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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatgagtgtagatgatttgaatcatttgatctactatatcaatcggtatccttagtaccttctcaaatatagttgacatcttaattgtttgtgctgtagGTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAAAAGTTATGTGAAGACTTGAGTAATCTG

Basic information

species Glycine max
transcript GLYMA20G29280.1
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|6455809|gb|AW186492.1|AW186492
EST:     CAACAGAAAGAATTCGTGTGGCCAAGCTAAAGGAAGAACAGGCACGGAAG                         GTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAA
genomic: CAACAGAAAGAATTCGTGTGGCCAAGCTAAAGGAAGAACAGGCACGGAAGgtctgttact ... tgtgctgtagGTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAA
EST: gi|6727086|gb|AW311440.1|AW311440
EST:     CAACAGAAAGAATTCGTGTGGCCAAGCTAAAGGAAGAACAGGCACGGAAG                         GTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAA
genomic: CAACAGAAAGAATTCGTGTGGCCAAGCTAAAGGAAGAACAGGCACGGAAGgtctgttact ... tgtgctgtagGTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAA
EST: gi|298198667|gb|HO042030.1|HO042030
EST:     CAACAGAAAGAATTCGTGTGGCCAAGCTAAAGGAAGAACAGGCACGGAAG                         GTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAA
genomic: CAACAGAAAGAATTCGTGTGGCCAAGCTAAAGGAAGAACAGGCACGGAAGgtctgttact ... tgtgctgtagGTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAA
EST: gi|213618278|gb|DB973048.1|DB973048
EST:     CAACAGAAAGAATTCGTGTGGCCAAGCTAAAGGAAGA-CAGGCACGGAAG                         GTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAA
genomic: CAACAGAAAGAATTCGTGTGGCCAAGCTAAAGGAAGAACAGGCACGGAAGgtctgttact ... tgtgctgtagGTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAA
EST: gi|213602217|gb|DB958477.1|DB958477
EST:     CAACAGAAAGAATTCGTGTGGCCAAGCTAAAGGAAGA-CAGGCACGGAAG                         GTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAA
genomic: CAACAGAAAGAATTCGTGTGGCCAAGCTAAAGGAAGAACAGGCACGGAAGgtctgttact ... tgtgctgtagGTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAA
EST: gi|151398262|gb|EV268140.1|EV268140
EST:     CAACAGAAAGAATTCGTGTGGCCAAGCTAAAGGAAGAACAGGCACGGAAG                         GTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAA
genomic: CAACAGAAAGAATTCGTGTGGCCAAGCTAAAGGAAGAACAGGCACGGAAGgtctgttact ... tgtgctgtagGTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtatccttagtaccttctcaaatatagttgacatcttaattgtttgtgctgtagGTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAAAAGTTATGTGAAGACTTGAGTAATCTG
                                  tcttaat  putative branch site (score: 3)
                    aaatatagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgagtgtagatgatttgaatcatttgatctactatatcaatcggtatccttagtaccttctcaaatatagttgacatcttaattgtttgtgctgtagGTGTGGGAATCAGCATCAAAAGTAGTAAGAGATGAGGAAGCATTAAAGCAAAAGTTATGTGAAGACTTGAGTAATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- -tgagtgt
- - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacatc