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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaacctctgagaaatttgacttttgatggcttaattgtcatttgtcacttgtatttttttgattttgcttaaggatgaatattatggtgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG

Basic information

species Glycine max
transcript GLYMA02G46620.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46620.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G26670.1 (Arabidopsis thaliana), 3'ss of exon 1
----------aaaaaacctctgagaaatttgactt-ttgatggcttaattgtcatttgtcacttgtatttttttgattttgcttaaggatgaatattatggtgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG
          ||| | | ||   |  ||  || |   |  ||  || |||   ||        || | || |   || ||   | |  ||      || | || | ||||||| | |||||||| ||||||||||| || |||||||| |||| ||| ||||||   | ||| |||
agttttcattaaagagcgtcaatgtgataagattggctactgatttgattacgat------gatggaattgtgaaatattatctcactata-----taagttgggattcagGTTCAGGATTGTTCAAGAAGAAAGGCTTCAAAGGATCATTTGCAGATGCAGGGCAGTCTGCTAAG

upper sequence: GLYMA02G46620.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G55510.1 (Arabidopsis thaliana), 3'ss of exon 1
-------aaaaaacctctgagaaatttgacttttgatggcttaattgtcatttgtcacttgtatttttttgattttgcttaaggatgaatattatggtgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG
            ||   |    ||||  |||||   || | |  || |  ||    |  |||  ||     ||    || | |||  ||||   ||||||   |||||  |||||||||||||||||||||| ||||||||||| ||||| || || ||    | |||||||
tatttagtgttgactaatagagaatt--actttgtgtgtcgttgttttttttatgaaactgtgattgaacaataaatctcacgga--aataagttggtgt---tcagGCTCTGGATTGTTTAAGAAGAAAGGGTTTAAAGGATCATTTGTGGATGCGGGTCAGTCTGCAAAG
















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|23727058|gb|BU761545.1|BU761545
EST:     CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|17153736|gb|BM143669.1|BM143669
EST:     CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|31468894|gb|CD410922.1|CD410922
EST:     CGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGCTTTTAAAGGATCCTTCGTAGAAGCAG
genomic: CGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|26047850|gb|CA784505.1|CA784505
EST:     CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|298181833|gb|HO026008.1|HO026008
EST:     CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|298174609|gb|HO017832.1|HO017832
EST:     CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|9898882|gb|BE607850.1|BE607850
EST:     CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|298184523|gb|HO029736.1|HO029736
EST:     CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|31311953|gb|CD397156.1|CD397156
EST:     CGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|298178521|gb|HO024256.1|HO024256
EST:     CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGGAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|298181875|gb|HO026050.1|HO026050
EST:     CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTATAGAAGCAG
genomic: CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|7925046|gb|AW831072.1|AW831072
EST:     CGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|6071305|gb|AW100692.1|AW100692
EST:     CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|24135852|gb|BU926362.1|BU926362
EST:     CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|298173707|gb|HO017043.1|HO017043
EST:     CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGTGTTTTAAAGGATCCTTTGTAGAAGCA
genomic: CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAG-GTTTTAAAGGATCCTTTGTAGAAGCA
EST: gi|15337011|gb|BI497667.1|BI497667
EST:     CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|18041339|gb|BM309633.1|BM309633
EST:     CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGGCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttctctctt ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcacttgtatttttttgattttgcttaaggatgaatattatggtgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG
              ttttgat  putative branch site (score: 4)
         tatttttttgattttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaacctctgagaaatttgacttttgatggcttaattgtcatttgtcacttgtatttttttgattttgcttaaggatgaatattatggtgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
aaaaaac
- - - - - - - - - - - - - tgatggc
- - - - - - - - - - - - - - - - - - - - - - -tgtcact