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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttcccctttgctaaacgaaactagaaaatatggatttgttctttctgattgtttagtcttgcatgacctctacttattgtttcctacttgaatactagGTGGTCACACCGGAAATGTTGACATTCATGCAAGAACTACGAAAG

Basic information

species Glycine max
transcript GLYMA09G39800.1
intron # 2
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|151397333|gb|EV267206.1|EV267206
EST:     GTTTAATTGCTTTGTTTGATGTTGACGGGACTCTTACAGCTCCCAGGAAG                         GTGGTCACACCGGAAATGTTGACATTCATGCAAGAACTACGAAAG
genomic: GTTTAATTGCTTTGTTTGATGTTGACGGGACTCTTACAGCTCCCAGGAAGgtatctgttt ... tgaatactagGTGGTCACACCGGAAATGTTGACATTCATGCAAGAACTACGAAAG
EST: gi|151394604|gb|EV264475.1|EV264475
EST:     GTTTAATTGCTTTGTTTGATGTTGACGGGACTCTTACAGCTCCCAGGAAG                         GTGGTCACACCGGAAATGTTGACATTCATGCAAGAACTACGAAAG
genomic: GTTTAATTGCTTTGTTTGATGTTGACGGGACTCTTACAGCTCCCAGGAAGgtatctgttt ... tgaatactagGTGGTCACACCGGAAATGTTGACATTCATGCAAGAACTACGAAAG
EST: gi|209714867|gb|BW682032.1|BW682032
EST:     GTTTAATTGCTTTGTTTGATGTTGACGGGACTCTTACAGCTCCCAGGAAG                         GTGGTCACACCGGANATGTTGACATTCATGCAAGAACTACGAAAG
genomic: GTTTAATTGCTTTGTTTGATGTTGACGGGACTCTTACAGCTCCCAGGAAGgtatctgttt ... tgaatactagGTGGTCACACCGGAAATGTTGACATTCATGCAAGAACTACGAAAG
EST: gi|192301212|gb|FG988977.1|FG988977
EST:     GTTTAATTGCTTTGTTTGATGTTGACGGGACTCTTACAGCTCCCAGGAAG                         GTGGTCACACCGGAAATGTTGACATTCATGCAAGAACTACGAAAG
genomic: GTTTAATTGCTTTGTTTGATGTTGACGGGACTCTTACAGCTCCCAGGAAGgtatctgttt ... tgaatactagGTGGTCACACCGGAAATGTTGACATTCATGCAAGAACTACGAAAG
EST: gi|19453591|gb|BM955001.1|BM955001
EST:     GTTTAATTGCTTTGTTTGATGTTGACGGGACTCTTACAGCTCCCAGGAAG                         GTGGTCACACCGGAAATGTTGACATTCATGCAAGAACTACGAAAG
genomic: GTTTAATTGCTTTGTTTGATGTTGACGGGACTCTTACAGCTCCCAGGAAGgtatctgttt ... tgaatactagGTGGTCACACCGGAAATGTTGACATTCATGCAAGAACTACGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgattgtttagtcttgcatgacctctacttattgtttcctacttgaatactagGTGGTCACACCGGAAATGTTGACATTCATGCAAGAACTACGAAAG
 ttctgat  putative branch site (score: 3)
                                    tttcctactt  putative PPT
                              ttattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttcccctttgctaaacgaaactagaaaatatggatttgttctttctgattgtttagtcttgcatgacctctacttattgtttcctacttgaatactagGTGGTCACACCGGAAATGTTGACATTCATGCAAGAACTACGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- ttcccct
- - - - - -gctaaac
- - - - - - - - - - - - agaaaata
- - - - - - - - - - - - - - - - -ggatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttcc