACTAGGAGCTGACAATCTTAAGGGTGTAAAAAATGAAGAACTCCTA

Basic information

species Glycine max
transcript GLYMA15G01150.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G01150.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g06730.t01 (Vitis vinifera), 3'ss of exon 1
gtgtgctctttctctgatctacttgcatactaaaaatagaaacttggtcttggtt--ctaactttttgattaactgaacccccagtggctttgtgattgcagTTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGTTAAACTAGGAGCTGACAATCTTAAGGGTGTAAAAAATGAAGAACTCCTA
 ||      |     | | | |||    | | |     |||  ||| || ||  |    |  || |||| | |||||        |     ||| ||||||| |||  |||||| || ||||| || || || || ||| | ||||||||||||||| | ||||| ||||||||||| || ||||||||||| || || || 
atgaatgaatgaatagctttgcttcagaaatgactgctgaa-tttgatcatgtatggtaagattgttgaattactgatttaaggtttatgctgt-attgcagATTTAGTGGAGTCCCAGCAGAAGAACGGCTGCATTGGAGATCTTTCTTGGTTAAATTGGGAGCGGACAATCTTAAAGGCGTAAAAAATGAGGAGCTTCTT
















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|7640128|gb|AW734436.1|AW734436
EST:     CCCGAGGAGTCGAGTTTCCAGTCGAGGATTGCGAAAGGGTGTACAATGGG                         TTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGT
genomic: CCCGAGGAGTCGAGTTTCCAGTCGAGGATTGCGAAAGGGTGTACAATGGGgtgattatgc ... gtgattgcagTTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGT
EST: gi|21888474|gb|BQ741687.1|BQ741687
EST:     CCCGAGGAGTCGAGTTTCCAGTCGAGGATTGCGAAAGGGTGTACAATGGG                         TTTTCATGGAGTTCCTGCA
genomic: CCCGAGGAGTCGAGTTTCCAGTCGAGGATTGCGAAAGGGTGTACAATGGGgtgattatgc ... gtgattgcagTTTTCATGGAGTTCCTGCA
EST: gi|9820182|gb|BE555692.1|BE555692
EST:     CCCGAGGAGTCGAGTTTCCAGTCGAGGATTGCGAAAGGGTGTACAATGGG                         TTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGT
genomic: CCCGAGGAGTCGAGTTTCCAGTCGAGGATTGCGAAAGGGTGTACAATGGGgtgattatgc ... gtgattgcagTTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGT
EST: gi|9204520|gb|BE330744.1|BE330744
EST:     CCCGAGGAGTCGAGTTTCCAGTCGATGATTGCGAAAGGGTGTACAATGGG                         TTTTCATGGAGTTCCTGCATAGGAGCGTCTACACTGGCGTTCTTTCTTGGT
genomic: CCCGAGGAGTCGAGTTTCCAGTCGAGGATTGCGAAAGGGTGTACAATGGGgtgattatgc ... gtgattgcagTTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGT
EST: gi|9820943|gb|BE556453.1|BE556453
EST:     CCCGAGGAGTCGAGTTTCCAGTCGAGGATTGCGAAAGGGTGTACAATGGG                         TTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGT
genomic: CCCGAGGAGTCGAGTTTCCAGTCGAGGATTGCGAAAGGGTGTACAATGGGgtgattatgc ... gtgattgcagTTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGT
EST: gi|6913962|gb|AW395492.1|AW395492
EST:     CCCGAGGAGTCGAGTTTCCAGTCGAGGATTGCGAAAGGGTGTACAATGGG                         TTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGT
genomic: CCCGAGGAGTCGAGTTTCCAGTCGAGGATTGCGAAAGGGTGTACAATGGGgtgattatgc ... gtgattgcagTTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGT
EST: gi|27425069|gb|CA936589.1|CA936589
EST:     CCCGAGGAGTCGAGTTTCCAGTCGAGGATTGCGAAAGGGTGTACAATGGG                         TTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGT
genomic: CCCGAGGAGTCGAGTTTCCAGTCGAGGATTGCGAAAGGGTGTACAATGGGgtgattatgc ... gtgattgcagTTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcttggttctaactttttgattaactgaacccccagtggctttgtgattgcagTTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGTTAAACTAGGAGCTGACAATCTTAAGGGTGTAAAAAATGAAGAACTCCTA
           taactttttgattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgctctttctctgatctacttgcatactaaaaatagaaacttggtcttggttctaactttttgattaactgaacccccagtggctttgtgattgcagTTTTCATGGAGTTCCTGCAGAGGAGCGTCTACACTGGCGTTCTTTCTTGGTTAAACTAGGAGCTGACAATCTTAAGGGTGTAAAAAATGAAGAACTCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
gtgtgct
- - - - - - - - - - - - gcatact
- - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggctt