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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtgtttcattttccttgatatattttcaaatgttaatctattgacatgaaagttttagcgtatgaattttgggatgcttttaaattatttcaaattctcataacagCTTGGGGAGGAATGGGATGACAGCGTACAATCAAAAGAACAAGTTGAAGCCAAGTTACTGAGCAAGTATGAAGCTTCTATGAGAAGAGAAAGAGCAATGG

Basic information

species Glycine max
transcript GLYMA10G05720.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G05720.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0040g02360.t01 (Vitis vinifera), 3'ss of exon 4
gtctgtgtttcattttccttgatatattttcaaatgttaatctattgacatgaaag---ttttagcgta-tgaattttgggatgcttttaaattatttcaaattctcataacagCTTGGGGAGGAATGGGATGACAGCGTACAATCAAAAGAACAAGTTGAAGCCAAGTTACTGAGCAAGTATGAAGCTTCTATGAGAAGAGAAAGAGCAATGG
              |||  ||| | ||| |  ||    |  |  ||  | |    |   ||| ||| |  ||  |||    |     |||   | ||| |||||    |||||| | ||||||||||||||||||||| ||||||||||||||||| |||||||     || | | |||| | |  ||  | |||||||||||||| ||| |||
----------ttgcttctgtgagagattcttgaacaa-agccagttatcctaggtggtttttcagctttctgcctttcttcagaaaattattgtttttgaaatt---gtaacagATGGGGGAGGAATGGGATGACAGCCTACAATCAAAAGAACAAATTGAAGCAGGCCTATTAAACAAGCAAGGGGCAGCAATGAGAAGAGAAAGGGCACTGG
















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|193419933|gb|FK385371.1|FK385371
EST:     AGAGCATGCGG                         CTTGGGGAGGAATGGGATGACAGCGTACAATCAAAAGAACAAGTTGAAGCC
genomic: AGAGCATGCGGgtctgtgttt ... ctcataacagCTTGGGGAGGAATGGGATGACAGCGTACAATCAAAAGAACAAGTTGAAGCC
EST: gi|207720112|gb|GD702611.1|GD702611
EST:     TACAAAAACAGCTCTTACAGAAGCACGCAAAAGAGCTAGAGAGCATGCGG                         CTTGGGGAGGAATGGGATGACAGTGTACAATCAAAAGAACAAGTTGAAGCC
genomic: TACAAAAACAGCTCTTACAGAAGCACGCAAAAGAGCTAGAGAGCATGCGGgtctgtgttt ... ctcataacagCTTGGGGAGGAATGGGATGACAGCGTACAATCAAAAGAACAAGTTGAAGCC
EST: gi|193548623|gb|FK509536.1|FK509536
EST:     TACAAAAACAGCTCTTACAGAAGCACGCAAAAGAGCTAGAGAGCATGCGG                         CTTGGGGAGGGAATGGGATGACAGCGTACAATCAAAAGAACAAGTTGAAGC
genomic: TACAAAAACAGCTCTTACAGAAGCACGCAAAAGAGCTAGAGAGCATGCGGgtctgtgttt ... ctcataacagCTTGGGGAGG-AATGGGATGACAGCGTACAATCAAAAGAACAAGTTGAAGC
EST: gi|193691616|gb|FK629733.1|FK629733
EST:     TACAAAAACAGCTCTTACAGAAGCACGCAAAAGAGCTAGAGAGCATGCGG                         CTTGGGGAGGAATGGGATG-CAGCGTACAATCAAAAGAACAAGTTGAAGCC
genomic: TACAAAAACAGCTCTTACAGAAGCACGCAAAAGAGCTAGAGAGCATGCGGgtctgtgttt ... ctcataacagCTTGGGGAGGAATGGGATGACAGCGTACAATCAAAAGAACAAGTTGAAGCC
EST: gi|208265095|gb|GE065423.1|GE065423
EST:     TACAAAAACAGCTCTTACAGAAGCACGCAAAAGAGCTAGAGAGCATGCGG                         CTTGGGGAGGAATGGGATGACAGCGTACAATCAAAAGAACAAGTTGAAGCC
genomic: TACAAAAACAGCTCTTACAGAAGCACGCAAAAGAGCTAGAGAGCATGCGGgtctgtgttt ... ctcataacagCTTGGGGAGGAATGGGATGACAGCGTACAATCAAAAGAACAAGTTGAAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttagcgtatgaattttgggatgcttttaaattatttcaaattctcataacagCTTGGGGAGGAATGGGATGACAGCGTACAATCAAAAGAACAAGTTGAAGCCAAGTTACTGAGCAAGTATGAAGCTTCTATGAGAAGAGAAAGAGCAATGG
                                           ttctcat  CT-rich tract
                          ttttaaattatttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtgtttcattttccttgatatattttcaaatgttaatctattgacatgaaagttttagcgtatgaattttgggatgcttttaaattatttcaaattctcataacagCTTGGGGAGGAATGGGATGACAGCGTACAATCAAAAGAACAAGTTGAAGCCAAGTTACTGAGCAAGTATGAAGCTTCTATGAGAAGAGAAAGAGCAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA