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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacaatttcacttacatagcttcaacattgttatttcattttcaattggttatttatttatttatttatgccagttccagctcttgatgaaagcttatcatcagttatttatttgttatcgatttgtcttttgaattatagtatttccgttcagtttttgtgtgtgtcgttgtgaaacagGTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGCTATTACAG

Basic information

species Glycine max
transcript GLYMA13G41580.5
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G41580.5 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 1
gtacacaatttcacttacatagcttcaacattgttatttcattttcaattggttatttatttatttatttatgccagttccagctcttgatgaaagcttatcatcagttatttatttgttatcgatttgtcttt--tgaattatagtatttccgttcagtttttgtgtgtgtcgttgtgaaacagGTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGCTATTACAG
                                                                                  | | ||  |||  ||||        ||  | ||| | || | |||  ||     |||  | ||||       || |    | ||   ||  | |||| | |||||||||||||||||||| ||||| |  ||||||   |||||||||||||||| ||||||
----------------------------------------------------------------------------------gatttttctgattgcttcatgggccttgatgattagataac-attgatcccagatgaggtttagttccataatttaaccatggttcctgg-gatgtgga-cagGTGCACTTTTTGTAATTCTTAATGAGACTCCCAACCTGAAGATGCTTGGGCTTTTACAG
















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|192300198|gb|FG989320.1|FG989320
EST:     TGCCGTAGCTCTTGCTCTTTCACTTGTTGGTGGTGTCAGCACTTCTATCG                         GTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGC
genomic: TGCCGTAGCTCTTGCTCTTTCACTTGTTGGTGGTGTCAGCACTTCTATCGgtacacaatt ... tgtgaaacagGTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGC
EST: gi|298174471|gb|HO014616.1|HO014616
EST:     TGCCGTAGCTCTTGCTCTTTCACTTGTTGGTGGTGTCAGCACTTCTATCG                         GTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGC
genomic: TGCCGTAGCTCTTGCTCTTTCACTTGTTGGTGGTGTCAGCACTTCTATCGgtacacaatt ... tgtgaaacagGTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGC
EST: gi|213617692|gb|DB967222.1|DB967222
EST:     TGCCGTAGCTCTTGCTCTTTCACTTGTTGGTGGTGTCAGCACTTCTATCG                         GTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGC
genomic: TGCCGTAGCTCTTGCTCTTTCACTTGTTGGTGGTGTCAGCACTTCTATCGgtacacaatt ... tgtgaaacagGTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGC
EST: gi|298198295|gb|HO039834.1|HO039834
EST:     TGCCGTAGCTCTTGCTCTTTCACTTGTTGGTGGTGTCAGCACTTCTATCG                         GTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTAAAGATGCTTGGGC
genomic: TGCCGTAGCTCTTGCTCTTTCACTTGTTGGTGGTGTCAGCACTTCTATCGgtacacaatt ... tgtgaaacagGTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGC
EST: gi|192323380|gb|FK017081.1|FK017081
EST:     TGCCGTAGCTCTTGCTCTTTCACTTGTTGGTGGTGTCAGCACTTCTATCG                         GTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGC
genomic: TGCCGTAGCTCTTGCTCTTTCACTTGTTGGTGGTGTCAGCACTTCTATCGgtacacaatt ... tgtgaaacagGTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGC
EST: gi|298167335|gb|HO010774.1|HO010774
EST:     TGCCGTAGCTCTTGCTCTTTCACTTGTTGGTGGTGTCAGCACTTCTATCG                         GTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGC
genomic: TGCCGTAGCTCTTGCTCTTTCACTTGTTGGTGGTGTCAGCACTTCTATCGgtacacaatt ... tgtgaaacagGTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttttgaattatagtatttccgttcagtttttgtgtgtgtcgttgtgaaacagGTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGCTATTACAG
     ttgaattatagtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacaatttcacttacatagcttcaacattgttatttcattttcaattggttatttatttatttatttatgccagttccagctcttgatgaaagcttatcatcagttatttatttgttatcgatttgtcttttgaattatagtatttccgttcagtttttgtgtgtgtcgttgtgaaacagGTGCACTTTTTGTAATTGTTAATAAAGCTCCCAGTTTGAAGATGCTTGGGCTATTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG