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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgatttttttttttttcattactacagttttagagagatgggttctgatctgaaggctctgagtggctactgactgtgccaatgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAGCCATACATTGCTTCCATGGGAGTGTATGTCTTCAAGAAGGAGATACTCC

Basic information

species Vitis vinifera
transcript Vv05s0020g02880.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 7
gtaatgatttttttttttttcattactacagttttagagagatgggttctgatctgaaggctctgagtggctactgactgtgccaatgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAGCCATACATTGCTTCCATGGGAGTGTATGTCTTCAAGAAGGAGATACTCC
          |     |  |  ||| || | |  || | |  |   |||        ||  |   | |  || || |   |||   | |  |||| ||||||||||||  || ||||| || |||| ||| |||||  ||||||| |||||||||||||||||||||||||| |||||||||||||||||||| |
---------gtaagcatcatgtttattatactgctaaaaaagt---ttcc-------agaattatattcactgctaatactgctt-tatatttagCAAGTAGATACAACCGTTTTGGGCCTTTCAAAGGACGAGGCTCAAAAGAAACCATACATTGCTTCCATGGGAGTGTACGTCTTCAAGAAGGAGATACTTC

upper sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 7
gtaatgatttttttttttttcattactacagttttagagagatgggttctgatctgaaggctctgagtggctactgactgtgccaatgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAGCCATACATTGCTTCCATGGGAGTGTATGTCTTCAAGAAGGAGATACTCC
    | |   |  | ||| | |  |||  |    || | | |||  |   ||  |  |   || | |    ||||| || |   |||    |||| ||||||||||||  || ||||| || |||| ||| |||||  | ||||| |||||||||||||||||||||||||| |||||||||||||||||||| |
---gtaagcctcatgtttattac-actgtaacactacaaa-atgtttcaagaattaca--ttcagtgctaatactg-ctttat-aat----ttagCAAGTAGATACAACCGTGTTGGGCCTTTCAAAGGATGAGGCTCAGAAGAAACCATACATTGCTTCCATGGGAGTGTACGTCTTCAAGAAGGAGATACTTC

upper sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S397_21V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------gtaatgatttttttttttttcattactacagttttagagagatgggttctgatct-gaaggctctgag--tggctactgactgtgccaatgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAGCCATACATTGCTTCCATGGGAGTGTATGTCTTCAAGAAGGAGATACTCC
                                          | | ||  ||| || |||  |  ||   | ||| |  |    |   ||   || | |   | ||| |   |  |  ||  ||||  | || |   ||| |||||||||||   ||  |||| || ||    || |||||  | |||||||| ||||| |||||||||||  | |||||||||||||||    | ||| 
gtaagctgattgtttcataacctcgaattaggttaaaaccttgaagtggatttcttatttc-cgctat--cggttgtcaatttctcattttcaattttggttgttctcacattatcgtcttgctgtttcgat-tgtgtagCAAGTAGATACATCTGTGCTGGGCCTGTCTTCCGAGGAGGCGAAGAAGAAGCCGTACATCGCTTCCATGGGCATCTATGTCTTCAAGAAGAGCGTTCTCA

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|110379176|gb|EC944355.1|EC944355
EST:     GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATG                         GAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
genomic: GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATGgtaatgattt ... atgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
EST: gi|351029658|gb|FQ427498.1|FQ427498
EST:     GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATG                         GAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
genomic: GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATGgtaatgattt ... atgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
EST: gi|351040871|gb|FQ438415.1|FQ438415
EST:     GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATG                         GAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
genomic: GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATGgtaatgattt ... atgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
EST: gi|351019209|gb|FQ429369.1|FQ429369
EST:     GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATG                         GAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAAGCAGAAAAGAAG
genomic: GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATGgtaatgattt ... atgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
EST: gi|110379174|gb|EC944353.1|EC944353
EST:     GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATG                         GAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
genomic: GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATGgtaatgattt ... atgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
EST: gi|351025236|gb|FQ433653.1|FQ433653
EST:     GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATG                         GAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
genomic: GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATGgtaatgattt ... atgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
EST: gi|351013646|gb|FQ429787.1|FQ429787
EST:     GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATG                         GAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGGGGCAGAAAAGAAG
genomic: GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATGgtaatgattt ... atgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
EST: gi|110373811|gb|EC938181.1|EC938181
EST:     GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATG                         GAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
genomic: GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATGgtaatgattt ... atgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
EST: gi|351015482|gb|FQ447311.1|FQ447311
EST:     GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATG                         GAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
genomic: GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATGgtaatgattt ... atgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
EST: gi|351034082|gb|FQ448000.1|FQ448000
EST:     GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATG                         GAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
genomic: GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATGgtaatgattt ... atgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
EST: gi|351013342|gb|FQ425047.1|FQ425047
EST:     GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATG                         GAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG
genomic: GGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATGgtaatgattt ... atgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgggttctgatctgaaggctctgagtggctactgactgtgccaatgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAGCCATACATTGCTTCCATGGGAGTGTATGTCTTCAAGAAGGAGATACTCC
                               tactgac  putative branch site (score: 1)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgatttttttttttttcattactacagttttagagagatgggttctgatctgaaggctctgagtggctactgactgtgccaatgtcattagGAAGTAGATACAAAAGTCTTGGGACTCTCAAGGGAAGAGGCAGAAAAGAAGCCATACATTGCTTCCATGGGAGTGTATGTCTTCAAGAAGGAGATACTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT