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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGCTAAGTGATCGTTTTCCTCAGCCTTATGCAAATGAACAAGCAGCTAGATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattttgttatagatcccttgatagaagtgaatggctgtccacccctacaataactgactctttgtcctctcag

Basic information

species Vitis vinifera
transcript Vv09s0002g05950.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G158479_T04 (Zea mays), 5'ss of exon 4
AAAGCTAAGTGATCGTTTTCCTCAGCCTTATGCAAATGAACAAGCAGCTAGATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattttgttatagatcccttgatagaagtgaatggctgtccacccctaca-ataactgactctttgtcctctcag-------
 || || || ||||| || || |||||||||||||| || ||||||||  | ||||||||||| || ||||| ||||| || || ||||||||||| |||||| |     |       ||   |||  ||   |   | |   ||  ||  | |  ||  || ||| ||     |   |        
TAAACTGAGCGATCGCTTCCCACAGCCTTATGCAAACGAGCAAGCAGCCCGGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaat-----tacagctaattttttg-cagtgatctgttgtgatcttccattgcgtatggcttactgttcacaatgcaatcattcag

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G032367_T01 (Zea mays), 5'ss of exon 4
AAAGCTAAGTGATCGTTTTCCTCAGCCTTATGCAAATGAACAAGCAGCTAGATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattttgttatagatcccttgatagaagtgaatggctgtccacccctacaataactgactctttgtcct---ctcag----
 || || || ||||| ||||| ||||||||||||||||| ||||||||  ||||||||||||| || || || || || || || ||||| ||||| |||||| |  |   ||||  | |       |         ||||  | |||    |  ||  || ||| ||||   |    |||     
TAAACTCAGCGATCGCTTTCCACAGCCTTATGCAAATGAGCAAGCAGCCCGATTTGCTAATGGTGGCGCCTACCCGCCGGACCTTAGTCTTATCACAAAGgtaat--tgcagttaatggtgttgcattgctttgatgtggcctttcactg--attatggcttactgtttgcattgcattcatccag

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G06700.1 (Glycine max), 5'ss of exon 5
AAAGCTAAGTGATCGTTTTCCTCAGCCTTATGCAAATGAACAAGCAGCTAGATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgta---ttaattttgttatagatcccttgatagaagtg---aatggctgtccacccctacaataactgactctttgtcctctcag
 || || |||||||||||||||||||| ||||||||||||  ||| ||||| ||||||||||||||||| ||||||||||||||||||||  | ||||| |||    ||||| | | ||||     |   | ||| |    ||||  |||| |||  |  ||||  |  |  | ||   | ||||
TAAACTCAGTGATCGTTTTCCTCAGCCATATGCAAATGAAGCAGCTGCTAGGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgctaattatttgatagtaatgtctttggaattttctaatgtatgtctacc--tgaaatatatatccttgtgatttttcag

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA19G24620.2 (Glycine max), 5'ss of exon 4
AAAGCTAAGTGATCGTTTTCCTCAGCCTTATGCAAATGAACAAGCAGCTAGATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgta---ttaattttgttatag--at-cccttgatagaagtgaatggctgtccacccctacaataactgactctttgtcctctcag
 || || || ||||||||||||||||| ||||||||||||  ||| ||||| ||||||||||||||||| |||||||||||||||||||| || ||||| |||    ||||| | | ||||  ||  | |||| |      ||||  |||| |||   | ||||  |  |  ||||   | ||||
TAAACTCAGCGATCGTTTTCCTCAGCCATATGCAAATGAAGCAGCTGCTAGGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTATTACCAAAgtaatgctaattatttgatagtaatatctttgaaattttctaatgtatgtctacctgaa-aatatatatccttttgatttttcag

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA05G07020.1 (Glycine max), 5'ss of exon 4
AAAGCTAAGTGATCGTTTTCCTCAGCCTTATGCAAATGAACAAGCAGCTAGATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattttgtta---tagatcccttgatagaagtgaatggctgtccacccctacaataactgactctttgtcctctcag
 || || |||||||| ||||| ||||| ||||||||||||  ||||||||| ||||||||||||||||| ||||||||||||||||||||  | ||||| ||| | | | |  |    |||   | |   ||||  |   |     |  |   |   ||||| |    | ||    | ||||
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgagtgtagtctgctagtaacgtctttagattttcttttgcttttatatcataaataattttacccttaatgtttcag

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 4
AAAGCTAAGTGATCGTTTTCCTCAGCCTTATGCAAATGAACAAGCAGCTAGATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattttgtta---tagatcccttgatagaagtga-atggctgtccacccctacaataactgactctttgtcctctcag
 || || |||||||| ||||| ||||| ||||||||||||  ||||||||| ||||||||||||||||| ||||||||||||||||||||  | ||||| ||| | | | |  |    |||     ||  ||||  |   || ||| |  |   |   ||||| |    | ||    | ||||
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactgtagtctgctagtaatgtttttagattttctattgct-tttatatcggaaataattttacccttaatatttcag

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 4
AAAGCTAAGTGATCGTTTTCCTCAGCCTTATGCAAATGAACAAGCAGCTAGATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtat--taattttgttatagatcccttga----tagaagtgaatggctgtcc-acccctacaataactg-actctttgtcctctcag
 || || ||||| || ||||||||||| ||||||||||||  ||| || || ||||||||||| ||||| |||||||| ||||||||||| || || ||||| |  |  |  |  | ||  |    |||      | ||  ||    |||        |  ||||  |  | | ||   |||  |||
TAAACTCAGTGACCGGTTTCCTCAGCCATATGCAAATGAATCAGCTGCAAGGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgctgctactttactttaactgaacatctgtagcaaacttgtgttttgtgttttaaatagttttaatgttctgccttccag

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|110377968|gb|EC943074.1|EC943074
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|30321061|gb|CD004323.1|CD004323
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|110698992|gb|EE077122.1|EE077122
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|34550509|gb|CF518727.1|CF518727
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|349813644|gb|FQ413878.1|FQ413878
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|351028222|gb|FQ426123.1|FQ426123
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACCATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|110429073|gb|EC995560.1|EC995560
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGT
EST: gi|110428516|gb|EC994990.1|EC994990
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|34547391|gb|CF515623.1|CF515623
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|34550428|gb|CF518646.1|CF518646
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|351033244|gb|FQ462016.1|FQ462016
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|34547301|gb|CF515533.1|CF515533
EST:     ATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCGATC                         G-ACGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCG
genomic: ATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACC-AAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCG
EST: gi|30320467|gb|CD003729.1|CD003729
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATGTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|18458621|gb|BM436899.1|BM436899
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTT
EST: gi|349808524|gb|FQ405668.1|FQ405668
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|110417035|gb|EC983057.1|EC983057
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|351017876|gb|FQ436229.1|FQ436229
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|110378867|gb|EC944022.1|EC944022
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
EST: gi|349809896|gb|FQ398521.1|FQ398521
EST:     GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAG                         GCCCGCCGCAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT
genomic: GATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattt ... gtcctctcagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGCTAAGTGATCGTTTTCCTCAGCCTTATGCAAATGAACAAGCAGCTAGATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattttgttatagatcccttgatagaagtgaatggctgtccacccctacaataactgactctttgtcctctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA