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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAACGAGGACCCGAGCTTGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTATAGGGACATTAGAGgtatgtatctataattacttgatctgcttttggttagttgtcaagttagggatattaatttcttagttcacctcattgtggaactaatatatactaccct...

Basic information

species Vitis vinifera
transcript Vv12s0055g00360.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0055g00360.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA15G05410.2 (Glycine max), 5'ss of exon 5
AGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAACGAGGACCCGAGCTTGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTATAGGGACATTAGAGgtatgtatctataattacttgatctgcttttggttagttgtcaagttagggatattaatttcttagttcacctcattgtggaactaatatatactaccct---
    || || |||||||||||||| ||||||||||||||||| || || ||||||||||||||||||||||||||||| || ||| | || ||  | |||||||  |||| | ||||||| |  || |||| |  |  | || |  ||    | |   |   | | | |    |||  || | ||  |   |   ||| |   
TACTACGGAACATGTTCCAAGGGTATTGCCAAAGAACGAGGATCCAAGTTTGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAGgtat--atctttgattactt-acttggttttagacatatctctatctatctctttctctagataattgctttccatgttgaatcttcttcctgagaccgtttt

upper sequence: Vv12s0055g00360.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G19640.1 (Glycine max), 5'ss of exon 5
-AGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAACGAGGACCCGAGCTTGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTATAGGGACATTAGAGgtatgtatctataattacttgatctgcttttggttagttgtcaagtt--agggatattaatttc--ttagttcacctcattgtggaactaatatatactaccct
 | | ||||| |||||||||||||| ||||| ||||| ||||| || || ||||||||||||||||||||||||||||| || ||| | || ||  | ||||||| |       |||||||| ||| ||     |  |||  | | |   | |||||  || |     |   | || |  || | ||  ||       ||| |  
TAAT-ACAGATCATGTTCCAAGGGTATTGCCTAAGAATGAGGATCCAAGTTTGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAGgtatatgatag--attacttgctctcctgacaat--gtttccgattcccatggataaaaaataaagattacttacttggttttagacatatctctatctatctc
















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|30255110|gb|CB971557.1|CB971557
EST:     TGGTTAATAGGAACAAAAGAATGTTGGGTGANCTTATAGGGACATTAGAG                         AAATTCAGAAAGGAAGACATGAAACTTTCAGGAACTGAGGCATTCATGCGT
genomic: TGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTATAGGGACATTAGAGgtatgtatct ... acttctccagAAATTCAGAAAGGAAGACATGAAACTTTCAGGAACTGAGGCATTCATGCGT
EST: gi|110722678|gb|EE099124.1|EE099124
EST:     TGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTATAGGGACATTANAG                         AAATTCAGAAAGGAAGACATGAAACTTTCAGGAACTGAGGCATTCCTGCGT
genomic: TGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTATAGGGACATTAGAGgtatgtatct ... acttctccagAAATTCAGAAAGGAAGACATGAAACTTTCAGGAACTGAGGCATTCATGCGT
EST: gi|161717479|gb|FC067864.1|FC067864
EST:     TGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTATAGGGACATTAGAG                         AAATTCAGAAAGGAAGACATGAAACTTTCAGGAACTGAGGCATTCATGCGT
genomic: TGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTATAGGGACATTAGAGgtatgtatct ... acttctccagAAATTCAGAAAGGAAGACATGAAACTTTCAGGAACTGAGGCATTCATGCGT
EST: gi|110711839|gb|EE088776.1|EE088776
EST:     TGGTTAATAGGAGCAAAAGAATGTTGGGTCAACTTATAGGGACATTAGAG                         AAATTCAGAAAGGAAGACATGAAACTTTCAGGAACTGAGGCATTCATGCGT
genomic: TGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTATAGGGACATTAGAGgtatgtatct ... acttctccagAAATTCAGAAAGGAAGACATGAAACTTTCAGGAACTGAGGCATTCATGCGT
EST: gi|161714363|gb|FC063204.1|FC063204
EST:     TGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTATAGGGACATTAGAG                         AAATTCAGAAAGGAAGACATGAAACTTTCAGGAACTGAGGCATTCATGCGT
genomic: TGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTATAGGGACATTAGAGgtatgtatct ... acttctccagAAATTCAGAAAGGAAGACATGAAACTTTCAGGAACTGAGGCATTCATGCGT
EST: gi|110712516|gb|EE090229.1|EE090229
EST:     TGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTATAGGGACATTAGAG                         AAATTCAGAAAGGAAGACATGAAACTTTCAGGAACTGAGGCATTCATGCGT
genomic: TGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTATAGGGACATTAGAGgtatgtatct ... acttctccagAAATTCAGAAAGGAAGACATGAAACTTTCAGGAACTGAGGCATTCATGCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAACGAGGACCCGAGCTTGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTATAGGGACATTAGAGgtatgtatctataattacttgatctgcttttggttagttgtcaagttagggatattaatttcttagttcacctcattgtggaactaatatatactaccct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agggata