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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcttatggctctatgtctcaattctactttagttttacatattaaatttgttttactaatacttgatgtttgtctcatttggattgtttatttgaagGGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATAAATCCAAAAAG

Basic information

species Glycine max
transcript GLYMA20G39080.1
intron # 5
splice site 3'
intron type U2

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|120491229|gb|EH219396.1|EH219396
EST:     TGCAGCAGCTGTCAAACAAGAAAGACATTGATGACATCTTTATTAAGCTG                         GGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATAAATCC
genomic: TGCAGCAGCTGTCAAACAAGAAAGACATTGATGACATCTTTATTAAGCTGgtaaggctta ... ttatttgaagGGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATAAATCC
EST: gi|193367957|gb|FK333021.1|FK333021
EST:     TGCAGCAGCTGTCAAACAAGAAAGACATTGATGACATCTTTATTAAGCTG                         GGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATAAATCC
genomic: TGCAGCAGCTGTCAAACAAGAAAGACATTGATGACATCTTTATTAAGCTGgtaaggctta ... ttatttgaagGGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATAAATCC
EST: gi|6481724|gb|AW200995.1|AW200995
EST:     TGCAGCAGCTGTCAAACAAGAAAGACATTGATGACATCTTTATTAAGCTG                         GGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATAAATCC
genomic: TGCAGCAGCTGTCAAACAAGAAAGACATTGATGACATCTTTATTAAGCTGgtaaggctta ... ttatttgaagGGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATAAATCC
EST: gi|31307409|gb|CD392612.1|CD392612
EST:     TGCAGCAGCTGTCAAACAAGAAAGACATTGATGACATCTTTATTAAGCTG                         GGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATAAATCC
genomic: TGCAGCAGCTGTCAAACAAGAAAGACATTGATGACATCTTTATTAAGCTGgtaaggctta ... ttatttgaagGGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATAAATCC
EST: gi|6454768|gb|AW185451.1|AW185451
EST:     TGCAGCAGCTGTCAAACAAGAAAGACATTGATGACATCTTTATTAAGCTG                         GGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATAAATCC
genomic: TGCAGCAGCTGTCAAACAAGAAAGACATTGATGACATCTTTATTAAGCTGgtaaggctta ... ttatttgaagGGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATAAATCC
EST: gi|10843741|gb|BF067004.1|BF067004
EST:     TGCAGCAGCTGTCAAACAAGAAAGACATTGATGACATCTTTATTAAGCTG                         GGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATANAATC
genomic: TGCAGCAGCTGTCAAACAAGAAAGACATTGATGACATCTTTATTAAGCTGgtaaggctta ... ttatttgaagGGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATA-AATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatttgttttactaatacttgatgtttgtctcatttggattgtttatttgaagGGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATAAATCCAAAAAG
                                            tttattt  CT-rich tract
     ttgttttactaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcttatggctctatgtctcaattctactttagttttacatattaaatttgttttactaatacttgatgtttgtctcatttggattgtttatttgaagGGATCTGATAAGGACAAGCGCAGAGAGACTCTTGAGAAGGAAGATAAATCCAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA