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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgtttgtggttaatttgatgattttttaaataattttttatgtcctttttttttaatttggaatttagttctgtgtggaccttagctaactgtgtagATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGATTTTGTCACCAAAGAGCTTCAGATTGACGACAGACTTGTCACTCTACAA

Basic information

species Glycine max
transcript GLYMA20G31150.1
intron # 2
splice site 3'
intron type U12 (go to U12 genes for details)

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|298193144|gb|HO033578.1|HO033578
EST:     GGTTGGGAAGACCTCGTTGATGAATCA                         ATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
genomic: GGTTGGGAAGACCTCGTTGATGAATCAgtatcctcac ... aactgtgtagATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
EST: gi|298186082|gb|HO036715.1|HO036715
EST:     GGTTGGGAAGACCTCGTTGATGAATCA                         ATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
genomic: GGTTGGGAAGACCTCGTTGATGAATCAgtatcctcac ... aactgtgtagATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
EST: gi|151399673|gb|EV269544.1|EV269544
EST:     GGAAGACCTCGTTGATGAATCA                         ATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
genomic: GGAAGACCTCGTTGATGAATCAgtatcctcac ... aactgtgtagATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
EST: gi|8827737|gb|BE211467.1|BE211467
EST:     GGTTGGGAAGACCTCGTTGATGAATCA                         ATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
genomic: GGTTGGGAAGACCTCGTTGATGAATCAgtatcctcac ... aactgtgtagATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
EST: gi|298167138|gb|HO010577.1|HO010577
EST:     GGTTGGGAAGACCTCGTTGATGAATCA                         ATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
genomic: GGTTGGGAAGACCTCGTTGATGAATCAgtatcctcac ... aactgtgtagATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
EST: gi|151393176|gb|EV263051.1|EV263051
EST:     GGTTGGGAAGACCTCGTTGATGAATCA                         ATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
genomic: GGTTGGGAAGACCTCGTTGATGAATCAgtatcctcac ... aactgtgtagATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
EST: gi|254337577|gb|GR849423.1|GR849423
EST:     GGTTGGGAAGACCTCGTTGATGAATCA                         ATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
genomic: GGTTGGGAAGACCTCGTTGATGAATCAgtatcctcac ... aactgtgtagATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
EST: gi|192321754|gb|FK013622.1|FK013622
EST:     GGTTGGGAAGACCTCGTTGATGAATCA                         ATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA
genomic: GGTTGGGAAGACCTCGTTGATGAATCAgtatcctcac ... aactgtgtagATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttttttttaatttggaatttagttctgtgtggaccttagctaactgtgtagATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGATTTTGTCACCAAAGAGCTTCAGATTGACGACAGACTTGTCACTCTACAA
                                   gaccttagc  putative branch site 
     tttttttaatttggaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgtttgtggttaatttgatgattttttaaataattttttatgtcctttttttttaatttggaatttagttctgtgtggaccttagctaactgtgtagATACGTGCACAAGAAGTTTAGTCAGCAATATAAGGCTACCATTGGAGCTGATTTTGTCACCAAAGAGCTTCAGATTGACGACAGACTTGTCACTCTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- -tgtttgt
- - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtgg