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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaattacaaaattcagcatcacataaatggcttgattttaactattcatggaatcagaaggagcttgaagttcattacttttcattcaatactctctttgcttccgtatgtatacttgtttgttgtcgcttgcatgttgacgacttatttgttttcctcaaaaactattacagCATCATTGGCAAGAGACTATTATGATGTTCTTGGTGTGAGTAAGAATGCAAGTTCTTCTGAAATAAAGAAAGCTTACTATGGG

Basic information

species Glycine max
transcript GLYMA09G00580.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G00580.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0064g01360.t01 (Vitis vinifera), 3'ss of exon 3
gtataaattacaaaattcagcatcacataaatggcttgattttaactattcatggaatcagaaggagcttga--agttcattacttttcattcaatactctctttgcttccgtatgtatacttgtttgttgtcgcttgcatgttgacgacttatttgttttcctcaaaaactattacagCATCATTGGCAAGAGACTATTATGATGTTCTTGGTGTGAGTAAGAATGCAAGTTCTTCTGAAATAAAGAAAGCTTACTATGGG
                                                                    ||||  ||||  ||| |||   ||   |  | ||||   ||    ||| | |     |||   |    |   |  |||     | |||| |||  |  ||    |    |  ||   || | |  || |||||||||   ||||||||||| |||||||| ||| | |||||||||||||||||||| ||||||
-----------------------------------------------------------------tctttgagcagtttgttaatttcttttt--tggtttctta--ttagacatgaagaaaaccttggaataagat---ttctgattttctgtttgctttgtttgaa--tcagCGTA-TATGGCTG-CTAATGATTATTATGATACACTTGGTGTGAGCAAGAATGCCAGTGCGTCTGAAATAAAGAAAGCTTATTATGGG
















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|192326652|gb|FK017309.1|FK017309
EST:     GGGAGCGGCAAATAAATATTGGGGGGCATCTAGATCAATTCATGGCTCGG                         CATCATTGGCAAGAGACTATTATGATGTTCTTGGTGTGAGTAAGAATGCAA
genomic: GGGAGCGGCAAATAAATATTGGGGGGCATCTAGATCAATTCATGGCTCGGgtataaatta ... actattacagCATCATTGGCAAGAGACTATTATGATGTTCTTGGTGTGAGTAAGAATGCAA
EST: gi|18040851|gb|BM309145.1|BM309145
EST:     GGGAGCGGCAAATAAATATTGGGGGGCATCTAGATCAATTCATGGCTCGG                         CATCATTGGCAAGAGACTATTATGATGTTCTTGGTGTGAGTAAGAATGCAA
genomic: GGGAGCGGCAAATAAATATTGGGGGGCATCTAGATCAATTCATGGCTCGGgtataaatta ... actattacagCATCATTGGCAAGAGACTATTATGATGTTCTTGGTGTGAGTAAGAATGCAA
EST: gi|151401621|gb|EV271434.1|EV271434
EST:     GGAGCGGCAAATAAATATTGGGGGGCATCTAGATCCAATTCGTGGCTCGG                         CATCATTGGCAAGAGACTATTATGATGTTCTTGGTGTGAGTAAGAATGCAA
genomic: GGAGCGGCAAATAAATATTGGGGGGCATCTAGATC-AATTCATGGCTCGGgtataaatta ... actattacagCATCATTGGCAAGAGACTATTATGATGTTCTTGGTGTGAGTAAGAATGCAA
EST: gi|15000262|gb|BI321076.1|BI321076
EST:     GGGAGCGGCAAATAAATATTGGGGGGCATCTAGATCAATTCATGGCTCGG                         CATCATTGGCAAGAGACTATTATGATGTTCTTGGTGTGAGTAAGAATGCAA
genomic: GGGAGCGGCAAATAAATATTGGGGGGCATCTAGATCAATTCATGGCTCGGgtataaatta ... actattacagCATCATTGGCAAGAGACTATTATGATGTTCTTGGTGTGAGTAAGAATGCAA
EST: gi|193641551|gb|FK592377.1|FK592377
EST:     GGGAGCGGCAAATAAATATTGGGGGGCATCTAGATCAATTCATGGCTCGG                         CATCATTGGCAAGAGACTATTATGATG
genomic: GGGAGCGGCAAATAAATATTGGGGGGCATCTAGATCAATTCATGGCTCGGgtataaatta ... actattacagCATCATTGGCAAGAGACTATTATGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttgtcgcttgcatgttgacgacttatttgttttcctcaaaaactattacagCATCATTGGCAAGAGACTATTATGATGTTCTTGGTGTGAGTAAGAATGCAAGTTCTTCTGAAATAAAGAAAGCTTACTATGGG
                tgttgac  putative branch site (score: 3)
                          ttatttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaattacaaaattcagcatcacataaatggcttgattttaactattcatggaatcagaaggagcttgaagttcattacttttcattcaatactctctttgcttccgtatgtatacttgtttgttgtcgcttgcatgttgacgacttatttgttttcctcaaaaactattacagCATCATTGGCAAGAGACTATTATGATGTTCTTGGTGTGAGTAAGAATGCAAGTTCTTCTGAAATAAAGAAAGCTTACTATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA