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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggccacccttatgagattcataatctctttcctacgaggttgttttactaccgaaagaatttcttattttgtgacttacaagtttatgaaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCACTCATATCTAAG

Basic information

species Glycine max
transcript GLYMA08G18560.1
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|8827757|gb|BE211487.1|BE211487
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|11412304|gb|BF424315.1|BF424315
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|58014741|gb|CX701483.1|CX701483
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|6914757|gb|AW396287.1|AW396287
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGG--                         -AGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|10233243|gb|BE802131.1|BE802131
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|254324562|gb|GR833987.1|GR833987
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|27426337|gb|CA937857.1|CA937857
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|7639980|gb|AW734290.1|AW734290
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|31472363|gb|CD414391.1|CD414391
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAGAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|192313316|gb|FK005088.1|FK005088
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|4298166|gb|AI442722.1|AI442722
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGG--                         -AGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|151411923|gb|EV281734.1|EV281734
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCC-AAAGCA---G                         GAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|19348889|gb|BM893421.1|BM893421
EST:     AGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: AGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|192313317|gb|FK005089.1|FK005089
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|31309242|gb|CD394445.1|CD394445
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAGAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|193376980|gb|FK340615.1|FK340615
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGG--                         -AGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|254324561|gb|GR833986.1|GR833986
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|31305685|gb|CD390888.1|CD390888
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAGAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|4313320|gb|AI460439.1|AI460439
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
EST: gi|6914456|gb|AW395986.1|AW395986
EST:     TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCA---G                         GAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA
genomic: TGGATGCATCTGATGAGTCAGCTAACATGCCATCACCCCAAAAGCAGGTGgtgttgggat ... aaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactaccgaaagaatttcttattttgtgacttacaagtttatgaaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCACTCATATCTAAG
                             gacttac  putative branch site (score: 2)
          aaagaatttcttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggccacccttatgagattcataatctctttcctacgaggttgttttactaccgaaagaatttcttattttgtgacttacaagtttatgaaccttgtagGAGGAGTCTGTAAAGAAAAAGTATGGAGGAATGCTGCCCAAAAAGCCACCACTCATATCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - -caccctt
- - - - - - - - - - - - - - - - - - -gaggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgactt