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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgttttcttttcaatttaatttcgggaaagtgtggggtgtaaatgcatgtctatgtggttctttgttattttttggttgttggtggtgaaatatagtcgtatgtgtatttcctttgtattatggcagAGAATGCAACTTGCGGTAAAACTACTTATGTTCACTGTAAAGCTGGTCGGGGGAGGAGTACAACAATTGTGCTTTGTTATCTG

Basic information

species Glycine max
transcript GLYMA05G36020.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G36020.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g02890.t01 (Vitis vinifera), 3'ss of exon 4
gtgggtgttttcttttcaatttaatttcgggaaagtgtggggtgtaaatgcatgtctatgtggttctttgttattttttggttgttggtggtgaaatatagtcgtatgtgtatttcctttgtattatggcagAGAATGCAACTTGCGGTAAAACTACTTATGTTCACTGTAAAGCTGGTCGGGGGAGGAGTACAACAATTGTGCTTTGTTATCTG
||| |   ||  | ||  | || |  || |  |  | ||             ||  | |  | | |  || | | |    ||||  | ||      | |  || | |  |  ||||| || |       ||||||||||| ||| ||||| ||||||||||||||| ||||||||||| || || ||||| ||||| ||||||||||| ||| ||
gtgagcaattcttctttgactttacatctgccagttctg-------------tgattcttagatgccatggtgtgt---agttga-gatgaaagtttcttttctttttgggttttcccttctgg-ggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG
















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|120533128|gb|EH261261.1|EH261261
EST:     CTTTGCCCCCTCATTTGTGGATATCAACCGGGCTGTGCAGTTCATTCATC                         AGAATGCAACTTGCGGTAAAACTACTTATGTTCACTGTAAAGCTGGTCGGG
genomic: CTTTGCCCCCTCATTTGTGGATATCAACCGGGCTGTGCAGTTCATTCATCgtgggtgttt ... attatggcagAGAATGCAACTTGCGGTAAAACTACTTATGTTCACTGTAAAGCTGGTCGGG
EST: gi|192302768|gb|FG993788.1|FG993788
EST:     CTTTGCCCCCTCATTTGTGGATATCAACCGGGCTGTGCAATTCATTCATC                         AGAATGCAACTTGCGGTAAAACTACTTATGTTCACTGTAAAGCTGGTCGGG
genomic: CTTTGCCCCCTCATTTGTGGATATCAACCGGGCTGTGCAGTTCATTCATCgtgggtgttt ... attatggcagAGAATGCAACTTGCGGTAAAACTACTTATGTTCACTGTAAAGCTGGTCGGG
EST: gi|15001047|gb|BI321861.1|BI321861
EST:     CTTTGCCCCCTCATTTGTGGATATCAACCGGGCTGTGCAGTTCATTCATC                         AGAATGCAACTTGCGGTAAAACTACTTATGTTCACTG
genomic: CTTTGCCCCCTCATTTGTGGATATCAACCGGGCTGTGCAGTTCATTCATCgtgggtgttt ... attatggcagAGAATGCAACTTGCGGTAAAACTACTTATGTTCACTG
EST: gi|192294262|gb|FG986351.1|FG986351
EST:     CTTTGCCCCCTCATTTGTGGATATCAACCGGGCTGTGCAGTTCATTCATC                         AGAATGCAACTTGCGGTAAAACTACTTATGTTCACTGTAAAGCTGGTCGGG
genomic: CTTTGCCCCCTCATTTGTGGATATCAACCGGGCTGTGCAGTTCATTCATCgtgggtgttt ... attatggcagAGAATGCAACTTGCGGTAAAACTACTTATGTTCACTGTAAAGCTGGTCGGG
EST: gi|120533275|gb|EH261408.1|EH261408
EST:     CTTTGCCCCCTCATTTGTGGATATCAACCGGGCTGTGCAGTTCATTCATC                         AGAATGCAACTTGCGGTAAAACTACTTATGTTCACTGTAAAGCTGGTCGGG
genomic: CTTTGCCCCCTCATTTGTGGATATCAACCGGGCTGTGCAGTTCATTCATCgtgggtgttt ... attatggcagAGAATGCAACTTGCGGTAAAACTACTTATGTTCACTGTAAAGCTGGTCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttgttggtggtgaaatatagtcgtatgtgtatttcctttgtattatggcagAGAATGCAACTTGCGGTAAAACTACTTATGTTCACTGTAAAGCTGGTCGGGGGAGGAGTACAACAATTGTGCTTTGTTATCTG
                                        tttgtattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgttttcttttcaatttaatttcgggaaagtgtggggtgtaaatgcatgtctatgtggttctttgttattttttggttgttggtggtgaaatatagtcgtatgtgtatttcctttgtattatggcagAGAATGCAACTTGCGGTAAAACTACTTATGTTCACTGTAAAGCTGGTCGGGGGAGGAGTACAACAATTGTGCTTTGTTATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG