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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctactgttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatcttcatgttttgtggggaattttgta...

Basic information

species Vitis vinifera
transcript Vv09s0002g04810.t01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctactgttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatcttc----atgttttgtggggaattttgta---
||||||| |||||||||||||||||||| |||||||||||||| ||  | ||||| || |||||  ||||||| || || || || |  ||  |||||| || | ||      | || || ||| |  | |||| | |  |       |      |||    |  | |||| | ||       || ||| |    ||||||||    
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagtt------gctgacttttgatccaaaacaatgagtttcttt-tattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 16
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctac-tgttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatc---ttcatgttttgtgg-ggaattttgta
||||||| |||||||||||||||||||| |||||||||||||| ||  ||||||  || |||||| ||||| | || || || || | |||  | |||||||   || | |  |||   ||| |  |   | ||  |    |      | ||    |  |   | |  ||| ||||   ||  | ||| ||   || |  || | 
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCAAAGGCACAATACAATAGgtttgttccaaaatgtaaactgatttttttctacgctcttttctctctctaa----tttatctttgcttttagatccgttttctatttcgtaacggcagattat-

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: GRMZM2G086015_T01 (Zea mays), 5'ss of exon 2
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctactgttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatc---ttcatgttttgtggggaattttgta
||||||| |||||||||||||||||||| |||||||||||||| ||  |||| |  || ||  || ||||| | || || || || |  ||  |||||||||   |   ||  | |   ||||   ||| |    |  | |           | ||  |     |  ||| || |   ||  | |||||| |   |     ||
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCAAAGGCGCAATATAATAGgtttgtgattatcggt--ttgtttcaaaatatatattgactttttcttttctaatt-tatctctgcttttagacccattttctattttgttgaagacaggtta

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctactgttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatc---ttcatgttttgtggggaattttgta-
||||||| |||||||||||||||||||| |||||||||||||| ||  |||| |  || ||  || ||||| | || || || || |  ||  |||||||||   |   ||    |   ||||   ||| |    |  | |           | |||       |  ||| || |   ||  | ||||||||   |     || 
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgattatcagt--ttgttccaaaatatatattgactttttttttctaatttat--ctctgcttttagacccattttctattttgtggaagacaggttat

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: GRMZM2G448913_T01 (Zea mays), 5'ss of exon 6
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctactgttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatc---ttcatgttttgtggggaattttgta
||||||| |||||||||||||||||||| |||||||||||||| ||  |||| |  || ||  || ||||| | || || || || |  ||  |||||||||   |   ||    |   ||||   ||| |    |  | |           | ||  |     |  ||| || |   ||  | ||||||||   |     ||
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCAAAGGCGCAATATAATAGgtttgtgattatcagt--ttgttccaaaatatatattgactttttcttttctaatt-tatctctgcttttagacccattttctattttgtggaagacaggtta

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 18
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctactgttggctgttggtaaaca-acagtaaaataagaggcaaacacttacaa--tgtagtatttggatc-ttcatgttttgtggggaattttgta
|||| |||||||||||||||||||| || |||||||||||||| ||  ||||||  || |||    ||||||| || || || || ||||| || || ||||    | ||  |  || |||||   ||      |||        |   ||||  |||        | | |||  ||  || |  ||| |   | |        
TACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAGgtgccatcctgtt--tgtctgttcaaaattttgtagtggttgttaatttaaacttttatgtgccccaatgtttatatgatttacttttggcttgcag-------

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 17
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaa-atttctactgttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatcttcatgttttgtggggaattttgta
| ||| | || ||||||||||||||||| |||||||||||||||||  ||||| ||||||||||| || |||| ||||| |||||||| |||||||| |||||  | ||    |||||   |    | |   |   |     || | | | | |  | |    ||    | | |  |  |  | || | || ||     | 
TGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCCAAAGAGCATCATAACAGgtaggacttaccttgttgcaagacaatgattgattttctttcaatatgtagaaatatgcttgatatgtgtagaaattaaaaatgtttttggtaacagaat-

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 17
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctactgttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatctt-catgttttgtggggaattttgta--------
||||| | ||||||||||| |||||||| ||||| |||||||||||  ||||| ||||||||||| || |||| |||||||| ||||| |||||||| |||||          |||   |  || ||           |||  ||  |  ||  |    || ||| | ||   | |   |||||||| |      ||| |         
TACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCTAAAGAGCATCATAACAGgtag-------tagttattttctgttatgttgttacggaat--gacccttactttctttatttagaaattatgtttgatatgttttgagaaaggcttttttgtaagggt

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 17
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctactgttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatcttcatgttttgtggggaattttgta--------
| ||| | || ||||||||||||||||| |||||||||||||||||  ||||| ||||||||||  || | || ||||| |||||||| |||||||| ||||| |  |     |||  ||  || ||     ||  | ||| |          ||| |||| |    ||   || | | || | ||||  ||| ||   |        
TGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCCAAAGAGCATCATAACAGgtagaagtta---gttaccttgtgttacgttgcaagataatgattaatt--ttctttcaatatg---ttgaaatatgcttgatatgtgtagaaattaaaaatgctttt

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 6
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctactgttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatctt-catgttttgtggggaattttgta--------
||||| | ||||||||||| |||||||| || || ||||| |||||  ||||| ||||||||||| || |||| |||||||| |||||  ||||||| |||||          |||   |  |  ||    |    | |||  ||     ||  | |  || ||| | ||   | |   |||||||| |      ||| |         
TACTTTTAAGTTTGATTGAATACAAGACACTAGTCATGCGCGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCTAAAGAGTATCATAACAGgtag-------tagttattttcttttatgttattacagaat--gacctttactttcattatttagaaattatgtttgatatgttttgagaaaggcttttttgtaaggga

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgta--aatttctactgttggctgttggtaaacaacagtaaaataagag-----gcaaacactta--caatgtagtatttggatcttcatgttttgtggggaattttgta------------------------------------------------
||||| | ||||||||||||||||||||||||||||||||||| ||  |||||| ||| |||||| | |||||||||||||| || || || |||||||||||  |   | | || |     |          ||||    || |  |     | |||||  ||  ||| ||   ||   | | |  ||  |||      | |   | |                                                
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 17
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGg-----taaatttctactgttggctgt--tggtaaacaacagtaaaataagaggcaaacact-tacaatgtagtatttggatcttcatgttttgtggggaattttgta
|  | || ||  |||||||||||||||||||||||||||| |||||  | ||    |||| |||| | |||||| ||||||| ||||| || ||||| |||     || || |  |||  ||  |||  | || |   |   |  |        |      | |   || | || || || | ||||| | ||  ||           
TGTTGCTAAGCCTGATTGAGTACAAGACTCTTGTGATGCGGGGTGATTTAGACAAAGCCAGTGAAATCTTACCTACAATTCCTAAAGATCAGCATAACAGgtatgctagatcttaacttctgtgtgtgcttgtgattcattctttatcgcacttctcttgttatgtgatat-gtcttaggtttttcatttctttaggaagg-------

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 17
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctact--gttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatcttcatgttttgtggggaattttgta-
| || || ||  ||||||| |||||||||||||||||||| || ||  ||||  | |||||| || |||||||| ||||||| ||||| || ||||| | |||  ||     |   || | | |   |      || | |  ||  |  ||  |  ||||  |   | ||||      |  |    ||    |   | || | 
TGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCTAAAGAGCAGCATAACAAgtatgttataggttattttggtctaaattttttgcattcacttataattcattc-tttac--tactgcattttatctcttgttgcctgctatgtcctatgaat

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|110728301|gb|EE103751.1|EE103751
EST:     GAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAG                         TGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGT
genomic: GAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttct ... gaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGT
EST: gi|161716849|gb|FC068107.1|FC068107
EST:     GAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAG                         TGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGT
genomic: GAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttct ... gaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctactgttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatcttcatgttttgtggggaattttgta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggaat