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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtcgtgtatatttttacttattattaaataaacatataacgtgaaatgaaaagcatgactaattattaaaacatgttcttatttttgctctttgcagGGATGTGATGCATCGGTTTTGTTAAAGAACACTGCAACTTTCACGGGCGAACAAGGTGCCTTCCCCAACGCTAATTCTCTAAGGGGTTTCGAAGTCATAG

Basic information

species Glycine max
transcript GLYMA03G04880.1
intron # 1
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|8283618|gb|BE021177.1|BE021177
EST:     GCATGGGTGCATCCTTGCTCCGTCTTCATTTCCATGATTGCTTTGTCCAA                         GGATGTGATGCATCGGTTTTGTTAAAGAACACTGCAACTTTCACGGGCGAA
genomic: GCATGGGTGCATCCTTGCTCCGTCTTCATTTCCATGATTGCTTTGTCCAAgtaagtcatt ... ctctttgcagGGATGTGATGCATCGGTTTTGTTAAAGAACACTGCAACTTTCACGGGCGAA
EST: gi|41145663|gb|CK605874.1|CK605874
EST:     GCATGGGTGCATCCTTGCTCCGTCTTCATTTCCATGATTGCTTTGTCCAA                         GGATGTGATGCATCGGTTTTGTTAAAGAACACTGCAACTTTCACGGGCGAA
genomic: GCATGGGTGCATCCTTGCTCCGTCTTCATTTCCATGATTGCTTTGTCCAAgtaagtcatt ... ctctttgcagGGATGTGATGCATCGGTTTTGTTAAAGAACACTGCAACTTTCACGGGCGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatgaaaagcatgactaattattaaaacatgttcttatttttgctctttgcagGGATGTGATGCATCGGTTTTGTTAAAGAACACTGCAACTTTCACGGGCGAACAAGGTGCCTTCCCCAACGCTAATTCTCTAAGGGGTTTCGAAGTCATAG
              gactaat  putative branch site (score: 2)
                                 ttcttatttttgctct  putative PPT
               actaattattaaaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtcgtgtatatttttacttattattaaataaacatataacgtgaaatgaaaagcatgactaattattaaaacatgttcttatttttgctctttgcagGGATGTGATGCATCGGTTTTGTTAAAGAACACTGCAACTTTCACGGGCGAACAAGGTGCCTTCCCCAACGCTAATTCTCTAAGGGGTTTCGAAGTCATAG

- - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - aaatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacatg