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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCATGTGCACATCAAGAGGCATTTGATGAAGGAATTGCCTGAAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtataccattgaaattgtcacagggttgtgttcttatgaaatatatgaagtttgcatgtttgaaacttaaaatatattttcagtgaataggaaagttt...

Basic information

species Vitis vinifera
transcript Vv08s0007g08110.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA19G32420.1 (Glycine max), 5'ss of exon 9
GTGCATGTGCACATCAAGAGGCATTTGATGAAGGAATTGCCTGAAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtataccattgaaattgtcacagggttgtgttcttatgaaatatatgaagtttgcatgtttgaaacttaaaatatattttcagtgaataggaaagttt---
|||||||| || |||||||||||||| |||||||||||||| ||||||||||| ||||  || ||||||||| ||||| ||||||| ||||||||| ||        || | |   |  ||| | || ||||    | |||    ||| |||    | | |   | ||   ||      |  |  |  | ||    
GTGCATGTTCATATCAAGAGGCATTTAATGAAGGAATTGCCAGAAACAGATGAGGCTGTTGCTCAATGGTGTCGAGATATATTTGTGGCCAAGgtgcatgttgaaagaacttttttactgttctattattatc---tctatttttttttcatcacaggatccacatattggttaatgtggtgtgagttaattgttt

upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA03G29600.1 (Glycine max), 5'ss of exon 9
GTGCATGTGCACATCAAGAGGCATTTGATGAAGGAATTGCCTGAAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtataccattgaaattgtcacagggttgtgttcttatgaaatatatgaagtttgcatgtttgaaacttaaaatatattttcagtgaataggaaagttt-
|||||||| || |||||||||||||||||||||||| |||| || |||||||| ||||  || ||||||||| ||||| ||||||| ||||||||| ||        || | |   |  ||| | || || |            ||   ||| || | || |     ||||  |  | |   | |     | | 
GTGCATGTTCATATCAAGAGGCATTTGATGAAGGAACTGCCAGATACAGATGAGGCTGTTGCTCAATGGTGTCGAGATATATTTGTGGCCAAGgtgcatgttgaaagaacttttttaccgttctattgtttttttcccctcactgtccacatattggtaaat-gtggtataaatataattgtttgttttttcta

upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA02G31320.1 (Glycine max), 5'ss of exon 9
GTGCATGTGCACATCAAGAGGCATTTGATGAAGGAATTGCCTGAAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtataccattgaaattgtcacagggttgtgttcttatgaaatatatgaagtttgcatgtttgaaacttaaaatatattttcagtgaat---aggaaagttt
||||||||||| || ||| |||||  ||||||||| ||||| |||  |||||| ||||  || ||||||||| ||||||| ||||| || ||||||| |   | |  ||  || |   ||||   |   ||| |  | |   |  ||| | | ||   | ||  | | ||| ||| |     |       | || |
GTGCATGTGCATATTAAGCGGCATGCGATGAAGGATTTGCCAGAAGAAGATGAAGCTGTTGCTCAATGGTGTCGAGATGTGTTTGTGGCTAAGgtgtgtgttaattgaaccgtaat--ggttac-tatgtattagctgtccaagattttcttattgctagctatataaataattttacaacgttcctactatgtct

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|83275962|gb|DV939970.1|DV939970
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAG                         GACGCCTTATTGGACGAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAG
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
EST: gi|110695893|gb|EE074430.1|EE074430
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAG                         GACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
EST: gi|110410507|gb|EC976190.1|EC976190
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAG                         GACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
EST: gi|110358248|gb|EC922324.1|EC922324
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTTTCGCCAAG                         GACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
EST: gi|110427310|gb|EC993745.1|EC993745
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAG                         GACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
EST: gi|30252653|gb|CB970204.1|CB970204
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAG                         GACGCCTTATTGGACGAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
EST: gi|110703094|gb|EE079637.1|EE079637
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAG                         GACGCGTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
EST: gi|110688154|gb|EE066378.1|EE066378
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAG                         GACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
EST: gi|110696827|gb|EE073281.1|EE073281
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAG                         GACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
EST: gi|110730631|gb|EE107931.1|EE107931
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAG                         GACGCGTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
EST: gi|83275755|gb|DV939763.1|DV939763
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAG                         GACGCCTTATTGGATGAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
EST: gi|110373043|gb|EC937250.1|EC937250
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAG                         GACGCCTTATTGGACGAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
EST: gi|110378825|gb|EC943977.1|EC943977
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAG                         GACGCCTTATTGGACGAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
EST: gi|110708022|gb|EE085087.1|EE085087
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAA                         GACGCGTTATTGGACAAACATAA
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAA
EST: gi|110388620|gb|EC953390.1|EC953390
EST:     AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAG                         GACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA
genomic: AAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtatacca ... aaccaaccagGACGCCTTATTGGACAAGCATAAGGTAGAAGACACATTTGGTGAAGGAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCATGTGCACATCAAGAGGCATTTGATGAAGGAATTGCCTGAAACAGATGATGCTGCAGCACAATGGTGTAGAGATGTATTTGTCGCCAAGgtgtataccattgaaattgtcacagggttgtgttcttatgaaatatatgaagtttgcatgtttgaaacttaaaatatattttcagtgaataggaaagttt

- - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaatata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaag