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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTGAAGCTAAACAAGTGGCTGCACAAGAGGCTGAAAGGGCCAAATTTGTTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaataaaaaacggtccatccatgccctaggaaatgcagatctttgtttccatttaagctgctgcagtgttgttctgaactaggattttctaccat...

Basic information

species Vitis vinifera
transcript Vv19s0085g00730.t01
intron # 6
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 6
lower sequence: LOC_Os07g15880.1 (Oryza sativa), 5'ss of exon 4
TATTGAAGCTAAACAAGTGGCTGCACAAGAGGCTGAAAGGGCCAAATTTGTTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaataa-----aaaacggtccatccatgcccta----ggaaatgcagatctttgtttc----catttaa-gctgctgcagtgttgttctgaactaggattttctaccat--------------------------
||||||||| ||||| || ||||||||||| |||||  | || || ||  |||| || |||||||||||||||||||||||||| |||||||| |||||||| ||||||       | | |  |      ||| | |     ||| || ||| |      | |     || ||| | |  |||  |    |    |  ||  ||| |||   |                           
TATTGAAGCCAAACAGGTTGCTGCACAAGAAGCTGAGCGTGCTAAGTTCATTGTTGAGAAAGCTGAGCAAGACAAGAGGAGTGCGATTATCAGGGCACAGgtaagaaatctgttttatagccattgcctgatgtcatgtgccggagatacagtttgacagtacatattatataatggttttgccattgcatgtctagttaacattgtctcttaaacatggcctttctcttctttcaacag

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 5'ss of exon 4
TATTGAAGCTAAACAAGTGGCTGCACAAGAGGCTGAAAGGGCCAAATTTGTTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgag-aaataaaaaacggtccatccatgccctaggaaatgcagatctttgtttccatttaagctgctgcagtgttgttctgaactaggattttctaccat-----------------------------------------------------------------------------------------
 |||||||| || || || ||||||||||| |||||  | || || ||  |||| || || ||||| ||||||||||||||||| || |||||||||||||| || ||| |   || ||   ||   ||   |||         | | |  |      | |   | || |  ||| ||| |         | ||    |||                                                                                         
AATTGAAGCCAAGCAGGTTGCTGCACAAGAAGCTGAGCGTGCAAAGTTCATTGTTGAGAAGGCTGAACAAGACAAGAGGAGTGCGATCATCAGAGCACAGgtaagcaaagatgcaatggattatttctggtttagatggctttcaccatattccttgataagtttactacc-tgtagttttagtgacaattgttaagacatatcaatggcactgtttatttcttcattgtttcatatatttcatttttgttggtgtgggttgagtctgactgtgaggcctgcttgaacag

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os03g60000.1 (Oryza sativa), 5'ss of exon 4
------------------------------------------------------------------------------------TATTGAAGCTAAACAAGTGGCTGCACAAGAGGCTGAAAGGGCCAAA-TTTGTTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaataaaaaacggtccatccatgccctaggaaatgcagatctttgtttccatttaagctgctgcagtgttgttctgaactaggattttctaccat
                                                                                     |||||||| || || || ||||||||||| |||||  | || ||| ||  |||| || || ||||| ||||||||||||||||| || |||||||||||||| || ||  |   |                                                                                     
GACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAGAGTTCACCCATGCAATTGAAGCCAAGCAGgttgctgcacaagaagctgagcgtgcaaaagttcattgttgagaaggctgaacaagacaagaggagtgcgatcatcagagcacaggtaagcaaagatgca-------------------------------------------------------------------------------------

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 5
TATTGAAGCTAAACAAGTGGCTGCACAAGAGGCTGAAAGGGCCAAATTTGTTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaataaaaaacggtccatccatgccctaggaaatgcagatctttgtttccatttaagctgctgcagtgttgttctgaactaggattttctaccat-----
 ||||||||||| || || ||||||||||| ||||| ||||| ||||||||||||||||||||||||||||||||||| |||||| | || |||||||||||||  |  ||  |    | |||  ||||   ||  ||  | | |  ||  | | | ||   ||||     |    ||   ||    | || | ||  |      
AATTGAAGCTAAGCAGGTAGCTGCACAAGAAGCTGAGAGGGCTAAATTTGTTGTGGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgatgataaattattaatgcatagatgc---agttaacactggtgcttagtacaagttt--ctgcaaattttacatttccaatacagtttgtgtattaaggaaa

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA09G30410.1 (Glycine max), 5'ss of exon 6
TATTGAAGCTAAACAAGTGGCTGCACAAGAGGCTGAAAGGGCCAAATTTGTTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaataaaaaacggtccatccatgccctaggaaatgcagatctttgtttccatttaagctgctgcagtgttgttctgaactaggattttctaccat---
 |||||||| || || || ||||||||||| ||||| ||||| ||||||||||| ||||||||||||||||||||||| |||||| | ||||||||||||||||  |  ||       | |||  ||||  |    | ||  |  ||| ||     |||   |||||    |  | ||   ||    |  | | ||  |    
AATTGAAGCAAAGCAGGTAGCTGCACAAGAAGCTGAGAGGGCTAAATTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAGgtgatgataaatttttaatgcatagatgcagttaacactgtggtgcttagtacaagttt---ctgctaattttatatttccaatacagcatgtgtattaagga

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA13G36940.1 (Glycine max), 5'ss of exon 5
TATTGAAGCTAAACAAGTGGCTGCACAAGAGGCTGAAAGGGCCAAATTTGTTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaataaaaaacggtccatccatgccctaggaaatgcagatctttgtttccatttaagctgctgcagtgttgttctgaactaggattttctaccat---
 |||||||| || || || ||||||||||| ||||| ||||| ||||||||||| ||||||||||||||||||||||| |||||| | || |||||||||||||  |  ||       | |||  ||||  |    | ||  |  ||| ||     |||   || ||    |  | ||   ||    |  | | ||  |    
AATTGAAGCAAAGCAGGTAGCTGCACAAGAAGCTGACAGGGCTAAATTTGTTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgacgataaatttttaatgcatagatgcagttaacactgtggtgcttagtacaagttt---cttctaattttatatttccaatacagtatgtgtattaagga

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA11G11670.2 (Glycine max), 5'ss of exon 5
TATTGAAGCTAAACAAGTGGCTGCACAAGAGGCTGAAAGGGCCAAATTTGTTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaataaaaaacggtccatccatgccctaggaaatgcagatctttgtttccatttaagctgctgcagtg-ttgttctgaactaggattttctaccat------
||||||||| || ||||| ||||| ||||| ||||| ||||| ||||||||||| ||||||||||| |||||||| || |||||| |||| ||||| ||||| | ||     |   |  ||||   | |  |    |       ||||  | |   |  ||   ||| |  |  || || | |  |  || || ||||||       
TATTGAAGCCAAGCAAGTTGCTGCTCAAGAAGCTGAGAGGGCTAAATTTGTTGTAGAAAAAGCTGAACAAGACAAAAGAAGTGCTGTTATTAGAGCTCAGgtaaaaat----agttgtcccatttttacatttaagaggat---tcttaatatttctacaactggctaccatactttttattatttctgaattgctaccaagccatg

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G01850.1 (Glycine max), 5'ss of exon 4
TATTGAAGCTAAACAAGTGGCTGCACAAGAGGCTGAAAGGGCCAAATTTGTTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaataaaaaacggtccatccatgccctaggaaatgcagatctttgtttccatttaagctg--ctgcagtgttgttctgaactaggattttctaccat-
||||||||| || || || ||||| ||||| ||||| || || ||||||||||| ||||||||||| ||||||||    |||||| |||| ||||| ||||| | |||||     |   |  |  |      ||   || |  |   ||  | | | |     ||  || |  |  | || | |  |  || || ||||||  
TATTGAAGCCAAGCAGGTTGCTGCTCAAGAAGCTGAGAGAGCTAAATTTGTTGTAGAAAAAGCTGAACAAGACAAACAAAGTGCTGTTATTAGAGCTCAGgtaa-aaatagttgtc--ccattttacatttaagatgattcttaatatttctacaagtggctatgggctaccatacttttattatttctgaattgctaccaaa

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S144_113V6.1 (Physcomitrella patens), 5'ss of exon 2
TATTGAAGCTAAACAAGTGGCTGCACAAGAGGCTGAAAGGGCCAAATTTGTTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtg----agaaataaaaaacggtccatccatgccctagga---------aatgcagatctttgtttcc----atttaagctgctgcagt---gttgttctgaactaggattttctaccat----------------------------------------------
| | ||||| || ||||| ||||| ||||||||||| || ||||| ||||| ||||| |||||||| ||||||||  | |||||||||||  | || ||||||    ||  ||    |  | | ||   |||     |           |||| ||||  | ||   |      ||  | || ||   |   |||  |||    | | ||    || | |                                              
TTTCGAAGCCAAGCAAGTTGCTGCTCAAGAGGCTGAGAGTGCCAAGTTTGTAGTGGAGAAAGCTGAACAAGACAAACGAAGTGCTATTATTCGTGCTCAGgtgctttagccatttgtattgtttcagttatgtttctgaggtagtttttaatggagattatcgtcctccgaagcttttgatgttggcatttggtttctcttcttttgaatagagtagcgtcattaattgtgaaaggtttttaagtttcttttgttgtatatctcag

upper sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S14_33V6.1 (Physcomitrella patens), 5'ss of exon 4
TATTGAAGCTAAACAAGTGGCTGCACAAGAGGCTGAAAGGGCCAAATTTGTTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaataaaaaacggtccatccatgccctaggaaatgcagatctttgtttccattt---aagctgctgcag-tgttgttctgaactagg-attttctaccat------------------------------------------------
 ||||||||||| ||||| ||||| || || ||||| ||||| |||||||| ||||| || || ||||| ||||| |||||||| |||||  | || ||||||    ||    |    | | |   | |  |  |  ||  | |  || |       ||   |||  ||||  | ||||| | |  | |  | |      |||||                                                
AATTGAAGCTAAGCAAGTTGCTGCCCAGGACGCTGAGAGGGCTAAATTTGTGGTGGAGAAGGCAGAGCAGGACAAAAGGAGTGCAATTATTCGTGCTCAGgtgctttatcttgactcttgcttgatttctttcagctatttacagtttgggaaggggtttgtaagaggctgtggatgttggtgttcattccgcaaggaagaccattgccaagtttggtcggatagtgaaatttcctttttttgtgtactccag

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|110360428|gb|EC923520.1|EC923520
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|110377275|gb|EC942338.1|EC942338
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|110417983|gb|EC984089.1|EC984089
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAG                         GGTGAGGCCAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|110696854|gb|EE073329.1|EE073329
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|32458718|gb|CD799892.1|CD799892
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|30126574|gb|CB911913.1|CB911913
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|110379537|gb|EC944738.1|EC944738
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|110688172|gb|EE066420.1|EE066420
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAAAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACA
EST: gi|161712704|gb|FC062276.1|FC062276
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|77581519|gb|DV219712.1|DV219712
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|110687081|gb|EE064178.1|EE064178
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCC
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCC
EST: gi|110708369|gb|EE085834.1|EE085834
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAAAGCACAG                         GGTGAAGCTAAAAGTGCC
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCC
EST: gi|71866994|gb|DT016049.1|DT016049
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTGAAGCTAAACAAGTGGCTGCACAAGAGGCTGAAAGGGCCAAATTTGTTGTGGAAAAAGCTGAGCAAGACAAGAGGAGTGCTATTATCAGAGCACAGgtgagaaataaaaaacggtccatccatgccctaggaaatgcagatctttgtttccatttaagctgctgcagtgttgttctgaactaggattttctaccat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaat