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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagggtgtagggttgttactaaatgtttgatttagagaatttcccctaaatgtttgatttagagaatttccactcacaacttctgtggctgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGGATGCGTTTGAGAGGGATTTCTTTCAGTTGAAACCTTATTATACAGATAC

Basic information

species Vitis vinifera
transcript Vv02s0025g02010.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G08690.1 (Glycine max), 3'ss of exon 2
atagggt--gtagggttgttactaaatgtttgatttagag--aatttcccctaaatgtttgat-ttagagaatttccactcacaacttctgtggctgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGGATGCGTTTGAGAGGGATTTCTTTCAGTTGAAACCTTATTATACAGATAC
 |||  |   |  | |  |  |||  | ||  ||  | ||  ||       || | |||| || |   ||  |||   |       || |    ||    | ||||||||||||||||||||||||||||||| ||||| || |  |||||||| ||||| || || ||||||||||| |||||||| ||||||||||||||| |
-tagcatcaatgagataatatctacttattaaatgaaaaggtaaaaaatgttagaagttttatgtctaagttttttttcctgttggtttttaaact----tccagGGGATATATATGAGCATGCTGTTGTCCTTAGTGTGAAAATTGAGGATCAAGATGCTTTCGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGC

upper sequence: Vv02s0025g02010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G25730.1 (Glycine max), 3'ss of exon 2
-atagggtgtagggttgttactaaatgtttgatttagagaatttcccctaaatgtttgatttagagaatttccactcacaacttctgtggctgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGGATGCGTTTGAGAGGGATTTCTTTCAGTTGAAACCTTATTATACAGATAC
 ||   || |      | |  ||  |  || ||| |  |||        |||||||    |   |   ||     |  |   |  | |     | || ||||||||||||| ||||||||||||||||| ||||| || |  |||||||| ||||| ||||| ||||||||||| |||||||| ||||||||||||||| |
tatttagtatcaataagattatagctactt-attaaatgaaaaagtaaaaaatgttaagatatcaagtttattttttcctgttggttttttaaacttccagGGGATATATACGAGCATGCTGTTGTCCTTAGTGTGAAAAATGAGGATCAAGATGCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGC

upper sequence: Vv02s0025g02010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G64520.1 (Arabidopsis thaliana), 3'ss of exon 2
atagggtgtagggttgttactaaatgtttgatttagagaatttcccctaaatgtttgatttagagaatttccactc--acaactt---ctgtggctgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGGATGCGTTTGAGAGGGATTTCTTTCAGTTGAAACCTTATTATACAGATAC
||     || |  | | | | |   |||||  ||   || ||     ||| | ||    |||  || | |||  |   | |||||   |  | | || |||  |||||| || ||||||||||||||||| ||||| ||||| || |||||||| ||||| |||||||| |||||||| ||| |||||||||| |||   ||| |
attaatcgttgaat-gctgc-attggtttggatt---gagttattggtaatttttgttcttattgattatccgtttctaaaactttgacaattggtgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGC

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|37188612|gb|CF607961.1|CF607961
EST:     ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAA                         GGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
genomic: ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAAgtatagttct ... tgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
EST: gi|349816270|gb|FQ399380.1|FQ399380
EST:     ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAA                         GGGATATATATGAGCATGCTGTTGTCCTAAGTGTC-AGACAGAGGATCAGG
genomic: ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAAgtatagttct ... tgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
EST: gi|30298118|gb|CB974912.1|CB974912
EST:     ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGACAATAGCAA                         GGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
genomic: ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAAgtatagttct ... tgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
EST: gi|161716840|gb|FC064955.1|FC064955
EST:     ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGACAATAGCAA                         GGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
genomic: ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAAgtatagttct ... tgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
EST: gi|110718356|gb|EE095093.1|EE095093
EST:     ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGACAATAGCAA                         GGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
genomic: ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAAgtatagttct ... tgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
EST: gi|110731735|gb|EE106407.1|EE106407
EST:     ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGACAATAGCAA                         GGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
genomic: ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAAgtatagttct ... tgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
EST: gi|110707571|gb|EE084124.1|EE084124
EST:     ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGACAATAGCAA                         GGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
genomic: ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAAgtatagttct ... tgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
EST: gi|110374493|gb|EC939283.1|EC939283
EST:     ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGACAATAGCAA                         GGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
genomic: ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAAgtatagttct ... tgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
EST: gi|351044575|gb|FQ443106.1|FQ443106
EST:     ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAA                         GGGATATATATGAGCATGCTGTTGTCCTAAGTGTC-AGACAGAGGATCAGG
genomic: ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAAgtatagttct ... tgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
EST: gi|351033177|gb|FQ461949.1|FQ461949
EST:     ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAA                         GGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
genomic: ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAAgtatagttct ... tgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
EST: gi|110410923|gb|EC976617.1|EC976617
EST:     ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAA                         GGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG
genomic: ACCATTGTTTGAGGACTCCCCCAATGCAGTTCATGAGTTGAAAATAGCAAgtatagttct ... tgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctaaatgtttgatttagagaatttccactcacaacttctgtggctgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGGATGCGTTTGAGAGGGATTTCTTTCAGTTGAAACCTTATTATACAGATAC
                          cactcac  putative branch site (score: 2)
        tttgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagggtgtagggttgttactaaatgtttgatttagagaatttcccctaaatgtttgatttagagaatttccactcacaacttctgtggctgaatttcagGGGATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGGATGCGTTTGAGAGGGATTTCTTTCAGTTGAAACCTTATTATACAGATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - gggttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacttc