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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaagaactgacaagctggatcacctgaactgaaaatggttctaagtgctggctgtgtgagctttatttgagtcttaatatttccaaactgtattgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAACTGTCATCGGGATAGATCTTGGAACAACCTACTCATGTGTTGGTGTTTA

Basic information

species Vitis vinifera
transcript Vv02s0025g02140.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 1
--agaaagaact-gacaagctggatcacctgaactgaaaatggttctaagtgctggctgtgtgagctttatttgagtcttaatatttccaaactgtattgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAACTGTCATCGGGATAGATCTTGGAACAACCTACTCATGTGTTGGTGTTTA
   ||| |||   ||| | ||   | || |||     |  | |   | | |       || |||| ||   |||    ||||| ||   | | |  || |||| || ||||  ||  |||||||||||||| |||||||| ||||||||||| || ||||| ||||| ||||||||||||||||| |||||||||||||||||
catgaatgaatgagactacctactttacgtgagtc--agtttgccatcaatttaactagtttgagtttacattgtaa-ttaatgttgagagagttcatcgcagTATGTCTATTTGTGATTTCCATTGCAAAGGAGGAAGCCACCAAGTTGGGGACGGTCATTGGGATTGATCTTGGAACAACCTATTCATGTGTTGGTGTTTA

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 1
agaaagaactgacaagctggatcacctgaactga---aaatggttctaagtgctggctgtgtgagctttatttgagtcttaatatttccaaactgtattgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAACTGTCATCGGGATAGATCTTGGAACAACCTACTCATGTGTTGGTGTTTA
   | |||   |  || |   | || | |   ||   |  | ||  | | |       || |||| ||   |||    ||||  ||   | | |  || ||||||| ||||  ||| |||||||||||||| |||||||| ||||||||||| || ||||| ||||| ||||||||||| ||||| |||||||||||||||||
--catgaataaatgagattacttactttacgcgagtcagtttgtcatgaatttaactagtttgagtttacattgtaa-ttaaccttgagagagttcatcgcagGATGTCTATTTGCGATTTCCATTGCAAAGGAGGAAGCCACCAAGTTGGGGACGGTCATTGGGATTGATCTTGGAACGACCTATTCATGTGTTGGTGTTTA

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 1
agaaagaactgacaagctggatcacctgaactgaaaatggttc--taagtgctggctgtgtgag-ctttatttgagtc-ttaatatttccaaactgtattgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAACTGTCATCGGGATAGATCTTGGAACAACCTACTCATGTGTTGGTGTTTA
    || |||   | |    |   |   || | |      ||   | |||    |   ||| |  ||  | ||  ||   ||| |||   | | | |     ||||| | ||  ||||||||||||||| || |||||||| || || ||||| || ||||||||||| ||||||||||| ||||| |||||||||||||||||
----agcactattatgtgcaaatgcagaaattaattccattttgatgagtttcagtgttgtaaaactgcaattatgtaactaacattgagatatttttccatagGATGTTTATTTGCAATTTCCATTGCTAAGGAGGAAGCCACAAAATTGGGGACGGTCATCGGGATTGATCTTGGAACGACCTATTCATGTGTTGGTGTTTA

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 1
agaaagaactgacaagctggatcacctgaactgaaaatggttctaagtgctg----gctgtgtgagctttatttgagtcttaatatttccaaactgtattgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAACTGTCATCGGGATAGATCTTGGAACAACCTACTCATGTGTTGGTGTTTA
    || ||    | |    |   |   || | |    | ||| | | | |     | |||   |  || | |       ||| |||   ||| |       ||||| ||||  ||| ||||||||||| || |||||||| |||||||| || || |||||||| || ||||||||||||||||| |||||||| ||||||||
----agcacaattatgtgcaaatgcagaaattaactgcgtttcgatgagtttaagtgttgtaaaaatttaactatgtaactaacattgagaaatttctccatagGATGTCTATTTGCGATTTCCATTGCTAAGGAGGAAGCCACCAAGTTAGGGACGGTCATCGGCATTGATCTTGGAACAACCTATTCATGTGTCGGTGTTTA

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 1
agaaagaactgacaagctggatcacctgaact--gaaaatggttc-taagtgct---ggctgtgtgagctttatttgagtcttaatatttccaaactgtattgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAACTGTCATCGGGATAGATCTTGGAACAACCTACTCATGTGTTGGTGTTTA
  |    | ||| ||    |   |  | |  |  || | |||||  |  ||| |   || | ||  || |||||| ||   || | ||||      |    | |||||| | ||  |||  |||||| ||||||||| || || || ||||| ||| | || || |||||||||||||| || || ||||| ||||||||||||||
-catttcattgataatagagtgaaattaagttttgagattggttgattggtgtttttggttttgatagttttatt-gacgattgaaattttt----tacgattcagGATGTTTATTTGCGTTTTCCACTGCAAAAGAAGAGGCTACGAAGTTAGGATCAGTTATTGGGATAGATCTTGGTACCACTTACTCTTGTGTTGGTGTTTA

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------------------agaaagaactgacaagctggatcacctgaactgaaaatg----------gttctaagtgctggctgtgtgagctttatttgagtcttaatatttccaaactgt---attgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAACTGTCATCGGGATAGATCTTGGAACAACCTACTCATGTGTTGGTGTTTA
                                                             |||||       |    |  |  || |||||  ||           ||  | |  ||      || || | |   |  || || |   ||  || || |   ||| |||||| | ||  |||  | |||  ||||| ||| || || || ||||| ||| | || || |||||||||||||| || || ||||| ||||||||||||||
gtgagtgattttccgatcttcttctccgatttagatctcctctacattgttgcttaatctcagaaccttttttcgttgttcctggatctgaatgtgtttgtttgcaatttcacgatcttaaaaggttagatctcgattggtattgacgattggaatctttacgatttcagGATGTTTATTTGCGTTGTCCTCTGCAATAGAAGAGGCTACGAAGTTAGGATCAGTGATAGGGATAGATCTTGGTACTACTTACTCTTGTGTTGGTGTTTA

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|110725909|gb|EE102862.1|EE102862
EST:     CTCGTGGAGAAGACGAGGGTCTTTGATCGTCGCGGCGATCGTGTGTTTCG                         GATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAA
genomic: CTCGTGGAGAAGACGAGGGTCTTTGATCGTCGCGGCGATCGTGTGTTTCGgtgagtgtcg ... tgtattgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAA
EST: gi|110709376|gb|EE084780.1|EE084780
EST:     CTCGTGGAGAAGACGAGGGTCTTTGATCGTCGCGGCGATCGTGTGTTTCG                         GATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAA
genomic: CTCGTGGAGAAGACGAGGGTCTTTGATCGTCGCGGCGATCGTGTGTTTCGgtgagtgtcg ... tgtattgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAA
EST: gi|110703620|gb|EE080624.1|EE080624
EST:     CTCGTGGAGAAGACGAGGGTCTTTGATCGTCGCGGCGATCGTGTGTTTCG                         GATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAA
genomic: CTCGTGGAGAAGACGAGGGTCTTTGATCGTCGCGGCGATCGTGTGTTTCGgtgagtgtcg ... tgtattgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAA
EST: gi|33401982|gb|CF207609.1|CF207609
EST:     CTCGTGGAGAAGACGAGGGTCTTTGATCGTCGCGGCGATCGTGTGTTTCG                         GATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAA
genomic: CTCGTGGAGAAGACGAGGGTCTTTGATCGTCGCGGCGATCGTGTGTTTCGgtgagtgtcg ... tgtattgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAA
EST: gi|110687283|gb|EE064556.1|EE064556
EST:     CTCGTGGAGAAGACGAGGGTCTTTGATCGTCGCGGCGATCGTGTGTTTCG                         GATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAA
genomic: CTCGTGGAGAAGACGAGGGTCTTTGATCGTCGCGGCGATCGTGTGTTTCGgtgagtgtcg ... tgtattgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgctggctgtgtgagctttatttgagtcttaatatttccaaactgtattgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAACTGTCATCGGGATAGATCTTGGAACAACCTACTCATGTGTTGGTGTTTA
                            tcttaat  putative branch site (score: 3)
                  tttatttgagtcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaagaactgacaagctggatcacctgaactgaaaatggttctaagtgctggctgtgtgagctttatttgagtcttaatatttccaaactgtattgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAACTGTCATCGGGATAGATCTTGGAACAACCTACTCATGTGTTGGTGTTTA

-gaaagaa
- - - - ctgacaa
- - - - - - - - - - - cacctga
- - - - - - - - - - - - - - - - gaaaatg
- - - - - - - - - - - - - - - - - - - - - - - gtgctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccaaac