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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattataaaccatgaggatggtgtgaaaaagaaaattgaaactgaagtttgatgtggtagatattgaaattcaattgactggatgatttcttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTGGACTGTTTTCTCTGACATTGAAAAGAAAGGCTGTAGTGCTGAGGATCTG

Basic information

species Vitis vinifera
transcript Vv05s0049g01180.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
tgattataaaccatgaggatggtgtgaaaaagaaaattgaaactgaagt-ttgatgtggtagatattgaaattcaattgactggatgatttcttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTGGACTGTTTTCTCTGACATTGAAAAGAAAGGCTGTAGTGCTGAGGATCTG
| | ||   |   |  |  |   |  |   |  || |||  |      |  | | |   |      || ||||  | | |     | |||| | |  ||||||||||||| ||||| || |||||||| || |||||| | ||||| || ||||| || ||||||||| |||| |||| ||| || || || || ||||| 
ttactactgattgtttgtgtttggatagttatcaacttgtcatgattatactaaggatatgtcctctgtaattttactcaa-atctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G107629_T05 (Zea mays), 3'ss of exon 3
tgattataaaccatgagga--tggtgtgaaaaagaaaattgaaactgaagtttgatgtggtagatattgaaattcaattgactggatgatttcttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTGGACTGTTTTCTCTGACATTGAAAAGAAAGGCTGTAGTGCTGAGGATCTG
 |||| | |    ||  ||  |  ||   ||  |   |   | |  |   ||  |  || || |  ||       |    |     || || |  || ||||||||||||| |||||||| |||||||| || |||||| | |||||||| ||| | || ||||| ||| | || || | |||||| |||||||| || |||
-gattgttattattggcgagtttctgcagaagcggggaacaacatcgtgcttccacatg-tacagtttactcaagatacaataatgtgtttgcactttgcagGTGTGAAGCCTTCTCGACCTATCCTCGAACATATGATCTTCTCCACGCATGGGCAGTCTTCTCCGACCTCGATAAAAGAGGCTGCAGTGCTGAAGACCTG

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 7
tgatta-taaaccatgaggatggtgtg-aaaaagaaaattgaaactgaagtttgatgtggtagatattgaaattcaattgactggatga-tttcttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTGGACTGTTTTCTCTGACATTGAAAAGAAAGGCTGTAGTGCTGAGGATCTG
| |||| ||   | |     |  |||  | ||  |||||   |       | |||| ||  | | | ||| ||| |  |||  | ||||   ||||||  |||||||||||| |  || || || || |||||||||||||||||||| || |||||||| || ||||||||||||| || ||| || ||| | |||||||| 
ttattagtagctcctccttgtattgttcagaatcaaaatctgagtatggatgtgat-tgacaaa-agtgatattta-ctgaaggaatgaacatcttttaacagGTGTGAAGCATATTCAACATACCCCCGGACTTATGATTTACTCCATGCATGGACTGTGTTTTCTGACATTGAAACGAGAGGGTGCAGTCCAGAGGATCTA

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G35120.1 (Glycine max), 3'ss of exon 6
---tgattataaaccatgaggatggtgtgaaaaagaaaattgaaactgaagtttgat-gtggtagatattgaaattcaattgactggatgatttcttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTGGACTGTTTTCTCTGACATTGAAAAGAAAGGCTGTAGTGCTGAGGATCTG
   | ||| || |   |       ||        | |  |||    || ||||      ||   |||    ||||   | |       ||||    ||   |||||||||||| || ||||| || || ||||| || |||||||| || || ||||||||  |||||||||| ||| ||||||| || ||| | |||||||| 
tgcttattctagattctagattcagtt----gttggattttgtttttgtagttcctccatgaatgatgagaaaataagagttttgatgtgataatcttaaacagGTGTGAAGCATTTTCGACATACCCCCGGACATACGATTTACTTCATGCATGGACTGTCCTCTCTGACATAGAACAGAAAGGTTGCAGTCCAGAGGATCTA

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 6
tgatta-taaaccatgaggatggtgtgaaaaagaaaattgaaactgaagtttgatgtggtagatattgaaattcaattgactggatga---tttcttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTGGACTGTTTTCTCTGACATTGAAAAGAAAGGCTGTAGTGCTGAGGATCTG
  |||| ||   | |     |  | |  | ||  ||| |     |   | | |||||| | || |   || |   ||| |||| | ||   | ||||||  |||||||||||| |  || || || || |||||||| ||||||||||| || |||||||| || |||||||||||||  | ||| || |||   |||||||| 
--attagtagctcctccttgtattattcagaatcaaaatctgggtatggatggatgtgattgaca--aaagtgatatttactgaaggaatatatcttttaacagGTGTGAAGCATATTCAACATACCCCCGGACTTACGATTTACTCCATGCATGGACTGTGTTTTCTGACATTGAAACAAGAGGGTGCAGTAAAGAGGATCTA

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 7
---tgattataaaccatgaggatggtgtgaaaaagaaaattgaaactgaagtttgat-gtggtagatattgaaattcaattgactggatgatttcttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTGGACTGTTTTCTCTGACATTGAAAAGAAAGGCTGTAGTGCTGAGGATCTG
   | ||| || |   |     | || ||  | |     |||    || || |     |||   |||    ||||   | |       ||||    ||   |||||||||||| || || || || || ||||| || |||||||| || || |||||||| ||||||||||| ||||| ||||| || |||   |||||||| 
tgcttattctagaatctagatttagt-tgttagatt---ttgtttttgtagctcctccgtgaatgatgagaaaataagagttttgatgtgataatcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATGGACTGTCTTCTCTGACATAGAAAATAAAGGTTGCAGTAAAGAGGATCTA

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 7
tgattataaaccatgaggatggtgtgaaaaagaaaattgaaactgaagtttgatgtggtagatattgaaatt-caattgactggatgatttcttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTGGACTGTTTTCTCTGACATTGAAAAGAAAGGCTGTAGTGCTGAGGATCTG
             | ||  |       ||      | | || |  || |    |    || || |     ||   ||| |  |  ||||    ||  ||||||||||||| ||||||||||| ||  ||||||| ||||||||||| || |||    |  | ||||| ||  | |||| ||| || || || || ||| ||
------------gtcagtttctcccttaacctttcacttaatc-aaaatccattagtatatatgtgcctcttatgatttatcgtctgataatatt--gcagGTGTGAAGCGTTCTCGACTTACCCGAGGACTTACGATTTACTCCATGCCTGGGACATCATATCTGATATCAAGAAGAGAGGTTGCAGCGCAGAAGATTTG

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|110699783|gb|EE077083.1|EE077083
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|56409526|gb|CX017778.1|CX017778
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|110363042|gb|EC926608.1|EC926608
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|110421752|gb|EC988052.1|EC988052
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|27580186|gb|CB002881.1|CB002881
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|110387794|gb|EC952491.1|EC952491
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|34545569|gb|CF513801.1|CF513801
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|34545484|gb|CF513716.1|CF513716
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|56409685|gb|CX017937.1|CX017937
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|351021835|gb|FQ437220.1|FQ437220
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|56409742|gb|CX017994.1|CX017994
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|110379730|gb|EC944949.1|EC944949
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|110374002|gb|EC938463.1|EC938463
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|71886266|gb|DT035321.1|DT035321
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCAGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|110694918|gb|EE072343.1|EE072343
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|110716290|gb|EE091140.1|EE091140
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|110726430|gb|EE102206.1|EE102206
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|110715719|gb|EE094088.1|EE094088
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|110694546|gb|EE071749.1|EE071749
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|110357653|gb|EC921295.1|EC921295
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
EST: gi|110715151|gb|EE092872.1|EE092872
EST:     ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTG                         GTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG
genomic: ACACTTAAACTGATCTATGACAGAGGTCTAATAGGCACTATCCATAACTGgtatgcatat ... cttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtttgatgtggtagatattgaaattcaattgactggatgatttcttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTGGACTGTTTTCTCTGACATTGAAAAGAAAGGCTGTAGTGCTGAGGATCTG
                            aattgac  putative branch site (score: 3)
                                          tttctttt  putative PPT
                atattgaaattcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattataaaccatgaggatggtgtgaaaaagaaaattgaaactgaagtttgatgtggtagatattgaaattcaattgactggatgatttcttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTGGACTGTTTTCTCTGACATTGAAAAGAAAGGCTGTAGTGCTGAGGATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - -aaaccat
- - - - - - - - - -tggtgtg
- - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - -aaactga
- - - - - - - - - - - - - - - - - - - - - - - - - tgatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaattcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgactgg