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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttaaatcatccaattatatgccacaatgttaatatgagattagttcttggtggaataggtttgtttcctgcatgcaaattgatgctctggcagctagttctactctgtgggttctctaaactctgtttttaactgaatataaaaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCAAAGACAAGCTTTAAGGCTAACACAAAGGCCCTAGCAGAAAATGAAGGAG

Basic information

species Vitis vinifera
transcript Vv05s0077g01210.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 11
gtaaatttaaatcatccaattatatgccacaatgttaatatgagattagttcttggtggaataggtttgtttcctgcatgcaaattgatgctctggcagctagttctactctgtgggttctctaaactctgtttttaactg--aatataaaaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCAAAGACAAGCTTTAAGGCTAACACAAAGGCCCTAGCAGAAAATGAAGGAG
                                                  | ||  || | | ||| ||| |||         |||| | || ||   |  |  |  ||  ||     | | | |  ||  |    || ||  |  |  |||  |  ||||| ||||| || || |||||||| || || ||||||||  |||||||||  ||||| |||||||||||||| ||||| ||  | ||||||||||||||||
--------------------------------------------------ttttactgtatttggtatgtatcc---------attgcttct-tgaaggggatctaaaccatgcaatctttatgatttccttgaccaagtgttatcaataaatattgcagCCACAAGCCAGAGAAAAAGCTGATAAAGAAGGATTTGAGATAAGTGTTGTTAAGACCAGCTTTAAGGCTAATACAAAAGCATTGGCAGAAAATGAAGGAG

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
----gtaaatttaaatcatccaattatatgccacaatgttaatatga--gattagttcttggtggaataggtttg----------tttcctgcatgcaaattgatgctctggcagctagttctactctg-tgggttctctaaactctgtttttaac--tgaatataa-----aaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCAAAGACAAGCTTTAAGGCTAACACAAAGGCCCTAGCAGAAAATGAAGGAG
    || |  |   ||  ||||||  ||          | || ||    ||    | ||||||  | |   ||||          |||| |   |  ||| | |     ||    | | |  | || || | || |  | || |  | |||   ||  | |  ||          ||  ||||| || || |||||||| ||||| ||||| ||||||||| ||||||||| |||||| || ||||||||||||||||||||||| ||||| ||||||||||
gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaactcttgctttgcttggctagcaaaccaatctttacgactctaatcattgttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G152958_T02 (Zea mays), 3'ss of exon 11
gtaaatttaaatcatccaattatatgccacaatgttaatatgagattagttcttggtggaataggtttgtttcctgcatgcaaattgatgctctggcagctagttctactctgtgggttctctaaactctgtttttaactgaatataaaaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCAAAGACAAGCTTTAAGGCTAACACAAAGGCCCTAGCAGAAAATGAAGGAG
                                                      | |    |   ||   | |    ||| ||    ||     |||| |  ||  || | | | | ||  | | ||| | |||||   ||||  |     ||| ||||| ||||| || ||||| || || || || |||||||| |||| |||||  ||||| ||||||||||||||||| || ||  | ||||||||||||||||
--------------------------------------------------ggccgttttgctcatttgactgcaattatggaaggatataaataggcaac--gtcttatttttttgcttaac-atactgtttttttttttgaaact-----ttctcagCCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTGAAGACTAGCTTTAAGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAG

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 11
--gtaaatttaaatcatccaattatatgccacaatgttaatatgagattagttcttggtggaataggtttgtttcct-gcatgcaaattgatgctctggcagctagttctactctgtgggttctctaaactctgtttttaactgaatataaaaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCAAAGACAAGCTTTAAGGCTAACACAAAGGCCCTAGCAGAAAATGAAGGAG
  |    |||   ||| |   ||| |   |   || ||  |  |   |||   ||| |   | |      ||||  |  | || | ||    ||| |   || | |       | |  |      | || | | ||  |  ||||  ||   |  | ||||||||||||| | |    ||||||||||||||||||  ||||||| ||||| ||||| ||||| || || || || ||||| ||||| ||||| || || |
gtgatggtttgggtca-ctgcttacaattc--tatatttgtgaggttttaccgcttagaatatttcaagagttttttcacgtggagatca--gctgtaatagatcgcatcgtacagaag------tgaagtttcttaatttctgagcatttca--tgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTG

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|110413521|gb|EC979310.1|EC979310
EST:     CAGCAGCTTGTTTCACTCATCCAGAAATCAGTATGGTTGGATTGACTGAG                         CCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCA
genomic: CAGCAGCTTGTTTCACTCATCCAGAAATCAGTATGGTTGGATTGACTGAGgtaaatttaa ... aaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCA
EST: gi|110398357|gb|EC964660.1|EC964660
EST:     CAGCAGCTTGTTTCACTCATCCAGAAATCAGTATGGTTGGATTGACTGAG                         CCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCA
genomic: CAGCAGCTTGTTTCACTCATCCAGAAATCAGTATGGTTGGATTGACTGAGgtaaatttaa ... aaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCA
EST: gi|34544811|gb|CF513043.1|CF513043
EST:     CAGCAGCTTGTTTCACTCATCCAGAAATCAGTATGGTTGGATTGACTGAG                         CCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCA
genomic: CAGCAGCTTGTTTCACTCATCCAGAAATCAGTATGGTTGGATTGACTGAGgtaaatttaa ... aaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCA
EST: gi|110381634|gb|EC934980.1|EC934980
EST:     CAGCAGCTTGTTTCACTCATCCAGAAATCAGTATGGTTGGATTGACTGAG                         CCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCA
genomic: CAGCAGCTTGTTTCACTCATCCAGAAATCAGTATGGTTGGATTGACTGAGgtaaatttaa ... aaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCA
EST: gi|110381614|gb|EC934930.1|EC934930
EST:     AGCAGCTTGTTTCACTCATCCATTAAATCAGTATGGTTGGATTGACTGAG                         CCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCA
genomic: AGCAGCTTGTTTCACTCATCCA-GAAATCAGTATGGTTGGATTGACTGAGgtaaatttaa ... aaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCA
EST: gi|34549728|gb|CF517960.1|CF517960
EST:     CAGCAGCTTGTTTCACTCATCCAGAAATCAGTATGGTTGGATTGACTGAG                         CCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCA
genomic: CAGCAGCTTGTTTCACTCATCCAGAAATCAGTATGGTTGGATTGACTGAGgtaaatttaa ... aaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctactctgtgggttctctaaactctgtttttaactgaatataaaaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCAAAGACAAGCTTTAAGGCTAACACAAAGGCCCTAGCAGAAAATGAAGGAG
                             ttttaac  putative branch site (score: 2)
                          tgtttttaactgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttaaatcatccaattatatgccacaatgttaatatgagattagttcttggtggaataggtttgtttcctgcatgcaaattgatgctctggcagctagttctactctgtgggttctctaaactctgtttttaactgaatataaaaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCAAAGACAAGCTTTAAGGCTAACACAAAGGCCCTAGCAGAAAATGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG