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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatttatttcttcgccacaactttttcttgcccagaaaagtttaatttattttttaatagtatttatttttccttgaagGATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCATAGCTTGGATGCTGATGCCCCCTTGTCAGAGCAG

Basic information

species Glycine max
transcript GLYMA08G20370.3
intron # 4
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|31560978|gb|CD486816.1|CD486816
EST:     GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGG                         GATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
genomic: GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGGgtatgcattt ... ttccttgaagGATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
EST: gi|21256834|gb|BQ453722.1|BQ453722
EST:     GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGG                         GATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
genomic: GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGGgtatgcattt ... ttccttgaagGATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
EST: gi|19937410|gb|BQ081279.1|BQ081279
EST:     GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGG                         GATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
genomic: GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGGgtatgcattt ... ttccttgaagGATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
EST: gi|7285995|gb|AW598482.1|AW598482
EST:     GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGG                         GATGATACTTGAAACAAATGGACCTCTTATTG
genomic: GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGGgtatgcattt ... ttccttgaagGATGATACTTGAAACAAATGGACCTCTTATTG
EST: gi|31470945|gb|CD412973.1|CD412973
EST:     GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGG                         GATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
genomic: GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGGgtatgcattt ... ttccttgaagGATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
EST: gi|8404161|gb|BE059795.1|BE059795
EST:     GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGG                         GATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
genomic: GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGGgtatgcattt ... ttccttgaagGATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
EST: gi|31305637|gb|CD390840.1|CD390840
EST:     GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGG                         GATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
genomic: GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGGgtatgcattt ... ttccttgaagGATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
EST: gi|7029699|gb|AW459482.1|AW459482
EST:     GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGG                         GATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
genomic: GAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGGgtatgcattt ... ttccttgaagGATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
EST: gi|151410805|gb|EV280620.1|EV280620
EST:     AGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTTGTTGATGGAGG                         GATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA
genomic: AGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATT-GTTGATGGAGGgtatgcattt ... ttccttgaagGATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgcccagaaaagtttaatttattttttaatagtatttatttttccttgaagGATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCATAGCTTGGATGCTGATGCCCCCTTGTCAGAGCAG
                           ttttaat  putative branch site (score: 3)
                                    tatttatttttcctt  putative PPT
         agaaaagtttaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcatttatttcttcgccacaactttttcttgcccagaaaagtttaatttattttttaatagtatttatttttccttgaagGATGATACTTGAAACAAATGGACCTCTTATTGCCGAAAAGGTGACCTCTCATAGCTTGGATGCTGATGCCCCCTTGTCAGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG