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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttaggtgatataggaattatattgcattctagttttctgcttgtgacctaggttttgatgtcaataatgtgttgatgtttacctattttcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG

Basic information

species Vitis vinifera
transcript Vv02s0025g01580.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 5
gcttaggtgatataggaattatattgcattctagttttctgcttgtgacctaggttttgatgtcaataatgtgttgatgtttacctattttcactt---tcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG---------------------
   |   | | |      | || |   |  |   | ||     | |    |   | |      ||| |   | ||  ||  |   | |  ||| ||   |||||| || |||||||| |||||||||||||| ||||||||||||||||| || |||   || |||    |  |  | ||||                     
---ttaattacagtttggtcatttattacccatttcttgaagatctacttttaatgtcttcaccaaaaggatcttactggatggttctcatcatttttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGGTATTATTCTAAAGTTTTCTT

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 5
gcttaggtgatataggaattatattgcattctagttttctgcttgtgacctaggttttgatgtcaataatgtgttgatgtttacctattttcacttt--cagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG
 ||| | ||          | |||| |    |  ||||     | |    |   |        ||| |   | ||  ||  |     || ||| |||  ||||| || |||||||| |||||||||||||| ||||||||||||||||| || |||   || |||    |  |  | ||||
tctttgttgggtgcatgcctttattacccatt--ttttgaagatctacttttaatgccttcaccaaaaggatcttactggatggtccttatcattttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAG

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G43540.1 (Glycine max), 3'ss of exon 5
gcttaggtgatataggaattatattgcattctagttttctgcttgtgacctaggttttgatgtcaataatgtgttgatgtttacctattttcacttt---cagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG
   |   | | |      | || |   |  |   | ||     | |    |   | |      ||| |   | ||  ||  |   | |  ||| |||   ||||| || |||||||| |||||||||||||| ||||||||||||||||| || |||   || |||    |  |  | ||||
---ttaattacagtttggtcatttattacccatttcttgaagatctacttttaatgtcttcaccaaaaggatcttactggatggttctcatcatttttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAG

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G02690.2 (Glycine max), 3'ss of exon 5
gcttaggtgatataggaattatattgcattctagttttctg-cttgtgacctaggttttgatgtcaataatgtgttgatgtttacctattttcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG
  |||     ||    |  | | | |||   ||  |   |  |   |  | ||  |  |      || | |   || || |     | |||||  |||||||| ||||||||||| |||||| ||||||| ||||||||||| ||||| || ||| | || ||     |  |  ||||||
-attaacaattaataaacatttttagcaacataactaaataacacatttcataactgatacaactaacacttgattaatatcctgattttttctttttcagGTTCGTGATTACATTCATGTTCTTGATTTAGCAGATGGGCATATTGCTGCGTTGCGTAAACTGGATGATCCTAAAATAG

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 5
gcttaggtgatataggaattatattgcattctagttttc----tgcttgtgacctaggttttgatgtcaataatgtgttgatgtttacctattttcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG
   |||      |  |     | || ||| |   | |||    | | |  || || |  || ||| ||   ||     | |     ||  |  ||   |||||||| ||||||||||| |||||| ||||||| ||||||||||| ||||| || ||| | || ||     |  |  ||||||
--atagtcacagtttggccattcttacatgcctatattcccatttcctaagatct-gccttagatttcttcaagaatcttacaga-acggaccttttttttcagGTTCGTGATTACATTCATGTTCTTGATTTAGCAGATGGGCATATTGCGGCATTGCGTAAACTCAATGATCCTAAAATAG

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|27586173|gb|CB008868.1|CB008868
EST:     CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGG                         GTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
EST: gi|110720449|gb|EE096391.1|EE096391
EST:     CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGG                         GTACGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
EST: gi|110358293|gb|EC922402.1|EC922402
EST:     CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGG                         GTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
EST: gi|110719820|gb|EE095280.1|EE095280
EST:     CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGG                         GTACGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
EST: gi|110718272|gb|EE094913.1|EE094913
EST:     CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGG                         GTACGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
EST: gi|110720256|gb|EE096017.1|EE096017
EST:     CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGGTGGTACCGGG                         GTACGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
EST: gi|110720916|gb|EE097257.1|EE097257
EST:     CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGG                         GTACGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
EST: gi|30329922|gb|CD013184.1|CD013184
EST:     CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGG                         GTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
EST: gi|110718494|gb|EE095391.1|EE095391
EST:     CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGG                         GTACGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
EST: gi|110720332|gb|EE096162.1|EE096162
EST:     CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGG                         GTACGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
EST: gi|110727091|gb|EE103475.1|EE103475
EST:     CTGCACTTACAGTTTTTGGAAATGACTATTCAACAAAGGATGGTACCGGG                         GTACGTGATTACATCCATGTTGTTGATTTGG
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGG
EST: gi|110385299|gb|EC949809.1|EC949809
EST:     CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGG                         GTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
EST: gi|110718330|gb|EE095043.1|EE095043
EST:     CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGG                         GTACGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
EST: gi|110719030|gb|EE096543.1|EE096543
EST:     CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGG                         GTACGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCT
EST: gi|110709164|gb|EE084386.1|EE084386
EST:     CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGG                         GTACGTGGAT-ACATCCATGTTGTTGA
genomic: CTGCACTTACAGTTTTTGGAAGTGACTATTCAACAAAGGATGGTACCGGGgtatgttttg ... tcactttcagGTCCGTG-ATTACATCCATGTTGTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacctaggttttgatgtcaataatgtgttgatgtttacctattttcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG
                          tgttgat  putative branch site (score: 4)
                                      cctattttcactttc  putative PPT
                 tcaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttaggtgatataggaattatattgcattctagttttctgcttgtgacctaggttttgatgtcaataatgtgttgatgtttacctattttcactttcagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - -ataggaa
- - - - - - - - - - - - -gcattct
- - - - - - - - - - - - - - - - - - - - gcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtc