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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaggttaccttcctattctttgctatgcttttcatgaacttgcatcttgggcattgcacagtctgtagtatgtttgtggctcatgatgctcatttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA

Basic information

species Vitis vinifera
transcript Vv04s0210g00180.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 1
gaggttaccttcctattctttgctatgcttttcatgaacttgcatcttgggcattgcacagtctgtagtatgtttgtggctca-tgatgctcatttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA------------
             |   |  ||  |||   | ||     ||   | |   |   |    ||  | |  |   | |  | |||| |||    | ||||  |||| ||||||||||| || || ||| | ||||| |||||||||||||||||||| ||||| |||||| |||||||||| ||||| ||||| ||||||||||            
------------attgccaatggaatgaaatgcacccttttttttttccagttctctg-agcttcttttccatcttagtctcactgactaacttttgtcaggtgataacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACATCATGAAGCTTG

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
-gaggttaccttcctattctttgctatgcttttcatgaacttgcatcttgggcattgcacagtctgtagtatgtttgtggctca-tgatgctcatttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA
    ||||| |   |   |  ||  |||   | ||     ||   | |   |   |    ||  | |  |   | |  | |||| |||    | ||||  |||| ||||||||||| || || ||| | ||||| |||||||||||||||||||| ||||| |||||| |||||||||| ||||| ||||| ||||||||||
ttgtgttacatgattgc-caatggaatgaaatgcacccttttttttttccagttctctg-agcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 3'ss of exon 1
gaggttaccttcctat--tctttgctatgcttttcatgaacttgcatcttgggcattgcacagtctgtagtatgtttgtggct--catgatgctcatttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA
    || |     ||     | ||  |   ||||  | |  || ||| |       |  |     | |  | | | ||   ||   |  |     |||| |||||| || ||||||||||| || ||  | ||||| || |||||||||||||| || ||||| |||||||||||||||||||| || ||||| ||||||||||
----tttctgaaatagaacgtatgtaaatgtttttgtcacttttcatttcatcatctaaaggaatttttttctatatggtactgttactaaatggatttactagGTGATCACAAAGTTCTGCTCTGAAAGGATTGCCAAGTATGCTTTTGAGTACGCGTACCTCAACAACAGAAAGAAAGTGACTGCCGTGCATAAAGCAAACA

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G006672_T02 (Zea mays), 3'ss of exon 1
gaggttaccttcctattctttgcta-tgcttttcatgaacttgc-atcttg--ggcattgcacagtctgtagtatgt-ttgtggctcatgatgctcatttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA
 |  ||        || |  |  |  ||||  |    |  |||| ||||    |||||| | |  | | || ||| |  | |  ||     || | ||||||||||| |||||||| ||||| || ||  | |||||||| ||||||||||||||||||||||| |||||  |||||||||||||||| ||||| ||||| || |
taatttgaaagtgcatgcaatattgctgctcctttctattttgccatctaaaaggcatttctccttat-tactatttactataactt----tgttgatttgctagGTGATAACAAAATTCTGCTCTGAAAGAATTGCAAAGTATGCTTTTGAGTATGCATACCTTAACAATCGAAAGAAAGTGACAGCAGTGCATAAAGCCAATA

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA11G08920.1 (Glycine max), 3'ss of exon 1
gaggttaccttcctattctttgctatgcttttcatgaacttgcatcttgggcattgc--acagtctgtagtatgtttgtggctcatgatgctcatttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA
    ||  | ||  ||  |    |||   | ||||||| ||    | | | |||||   || ||  ||  ||||||||   |||||  |  || ||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||| ||||||||||| ||||| |||||||||||||||||||
--ctttttcatctaatcttcaattatatatctcatgaagttagcgccttgacattgtgaactgtgagttttatgtttgcacctcatactaatcttttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G04780.1 (Glycine max), 3'ss of exon 1
gaggttaccttcctattctttgc-tatgcttttcatgaacttgcatcttgggcattgcacagtctgtagtat--gtttgtg---gctcatgatgctcat---ttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA
        | |   ||  ||    |||   | |||||||  |    | | |  | ||  | |  || |||||  |||| ||   |||  |||| |||||   || |||||||||||||||||| ||||||||||| ||||| |||||||| || |||||||| ||||| || ||||||||||| ||||| || |||||||||||||| |
--------catgtgatctttgatgtatatatgtcatgaaggtatcaccttgatactgtcctga-tgcagtatgggtttatgtttgctgttgatactcatattttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G22640.1 (Glycine max), 3'ss of exon 1
gaggttaccttc--ctattctttgctatgcttttcatgaacttgcatcttgggcattgcacagtctgtagtatgtttgtggctcatgatgctcatttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA
 | || | |||       | | ||  |||   || || ||||||   ||       ||||  ||  ||  |||||||   | | ||  |  |  ||| |||||||||||| ||||||||||||||||| ||||| |||||||| || |||||||| ||||| || ||||||||||| ||||| || |||||||||||||| |
catgtgatctttgatgcatatatgtcatgaagtt-atcaacttgatactgtcctgatgcagtgtgggtt-tatgttttctgttgatcctcatattttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G35650.1 (Arabidopsis thaliana), 3'ss of exon 1
gaggttaccttcctattctttgctatgcttttcatgaacttgcatcttgggcattgcacagtctgtagtatgtttgtggctcatgatgctcatttgc-tagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA
             ||  |  |  |||  || |   ||   |   |  |    ||||      || | ||||   ||  | |  |||   |  ||||  ||||| ||||||||||| ||||| ||| | || || | |||||| ||||||||||| || |||||||| || ||||||||||| ||||| || ||||| ||||
------------gtaaaccata-tataattatagggattgtttttagtccaaattgtgatcccttttgtatacatgatgttgttgaa--ttgtttgtgtagGTGATAACAAAGTTTTGTTCTGAGAGAATAGCGAGATATGCATTTGAGTATGCGTATCTAAACAATAGGAAGAAAGTGACTGCTGTTCATAAAGCTAACA

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S101_151V6.1 (Physcomitrella patens), 3'ss of exon 1
gaggttaccttcctattctttgc-tatgcttttcatgaacttgcatcttgggcattgcacagtctgtagta-tgtttgtggctcatgatgctcatttgct-agGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA
    |  |||    || |||     ||  |    || | |||   |  || |   | |        || |  |||  ||| || |   |||  |  || | ||||||| || |||||||| || ||||||||||| ||||| || ||||||||||| || || |||||| | |||| ||| ||||| |||||||| || ||||
---atctcctcgtcatgcttcatgcattgtggaaataatcttatctactgcgtggtacctgtcaaataattctgtaagtgccttacagtgccaagatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTATGCTTATCTCAACAACCGCAAGACAGTAACAGCAGTGCACAAGGCCAACA

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 1
gaggttaccttcctattctttgctatgcttttcat-gaacttgcatcttgggcattgcacagtctgtagtatgtttgtggctcatgatgctc----atttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA
      |     ||  ||  ||  |||  | | || | |  ||||  ||    | |   |  ||| |   ||   || |  || | ||| |     | |||  |||| || ||||| ||||| || |||||||| ||||||||||||||||| |||||||| || |||||| | ||||  || ||||| |||||||| || ||||
----caagagggcttgtcagtgtcatgtgtatgatcgtatctgcaggtttcctact-tgccatctatgagattgatgagattcctaatggtgccaaaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA

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|161716145|gb|FC069488.1|FC069488
EST:     ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAG                         GTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCCTTTGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAGgttttgattt ... catttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTAT
EST: gi|110702504|gb|EE081292.1|EE081292
EST:     ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAG                         GTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAGgttttgattt ... catttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTAT
EST: gi|110383796|gb|EC948197.1|EC948197
EST:     ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAG                         GTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAGgttttgattt ... catttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTAT
EST: gi|71869488|gb|DT018543.1|DT018543
EST:     ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAG                         GTAATAACAAAGTTCTGTTCAG
genomic: ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAGgttttgattt ... catttgctagGTAATAACAAAGTTCTGTTCAG
EST: gi|110415520|gb|EC981433.1|EC981433
EST:     ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAG                         GTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAGgttttgattt ... catttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTAT
EST: gi|110374228|gb|EC938864.1|EC938864
EST:     ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAG                         GTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAGgttttgattt ... catttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTAT
EST: gi|161720273|gb|FC070534.1|FC070534
EST:     ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAG                         GTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAGgttttgattt ... catttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTAT
EST: gi|351046732|gb|FQ453348.1|FQ453348
EST:     ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAG                         GTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAGgttttgattt ... catttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgggcattgcacagtctgtagtatgtttgtggctcatgatgctcatttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA
                                           ctcattt  CT-rich tract
                       tatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaggttaccttcctattctttgctatgcttttcatgaacttgcatcttgggcattgcacagtctgtagtatgtttgtggctcatgatgctcatttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - -ccttcct
- - - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - catgaac
- - - - - - - - - - - - - - - - - - - - tgcatct
- - - - - - - - - - - - - - - - - - - - - - - - - -cattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcatga