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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagagtgttatgtcttcttttctctgatttgttgattattatagtatattacataactgaggcatctgaaaaattaaattttgtctactcaaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATACTTGCTTCTGGAGTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAAC

Basic information

species Glycine max
transcript GLYMA20G32790.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32790.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g73680.1 (Oryza sativa), 3'ss of exon 7
taagagtgttatgtct-----tcttttctctgattt-gttgattattatagtatattacataactgaggcatctgaaaaattaaattttgtctactcaaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATACTTGCTTCTGGAGTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAAC
  ||  |||    |||     ||||| || |  |   | |||||  | |  || | ||||| | ||||   | |||  ||||  | |   | ||   |   |  |||||||||  || || ||||| ||||| ||||| ||||| || ||||| |||||||||||||| |||||||| || || ||||||||||| ||| |||| |
-cagcatgtgtcatctagaagtctttacttttgtaaagctgatttgtctt-tagaatacatgaatgag---tttgaggaattgcactg-atgtatatagcttatagGAATTTGTTGTAAGGAATGATATGGGCTGTGGTTCAACTATTGGCCCCATACTTGCTTCTGGTGTTGGCATACGGACTGTTGACTGTGGTATTCCTCAGC

upper sequence: GLYMA20G32790.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G061127_T01 (Zea mays), 3'ss of exon 3
taagagtgttatgtcttcttttctctgatttgttg-attattatagtatattacataactga-ggcatctgaaaaattaaattttgtctactcaaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATACTTGCTTCTGGAGTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAAC
||| | |||||  |  |       |    |  |   |  || |  |    || |     ||| ||  | || |    |     |  | ||   |      |||||||||  || || ||||| ||||||||||| || || || || || |||||||||||||| |||||||| || || || |||||||| ||  |||| |
taaaaatgttaaatgctagagaaacaagatgataacacaatcactgagccttccgc--ttgatggtttttggagtgatttgactgatgtaaataccacacagGAATTTGTTGTGAGGAATGATATGGGATGTGGCTCCACTATTGGACCCATACTTGCTTCTGGTGTTGGCATACGGACTGTAGACTGTGGTATCCCTCAGC

upper sequence: GLYMA20G32790.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G04710.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------taagagtgttatg--tcttcttttctctgatttgttgattattatagtatattaca--------taactgaggcatctgaaaaattaaattttgtctactcaaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATACTTGCTTCTGGAGTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAAC
               |||   |   |||  ||| |   ||   ||| |  |   |  | |    || | ||        |||    |  ||    | | ||| |||||  ||| |    ||| |||| |||| ||| ||||| || ||||||||||| ||||| ||||| || ||| | ||||| ||||| || |||||||| ||||| ||||| || ||||| |
gttaggtgttcttcttaatgttaagatgaatctacacatcatagatcttctagatgctctgcactaatccacccacatttaagaatgaaatactgacatttagatttttgctattt---ctgcagGAGTTTGTGGTGAGAAACGATATGGGATGTGGTTCAACAATAGGACCTATATTGGCTTCAGGAGTAGGGATCCGAACCGTTGATTGTGGCATAGCTCAGC

upper sequence: GLYMA20G32790.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0106g00700.t01 (Vitis vinifera), 3'ss of exon 8
taagagtgttatgtcttcttttctctgatttgttgattattatagtatattacataactgaggcatctgaaaaattaaattttgtctactcaaa---ctgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATACTTGCTTCTGGAGTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAAC
  ||| | |   |   |   ||   || ||   |  |  | ||   |   |  | || |||| || | ||||    |  |  |  | | |||     ||| |||||||||  || ||||| || |||||||||||||| |||||||| || ||||| |||||||| ||||||||||| || ||||| ||||| |||||||| |
--agaatatatagaggtagattacatgtttcactt-tcttcatttcaagatttaaaattgagacaccagaaactgcatctacttaccattcatttctctgtagGAATTTGTTGTGAGAAACGATATGGGATGTGGATCTACCATAGGTCCCATACTAGCTTCTGGGGTTGGCATCCGCACTGTTGATTGTGGTATTGCTCAGC

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|16347296|gb|BI972891.1|BI972891
EST:     CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAG                         GAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATA
genomic: CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAGgtagttcttc ... caaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATA
EST: gi|151401885|gb|EV271698.1|EV271698
EST:     CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAG                         -AATTTGCGGTTAGAA-TGACATGGGATGTGGATCAACCATAG-CCCAATA
genomic: CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAGgtagttcttc ... caaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATA
EST: gi|14258779|gb|BG881687.1|BG881687
EST:     CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAG                         GAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATA
genomic: CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAGgtagttcttc ... caaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATA
EST: gi|10232725|gb|BE801613.1|BE801613
EST:     CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAG                         GAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATA
genomic: CATCTTTTCTTTTTAAAGAAGTTGGAAAAATCCATAACCTTCCAACTCAGgtagttcttc ... caaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattacataactgaggcatctgaaaaattaaattttgtctactcaaactgaagGAATTTGCGGTTAGAAATGACATGGGATGTGGATCAACCATAGGCCCAATACTTGCTTCTGGAGTTGGCATCCGAACAGTTGACTGTGGAATTGCTCAAC
      acataac  putative branch site (score: 3)
                                       tctactc  putative PPT
                   atctgaaaaattaaat  TA-rich tract