Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattttctgacag

Basic information

species Vitis vinifera
transcript Vv09s0002g00150.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: LOC_Os10g25090.1 (Oryza sativa), 5'ss of exon 14
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattttctgacag
|||| |||| |||| | || || ||||| || |||||||||||||| || ||||| || ||||||||||||||  |  | || || ||||||||||| |||||    | ||   || ||     | || |   |  |||   | |    |      | |   |  |||  |   | |    ||    || ||| || ||| ||  | |  |  |||
CTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctatttttct-ctgattctgca-tccctgaattgtttatgcctacatttgatgattcctaatt-tcttagtcctgaccc--ctgactgttgtgtcaaactatcgtctcag

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 14
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattttctgacag
| ||||| | |||| | ||||| || || |||||||| ||||| ||||| ||||| ||||||||||| |||||| |  | ||||| | ||| || |||||||||     |||  || ||   ||  |  | |     || |   ||  | | |   |   |  |    |  ||   |    || | | ||   ||  |||  || ||   | ||||
CAGAGGTGGACATGACTGGTCAGTACACACTGAAGAGCGATGTCTACAGCTTTGGAGTAGTCATGCTAGAGCTTTTGACGGGACGCAGACCTTTCGATAGgtaac----ttgatcttctcatcagtcg-taaccagtttccagcttgcgcataactataaatttagtgctaactgatga--acctcggta-taatcgtgt-gactttgcattacag

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: LOC_Os03g27990.1 (Oryza sativa), 5'ss of exon 14
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaa---tgttgcac-tactagccatccaat-gattccatt----accttttttgaagagaaaaggacctgaatcataccattttctac----ttagctaactattatgttaacattttctgacag
| |||||  ||||||| || || ||  |||  ||||||||||| ||||||||||| || |||||||| ||||| ||  ||||  | ||| ||||||| |||| ||||    | ||  | ||| | |  | || | || || |      |  |  | ||||  ||         |||    |  | |   |||      ||  ||| ||| |  |   |   | |  |||
CCGAGGTGACCATGTCTGGACAGTACTCTCAAAAGAGTGATGTGTACAGTTTTGGAGTCGTCATGCTAGAGCTCCTGACTGGCAGGAAAGCATTTGACAGgtgaaaagtcagctgtccataccaacatttcacttgaatctacactcaaattcctctgaaatgactgaattgagaagacaatgagtccttacagtaacagaaaacaattgttgtctgaaactattgcag

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM2G330907_T01 (Zea mays), 5'ss of exon 14
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattttctgacag
| || || | |||| | ||||| || || || ||||||||||||||||| ||||| || |||||||| ||||| ||  | ||||||| ||||||||| |||||         |||| | | |||||   |  ||    | ||||||| |     ||   |  ||  || ||   || | | |    || |    || |  | |||           
CAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTTTACAGCTTTGGAGTTGTCATGCTTGAGCTACTGACAGGACGTAGACCATTTGACAGgta---------cact-ccaaccatctgttt-ttaagcttcctttttagttataaatttggtcttgatgatcagatatgccatcatgccactgtttttcatcacag----------

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM2G004572_T01 (Zea mays), 5'ss of exon 14
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattttctgacag
||||||| |  ||||| ||||| ||||| || ||||||||||| ||||| ||||| || ||||||||||| ||  |  | || |||||||||||||| |||||    | |  ||  |||||  || | |  | | | |||      |||            ||        | |  ||| |  | | || ||||| || | |  |  || |  |||
CTGAGGTCGAGATGTCCGGTCAGTATACCCTCAAGAGTGATGTCTACAGCTTTGGGGTCGTCATGCTGGAACTCTTGACAGGCCGTAAACCATTTGACAGgtatgcctat--catcactag--atgccagcactgcgttaaacccattg------------ccca---tgcagcggtttttggtgacctgactatgatttcacaacattatcgcag

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA07G05230.1 (Glycine max), 5'ss of exon 14
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaa--tgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattttctgacag
| || |||| | |||| ||||| |||||||| |||||||||||||| || ||||| || |||||| |||| ||||||  |||||| |||||||||||||||| |||   || |  ||   ||   | |  || |     |||| |||    |   | | |     | || ||||  | |    || |  || | | |||         ||  | |   
CCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagattgatatacctttaagtaac--ataacagttttactttt----acatgtacacactttcaaacata--aatgggcacatgcctgattgttaaaacgttccttcttcag--

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA16G01790.1 (Glycine max), 5'ss of exon 14
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattt-tctgacag
| || ||||   |||| ||||| |||||||| |||||||||||||| || || || || |||||| |||| ||||||  |||||| ||||| |||||||||||| | || |  ||   ||   | |  || |     |||| |||    |   | | |     | || |||   | |    || |   | | | |||    ||| ||  |   ||||
CCGAAGTTGGTTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTCGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCGTTTGATAGgtaagattgatatacctttaagtagc--ataacagttttactttt----acatgtacacactttcaaacat--taatgggcacatgcatgattgttaa---aacgttccttctacag

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA03G42360.1 (Glycine max), 5'ss of exon 16
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaa--aatg-ttgcactactagcc--atccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattttctgacag
|||| |||||| |||| ||||| |||||| |||| |||||||| ||||| ||||| || |||||| |||| |||||    ||||| |||||||||||||||| ||  |||| ||    |  | | |   ||  | | ||        | || || ||| |     |        |||  ||  | |  |   || | |   |    |||||| | | ||||
CTGAAGTTGCCTTGTCTGGTCAGTATACTTTGAAAAGTGATGTCTACAGCTTTGGAGTTGTCATGTTGGAACTTCTCAGCGGACGGAAACCATTTGATAGgtgaattaatggttttttttttggtctgctctcacgtttttgagcaatattctgcagaaattgaaattatgtagatataataatgttgtctcctgattgcga----aacattctgtaacag

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: AT3G14350.3 (Arabidopsis thaliana), 5'ss of exon 15
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactatta-tgttaacattttctgacag
| ||   | | |||||||| |||||  || ||||||| ||||||||||||||||| ||||| ||||| |||||| |  | ||| | |||||||| || |||||            ||| | ||||        ||| |  ||||  |  || |    | ||        |     ||    | | |  ||| |  |  || |     | | ||||||
CAGAAACTTCAATGTCAGGCCAATACTCTTTGAAGAGCGATGTTTACAGTTTTGGAGTAGTGATGCTCGAGCTTTTAACCGGAAGAAAACCATTCGACAGgtac--------ttttacaatccata-------tccctcgccttcctaaaaaaacttaagagtgatgcaaatgtgttcagaattgaagtaagtcctggtgattgttgtgtgtgacag

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: AT1G53730.1 (Arabidopsis thaliana), 5'ss of exon 14
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattttctgacag
|||| ||  | |||||||| |||||| || ||||||||||  ||||||||||||| ||||| ||||| || ||| |  ||||  | ||||||||||| |||||||     |  | ||  | |||  | | | ||    ||  |  ||    |||||| |    |   |   |  || ||  |     ||   ||| || | | ||           
CTGAAGTATCAATGTCAGGCCAATATTCTTTGAAGAGTGACATTTACAGTTTTGGAGTAGTGATGCTTGAACTTTTAACTGGGAGAAAACCATTTGACAGgtaaa----ctctattatgatccaaactaggcttgatgtatgtagtt----gagaaatgtgtttctgtttga--atcttaca----actggttataatttgagcag----------

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: AT1G53730.2 (Arabidopsis thaliana), 5'ss of exon 14
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattttctgacag
|||| ||  | |||||||| |||||| || ||||||||||  ||||||||||||| ||||| ||||| || ||| |  ||||  | ||||||||||| |||||||     |  | ||  | |||  | | | ||    ||  |  ||    |||||| |    |   |   |  || ||  |  | | ||    ||  |                 
CTGAAGTATCAATGTCAGGCCAATATTCTTTGAAGAGTGACATTTACAGTTTTGGAGTAGTGATGCTTGAACTTTTAACTGGGAGAAAACCATTTGACAGgtaaa----ctctattatgatccaaactaggcttgatgtatgtagtt----gagaaatgtgtttctgtttga--atcttacaactggttataatttgag-----------------

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|110375773|gb|EC940790.1|EC940790
EST:     TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAG                         CTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
genomic: TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgt ... tttctgacagCTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
EST: gi|110701239|gb|EE078596.1|EE078596
EST:     TTTGGTGTAGTCATGCTGGAACTTCTTTCTGGACGTAAACCATTTGATAG                         CTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCANCT
genomic: TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgt ... tttctgacagCTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
EST: gi|349830454|gb|FQ416752.1|FQ416752
EST:     TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAG                         CTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
genomic: TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgt ... tttctgacagCTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
EST: gi|110391079|gb|EC956033.1|EC956033
EST:     TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAG                         CTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
genomic: TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgt ... tttctgacagCTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
EST: gi|110363514|gb|EC927108.1|EC927108
EST:     TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAG                         CTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGG
genomic: TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgt ... tttctgacagCTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGG
EST: gi|110360391|gb|EC923453.1|EC923453
EST:     TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTG--A-                         -T--AGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
genomic: TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgt ... tttctgacagCTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
EST: gi|110379506|gb|EC944705.1|EC944705
EST:     TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAG                         CTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
genomic: TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgt ... tttctgacagCTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
EST: gi|30321691|gb|CD004953.1|CD004953
EST:     TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAG                         CTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
genomic: TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgt ... tttctgacagCTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
EST: gi|34319519|gb|CF372273.1|CF372273
EST:     TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAACCCATTTGATAG                         CTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
genomic: TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgt ... tttctgacagCTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCT
EST: gi|27579137|gb|CB001832.1|CB001832
EST:     TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAG                         CTCCAGGTCCAGATCTGAGCAATCTTTG
genomic: TTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgt ... tttctgacagCTCCAGGTCCAGATCTGAGCAATCTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattttctgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT