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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGGGCTTGGTTTGTATGGAGCTATTAACAGTCTGTACAATGTTGAGGGAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcatttccccttggtttcttgcatatgagacctgaaatccattaaattatttttgtctctgcttatatggttttttgggtaattgcttttagattt...

Basic information

species Vitis vinifera
transcript Vv19s0085g00730.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G30410.1 (Glycine max), 5'ss of exon 3
TGGTGGGCTTGGTTTGTATGGAGCTATTAACAGTCTGTACAATGTTGAGGGAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcatttccccttggtttcttgcatatgagacctgaaatccattaaattat----ttttgtctctgcttatatggttttttgggtaattgcttttagattt-
||||||  ||||||||||||  |||  ||||||||| ||||||||||| |||||||| || |||||||| || || ||  ||||||||||||| ||||||||| | || |            ||| | |||     ||  ||  | |  |||       ||||  | || || |  ||| || ||  | ||   ||| |||    
TGGTGGAATTGGTTTGTATGCTGCTGCTAACAGTCTCTACAATGTTGATGGAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatatgaagaaaaaaa-ttgaaaatgt--tttgctatttactgcattgcagtgctttggttatgattgt--ggtgttatgcttgatgtttttcagaagag

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA12G01850.1 (Glycine max), 5'ss of exon 1
TGGTGGGCTTGGTTTGTATGGAGCTATTAACAGTCTGTACAATGTTGAGGGAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgtt-ctcatttccccttggtttcttgcatatgagacctgaaatccattaaatta-tttttgtctctgcttatatggttttt--tgggtaattgcttttagattt--
||||||||||| | | ||||| |||   |||||  ||||||||||||||||||||||||| |||||||| || |||||  | || ||||||||||| ||||||  ||  ||  || ||  |  |   | ||||    |||  ||| |||| |||  ||    ||||  ||  ||  | |||  | |     ||   | | ||    
TGGTGGGCTTGTTGTTTATGGGGCTGCAAACAGCTTGTACAATGTTGAGGGAGGTCATCGAGCCATTGTCTTCAATCGTGTTGTCGGTGTCAAGGATAAGgttattccattgtccatgactgtt---aaatgaa---tgatttcctttaatttaacttgcaactctttttgcatcatctttagttgaagtctgtactcaaatgaaa

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 2
TGGTGGGCTTGGTTTGTATGGAGCTATTAACAGTCTGTACAATGTTGAGGGAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcatttccccttggtttcttgcatatgagacctgaaatccattaaatta---tttttgtctctgcttatatggttttttgggtaattgcttttagattt
||||||  ||||||| |||| ||||  ||||||||| ||||| ||||| |||||||| || |||||||| || || ||  ||||||||||||| ||||||||| | || |                  |   |   ||   |  | |  |||    |  |||    |  |||   |||| |    ||    |  |||      
TGGTGGAATTGGTTTATATGCAGCTGCTAACAGTCTCTACAACGTTGAAGGAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatatgaagaaaaaaaaaattgaaaacggtttgctgtttactgcattggagtgcttgatgattgttactcggttatgattgtggcagtctttgtg---

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA13G36940.1 (Glycine max), 5'ss of exon 2
-------TGGTGGGCTTGGTTTGTATGGAGCTATTAACAGTCTGTACAATGTTGAGGGAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcatttccccttggtttcttgcatatgagacctgaaatccattaaattatttttgtctctgcttatatggttttttgggtaattgcttttagattt----
       ||||||  |||||||||||| ||||  ||||||||| ||||||||||| |||||||| || |||||||| || ||        |||||||||| ||||||||| | || |            ||| | |||     ||  ||  | |  |||    |  |   ||  |   |  ||  ||  |    || | |||   ||    
GGATTGTTGGTGGAATTGGTTTGTATGCAGCTGCTAACAGTCTCTACAATGTTGAAGGAGGTCACCGAGCCATTGTTTTCAAC-------TTGGTGTCAAAGACAAGgttattatatgaagaaaaaaa-ttgaaaatgt--tttgctatttactgcattgcagtgcttgatgactgc-tacttggttatgattgtggtgttatgcttgatg

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA11G11670.2 (Glycine max), 5'ss of exon 2
TGGTGGGCTTGGTTTGTATGGAGCTATTAACAGTCTGTACAATGTTGAGGGAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcatttccccttggtttcttgcatatgagacctgaaatccattaaattatttttgtctctgcttatatggttttttgggtaattgcttttagattt
||||||||||| | | ||||| |||   |||||  ||||||||||||||||||||||||| |||||||| || |||||  | || |||||||| || |||||| |    |   |   |  | ||| ||    ||  |        | |    | ||    | |   ||  ||    ||| |   || |   | |  | | 
TGGTGGGCTTGTTGTATATGGGGCTGCAAACAGCTTGTACAATGTTGAGGGAGGTCATCGAGCCATTGTCTTCAATCGTGTTGTCGGTGTCAAAGATAAGgttattccattgtccatgactgttgaatgaatgatttttttaatgtaatgcaacttgcaacgccttttgcatcaactttagttgaagtctgtatgtactc

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G20530.2 (Arabidopsis thaliana), 5'ss of exon 3
TGGTGGGCTTGGTTTGTATGGAGCTATTAACAGTCTGTACAATGTTGAGGGAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcatttcc---ccttggtttct--tgcatatgagacctga-aatccattaaattatttttgtctctgcttatatggttttttgggtaattgcttttagattt
||| |||||  || | || || ||||   ||| ||| |||||||| || ||||||||||| |||||||| ||||| ||  | |||||| |||| |||||||||      | |     |||||||||  || || ||     ||| |||  ||    |  || |    |||   |  |      || || | |    |  |      
TGGGGGGCTCAGTCTTTACGGTGCTACGCACACTCTCTACAATGTCGATGGAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAGgttagtccctgcaaaaattggtttcttctgaatctgtatattgacaatgaatcttgtggttgtgacatctagctgaagttaggttaggcttagcattact------

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT4G28510.1 (Arabidopsis thaliana), 5'ss of exon 2
TGGTGGGCTTGGTTTGTATGGAGCTATTAACAGTCTGTACAATGTTGAGGGAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttc-tcatttccccttggtttcttgcatatgagacctgaaatccattaaat-tatttttgtctctgcttatatggttttttgggtaattgcttttagattt--
||||||||||||| | ||||| ||||   ||||||| ||||||||||| ||||| ||||| |||||  |||| |||||  |||| ||| | || || ||||||  ||| |    |||    |   |  | |  |   |    | || ||||| ||||||         || | | | | |||| |  |||    | | ||||  
TGGTGGGCTTGGTCTCTATGGTGCTACGCACAGTCTCTACAATGTTGAAGGAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagtgtttcttcaaattgggtctttttggatt----ttcagtaaatgtattttcccaatgagtttttttgctgtttgtgagatttggatgaaattttc

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S41_59V6.1 (Physcomitrella patens), 5'ss of exon 1
TGGTGGGCTTGGTTTGTATGGAGCTATTAACAGTCTGTACAATGTTGAGGGAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcatttccccttg-gtttcttgcatatgagacctgaaatccattaaattatttttgtctctgcttatatggttttttgg--gtaattgcttttagattt----------
 |||||  ||||  ||||||  ||  | |||    |||||||||| |||||||| || || |||||||||||||||||||| || ||||||||||| |||||       |      | ||   |||||| ||     |||        || ||   ||||| |  |  | |    |||   |   ||    | |||      |          
CGGTGGCATTGGGGTGTATGCTGCGGTCAACTCGTTGTACAATGTGGAGGGAGGGCACCGAGCCATTGTGTTTAATCGCATTGTAGGTGTCAAGGATAAGgtgagtgagtgagtgagtgtgaattgcat-tggtctttgatgagacggaatttggatttgttttagggtttggattttgacgatcgtggcggatttcgaggatggccttgcag

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|110733003|gb|EE108782.1|EE108782
EST:     GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAG                         GTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
genomic: GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcattt ... ggatatgcagGTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
EST: gi|71867260|gb|DT016315.1|DT016315
EST:     AGGTCATCGGGCCATTGTGTTTTAATCGCATAGTTGGTGTCAAGGACAAG                         GTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
genomic: AGGTCATCGGGCCATTGTG-TTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcattt ... ggatatgcagGTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
EST: gi|71870697|gb|DT019752.1|DT019752
EST:     GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAG                         GTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
genomic: GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcattt ... ggatatgcagGTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
EST: gi|110688172|gb|EE066420.1|EE066420
EST:     GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAG                         GTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
genomic: GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcattt ... ggatatgcagGTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
EST: gi|77588331|gb|DV223379.1|DV223379
EST:     GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAG                         GTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
genomic: GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcattt ... ggatatgcagGTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
EST: gi|110687081|gb|EE064178.1|EE064178
EST:     GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAG                         GTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
genomic: GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcattt ... ggatatgcagGTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
EST: gi|110731197|gb|EE109145.1|EE109145
EST:     GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAG                         GTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
genomic: GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcattt ... ggatatgcagGTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
EST: gi|161716392|gb|FC068402.1|FC068402
EST:     GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAG                         GTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
genomic: GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcattt ... ggatatgcagGTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
EST: gi|110708369|gb|EE085834.1|EE085834
EST:     GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAG                         GTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC
genomic: GAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcattt ... ggatatgcagGTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGGGCTTGGTTTGTATGGAGCTATTAACAGTCTGTACAATGTTGAGGGAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcatttccccttggtttcttgcatatgagacctgaaatccattaaattatttttgtctctgcttatatggttttttgggtaattgcttttagattt

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