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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttttttcggcctgaagcacacgtacttttgatttggaagtgcaaaaatgtcctccaaattgtgtgctttttcagttaataggtttttaaaaattgcagGGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGTTGGATGGTGGATTTCTGATAACACAGACCAACTCATTTGGGCACATGTT

Basic information

species Glycine max
transcript GLYMA08G21300.1
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|192310996|gb|FK001605.1|FK001605
EST:     AACCCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTG                         GGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
genomic: AACCCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTGgtaaattttt ... aaaattgcagGGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
EST: gi|15204297|gb|BI427065.1|BI427065
EST:     AACCCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTG                         GGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
genomic: AACCCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTGgtaaattttt ... aaaattgcagGGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
EST: gi|151397267|gb|EV267140.1|EV267140
EST:     AACCCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTG                         GGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
genomic: AACCCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTGgtaaattttt ... aaaattgcagGGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
EST: gi|13312797|gb|BG406448.1|BG406448
EST:     AACCCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTG                         GGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
genomic: AACCCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTGgtaaattttt ... aaaattgcagGGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
EST: gi|254329842|gb|GR839395.1|GR839395
EST:     AACCCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTG                         GGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
genomic: AACCCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTGgtaaattttt ... aaaattgcagGGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
EST: gi|151396455|gb|EV266332.1|EV266332
EST:     CCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTG                         GGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
genomic: CCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTGgtaaattttt ... aaaattgcagGGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
EST: gi|163921518|gb|EH039303.1|EH039303
EST:     AACCCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTG                         GGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
genomic: AACCCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTGgtaaattttt ... aaaattgcagGGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
EST: gi|192295399|gb|FG987013.1|FG987013
EST:     AACCCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTG                         GGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT
genomic: AACCCTTGGAGTCAACATGACTATCCTCATTGAGCAATCTGATCACTTTGgtaaattttt ... aaaattgcagGGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatgtcctccaaattgtgtgctttttcagttaataggtttttaaaaattgcagGGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGTTGGATGGTGGATTTCTGATAACACAGACCAACTCATTTGGGCACATGTT
                             agttaat  putative branch site (score: 4)
                       tttttcagttaatagg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttttttcggcctgaagcacacgtacttttgatttggaagtgcaaaaatgtcctccaaattgtgtgctttttcagttaataggtttttaaaaattgcagGGGCTGAAGTAGAGGCAAAGACTGAACCAATAAATGAGAGAGAACTGGTGTTGGATGGTGGATTTCTGATAACACAGACCAACTCATTTGGGCACATGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - -ggcctga
- - - - - - - - agcacac
- - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - -agtgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - -tcctcca