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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttaaaagcataggcctgaaattttctgcaacacacatacatgtaaatgataatgtgttcttaccaaagtttttttcctttgaatctcagGTATCGTTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACGTG

Basic information

species Glycine max
transcript GLYMA09G31980.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G31980.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 2
gtc-ttaaaagcataggcctgaaattttctgcaacacacatacatgtaaatgataatgtgttcttaccaaagtttttttcctttgaatctcagGTATCGTTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACGTG
||| || | | ||| |   ||| | ||||     |   ||| ||||| || |||  | ||| ||| | |||   ||||  |||||  |||||||| || |||||||||||||||||||||||||||||||||||||||||| ||
gtcatttagaacatggatgtgagaatttc-----ctagcattcatgttaaggat--tatgtccttgctaaaacattttaactttgcctctcagGTTTCATTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACATG
















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|192308963|gb|FK001739.1|FK001739
EST:     TTACATGTGGATTTGTGAAAGACCTGCATATTGATAAAGCTCTAGGAGAG                         GTATCGTTTCGGCTAGAGCTCACTACACCAGCATGTCCAATCAAGGACGTG
genomic: TTACATGTGGATTTGTGAAAGACCTGCATATTGATAAAGCTCTAGGAGAGgtcttaaaag ... tgaatctcagGTATCGTTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACGTG
EST: gi|213608309|gb|DB963085.1|DB963085
EST:     TTACATGTGGATTTGTGAAAGACCTGCATATTGATAAAGCTCTAGGAGAG                         GTATCGTTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACGTG
genomic: TTACATGTGGATTTGTGAAAGACCTGCATATTGATAAAGCTCTAGGAGAGgtcttaaaag ... tgaatctcagGTATCGTTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACGTG
EST: gi|192332938|gb|FK025035.1|FK025035
EST:     TTACATGTGGATTTGTGAAAGACCTGCATATTGATAAAGCTCTAGGAGAG                         GTATCGTTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACGTG
genomic: TTACATGTGGATTTGTGAAAGACCTGCATATTGATAAAGCTCTAGGAGAGgtcttaaaag ... tgaatctcagGTATCGTTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACGTG
EST: gi|7283383|gb|AW595992.1|AW595992
EST:     TTACATGTGGATTTGTGAAAGACCTGCATATTGATAAAGCTCTACGAGAG                         GTATCGTTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACGTG
genomic: TTACATGTGGATTTGTGAAAGACCTGCATATTGATAAAGCTCTAGGAGAGgtcttaaaag ... tgaatctcagGTATCGTTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catacatgtaaatgataatgtgttcttaccaaagtttttttcctttgaatctcagGTATCGTTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACGTG
                      ttcttac  putative branch site (score: 2)
                                  tttttttccttt  putative PPT
     atgtaaatgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttaaaagcataggcctgaaattttctgcaacacacatacatgtaaatgataatgtgttcttaccaaagtttttttcctttgaatctcagGTATCGTTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA