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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaaatgtgattgcattataatattctctgatgttgtaactttagcttcatgattaactatgaatagtaaagtttcatatgaatctttcttctctttcagGGTTTCAAGAAGGTAGTTGCTGACAGATGGGAGTTTGCAAATGAGTACTTCAGAAAAGGAGCTAAGCACCTTTTATGTGAAATTCACAGGAGAAAAGCAC

Basic information

species Glycine max
transcript GLYMA20G08250.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G08250.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0009g02730.t01 (Vitis vinifera), 3'ss of exon 1
ctaaatgtgattgcattataatattctctgatgttgtaactttagcttcatgatta-actatgaata-gtaaagtttcatatgaatctttcttctc--tttcagGGTTTCAAGAAGGTAGTTGCTGACAGATGGGAGTTTGCAAATGAGTACTTCAGAAAAGGAGCTAAGCACCTTTTATGTGAAATTCACAGGAGAAAAGCAC
    ||||| |   || |  || |||  |    | |||  | || ||  ||   || | ||| |  | ||     || || |   |||  | |  |  || ||||||||||||||| ||||||| || |||||||||||||||||||||||||||||||||||||  |||||| | || | |||||| ||||| |||||| | |
--tcatgtggtctaatgaatattttcattaggatagta--tataactatatatctatagtataagaatgtttttcttaatttatttctcccattacatttccagGGTTTCAAGAAGATAGTTGCAGATAGATGGGAGTTTGCAAATGAGTACTTCAGAAAAGGAGGGAAGCACATGTTGTCTGAAATCCACAGAAGAAAAACCC
















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|151397816|gb|EV267689.1|EV267689
EST:     ATTTTAAACACAACAACTTCTCAAGCTTTGTTAGGCAACTCAACACCTAT                         GGTTTCAAGAAGGTAGTTGCTGACAGATGGGAGTTTGCAAATGAGTACTTC
genomic: ATTTTAAACACAACAACTTCTCAAGCTTTGTTAGGCAACTCAACACCTATgtaagcatcc ... tctctttcagGGTTTCAAGAAGGTAGTTGCTGACAGATGGGAGTTTGCAAATGAGTACTTC
EST: gi|151411753|gb|EV281564.1|EV281564
EST:     ATTTTAAACACAACAACTTCTCAAGCTTTGTTAGGCAACTCAACACCTAT                         GGTTTCAAGAAGGTAGTTGCTGACAGATGGGAGTTTGCAAATGAGTACTTC
genomic: ATTTTAAACACAACAACTTCTCAAGCTTTGTTAGGCAACTCAACACCTATgtaagcatcc ... tctctttcagGGTTTCAAGAAGGTAGTTGCTGACAGATGGGAGTTTGCAAATGAGTACTTC
EST: gi|208192152|gb|GD990658.1|GD990658
EST:     ATTTTAAACACAACAACTTCTCAAGCTTTGTTAGGCAACTCAACACCTAT                         GGTTTCAAGAAGGTAGTTGCTGACAGATGGGAGTTTGCAAATGAG
genomic: ATTTTAAACACAACAACTTCTCAAGCTTTGTTAGGCAACTCAACACCTATgtaagcatcc ... tctctttcagGGTTTCAAGAAGGTAGTTGCTGACAGATGGGAGTTTGCAAATGAG
EST: gi|193541128|gb|FK497844.1|FK497844
EST:     ATCTTAAACACAACAACTTCTCAAGCTTTGTTAGGCAACTCAACACCTAT                         GGTTTCAAGAAGGTAGTTGCTGACAGATGGGAGTTTGCAAATGAGTACTTC
genomic: ATTTTAAACACAACAACTTCTCAAGCTTTGTTAGGCAACTCAACACCTATgtaagcatcc ... tctctttcagGGTTTCAAGAAGGTAGTTGCTGACAGATGGGAGTTTGCAAATGAGTACTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcatgattaactatgaatagtaaagtttcatatgaatctttcttctctttcagGGTTTCAAGAAGGTAGTTGCTGACAGATGGGAGTTTGCAAATGAGTACTTCAGAAAAGGAGCTAAGCACCTTTTATGTGAAATTCACAGGAGAAAAGCAC
      gattaac  putative branch site (score: 2)
                                      tctttcttctctttc  putative PPT
       attaactatgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaaatgtgattgcattataatattctctgatgttgtaactttagcttcatgattaactatgaatagtaaagtttcatatgaatctttcttctctttcagGGTTTCAAGAAGGTAGTTGCTGACAGATGGGAGTTTGCAAATGAGTACTTCAGAAAAGGAGCTAAGCACCTTTTATGTGAAATTCACAGGAGAAAAGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - -tgcatta
- - - - - - - - - - - - - - -gatgttg
- - - - - - - - - - - - - - - - - - - - - - - ttcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgaa