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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggtgaaaaaaatctttgagaaatttgtcttttgatggcttaattaccacttgtatttttctgattttgcttaaggatgcatgttctggtgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGATCTTATGCAAAG

Basic information

species Glycine max
transcript GLYMA14G02050.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G02050.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G26670.1 (Arabidopsis thaliana), 3'ss of exon 1
-----ttggtgaaaaaaatc--tttgagaaatttgtcttttgatggcttaattaccact-tgtatttttctgattttgcttaaggatgcatgttctggtgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGATCTTATGCAAAG
     |   | || |   ||  | ||| ||  ||| ||  ||||   || ||||| |   || | || |   || ||   | |  ||  | |||     | | ||||||| | |||||||| ||||||||||| || |||||||| |||| ||| |||||    | ||| |||
agttttcattaaagagcgtcaatgtgataagattggctactgat---ttgattacgatgatggaattgtgaaatattatctcactatataagtt-----gggattcagGTTCAGGATTGTTCAAGAAGAAAGGCTTCAAAGGATCATTTGCAGATGCAGGGCAGTCTGCTAAG

upper sequence: GLYMA14G02050.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G55510.1 (Arabidopsis thaliana), 3'ss of exon 1
---ttggtgaaaaa-aatctttgagaaatttgtcttttgatggcttaattaccac-ttgtatttttctgattttgcttaaggatgcatgttctggtgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGATCTTATGCAAAG
   || |||   |  |||     |  | ||||| | | | ||  ||  |||  |   |||  ||     ||    || | |||   | ||  ||||||   |||||  |||||||||||||||||||||| ||||||||||| ||||| || || ||    | |||||||
tatttagtgttgactaatagagaattactttgtgtgtcgttgttttttttatgaaactgtgattgaacaataaatctcacggaaataagt--tggtgt---tcagGCTCTGGATTGTTTAAGAAGAAAGGGTTTAAAGGATCATTTGTGGATGCGGGTCAGTCTGCAAAG

upper sequence: GLYMA14G02050.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0090g01590.t01 (Vitis vinifera), 3'ss of exon 1
---ttggtgaaaaaaatctttgagaaatttgtcttttgatggcttaattaccacttgtatttttctgattttgcttaaggatgcatgttctggtgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGATCTTATGCAAAG
       |   |      |   | ||    ||| |||  |  |||  ||      ||| ||  | ||||     | || |    || |       ||||||||||   || ||| ||||||| ||||| |||||||||||||||| ||| || ||||||| ||| |||
gttaaaatttgatggtgttaccataagccagtcattttgtctcttc-ttggaggatgtgttactgtgat--gaataaatgccttatatggatacatgtttcagGTTTGGGTTTGGTTAAGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG

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|207781490|gb|GD754013.1|GD754013
EST:     CCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CCGTCTTTGGATACGgttcttctct ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|193354243|gb|FK319829.1|FK319829
EST:     CGCCACCGACTCCGCCGCCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGCCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttcttctct ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|298164009|gb|HO013654.1|HO013654
EST:     CGCCACCGACTCCGCCGCCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGCCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttcttctct ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|298194244|gb|HO040892.1|HO040892
EST:     CGCCACCGACTCCGCCGCCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGCCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttcttctct ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|298185481|gb|HO030694.1|HO030694
EST:     CGCCACCGACTCCGCCGCCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGCCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttcttctct ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|8825817|gb|BE209547.1|BE209547
EST:     CGCCACCGACTCCGCCGCCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGCCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttcttctct ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|298163114|gb|HO011847.1|HO011847
EST:     CGCCACCGACTCCGCCGCCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGCCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttcttctct ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|193355914|gb|FK322599.1|FK322599
EST:     GCCACCGACTCCGCCGACCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: GCCACCGACTCCGCCG-CCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttcttctct ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
EST: gi|193421710|gb|FK387909.1|FK387909
EST:     CGCCACCGACTCCGCCGCCGGCGCTCTCATGGGCTCCGTCTTTGGATACG                         GTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG
genomic: CGCCACCGACTCCGCCGCCGGCGCTCTCATGGGCTCCGTCTTTGGATACGgttcttctct ... tgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccacttgtatttttctgattttgcttaaggatgcatgttctggtgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGATCTTATGCAAAG
              ttctgat  putative branch site (score: 3)
         tatttttctgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggtgaaaaaaatctttgagaaatttgtcttttgatggcttaattaccacttgtatttttctgattttgcttaaggatgcatgttctggtgtgtttcagGTGCTGGATTGTTTAAGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGATCTTATGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - aaaaaaa
- - - - - - - - - - - - - - - - -tgatggc
- - - - - - - - - - - - - - - - - - - - - - - -ccacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgtt