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

gtgtttatcttatatgctagtatatgtgtgtatttgaactttacttgtttgtaattctgatagatctttggttattgataatctgtttttataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAGTTAGAGAAGAGGAAGAGTGAGGGCACATACAAATACAAAGGTCACTTTA

Basic information

species Vitis vinifera
transcript Vv10s0116g00360.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 10
gtgtttatcttatatgctagtatatgtgtgtatttgaactttacttgtttg--taattctgatagatctttggttattgataatctgtttttataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAGTTAGAGAAGAGGAAGAGTGAGGGCACATAC------AAATACAAAGGTCACTTTA
    | | |   |||  |  |   |  |   |  |||  |||   ||      |  |  |  ||  ||  |   |  || |      ||||| |   ||||||||||||||| ||||||||||||||||||||    |||||||| || || || |||||||| ||   |||||| |  |||       | | || ||| |      
---gtaaacagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaagtccctaactggtgttggaa-atttttgt-ttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCC------

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 3
---------gtgtttatcttatatgctagtatatgtgtg-tatttgaactttacttgtttgtaattctgatagatctttggttattgataatctgtttttataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAGTTAGAGAAGAGGAAGAGTGAGGGCACATACAAATACAAAGGTCACTTTA-
         | |  |||  | ||   |  |   | | |  ||   | | | |   || | | ||   |   ||    || |  || | | |   || ||  |   ||||||||||||||| ||||| ||||||||||||||    ||||| ||||| ||  | |||||||| ||   |||||| | ||||   | || |  |||    | 
gtaaagactgggaatattgtttaactttcttggtctcttctaacaggattctttctgct-gaaaggataccagtaacttagacat-gctcactagtcttgttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAAGCTGAGGGGAGATACTC-TGCACATTTCAGAGGAC

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 10
gtgtttatcttatatgctagtatatgtgtgtatttgaactttacttgtttgt--aattctgatagat-ctttggttattgataatctgtttttataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAGTTAGAGAAGAGGAAGAGTGAGGGCACATACAAATACAAAGGTCACTTTA
|||  ||   |   |  |    ||| |   |   |  | ||  ||  | | |  ||||   || |   | |  |||| |  |   |||| ||   |  ||||||||| || ||||||||||||||||||||||| |||||||||||||| ||||| |||||||| |||   || |||| |||||||  | ||  | |     
gtgcctaatgttgttattgtgctatcttgctgggttgatttggctcctctatccaatttaaatcggcacctatgttaatcttg-cctgtattcccat-ttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAAGAAGGCAAATACAAAGGCGAATTTAAAGGGC

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 10
gtgtttatcttat-atgctagtatatgtg-tgtatttgaactttacttgtt-tgtaattctgatagatctttggttattgataatctgtttttataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAGTTAGAGAAGAGGAAGAGTGAGGGCACATACAAATACAAAGGTCACTTTA-
||| |||   ||| ||  |  ||||  || ||| |||  |  || | |||  || ||||    ||   ||     | ||| || | | |||  ||   ||||||||| || ||||||||||||||||||||||| |||||||||||||| ||||| |||||||| |||    |||||||||| |||   |    | |      
gtgcttaatgtattatagttctatacttgctgtgttt--atcttgcctgtaatgcaatttgactaagcctcaa--tgttggta-tatatttccat---ttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCACATATAAAGG-AGGATTTAGGGGGC

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 8
gtgtttatcttatatgctagtatatgtgtgtatttgaactttacttgtt-tgtaattctgatagatctttggttattgataatctgtttttataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAGTTAGAGAAGAGGAAGAGTGAGGGCACATACAAATACAAAGGTCACTTTA
||| |||   | |||  ||||       | || || | |||  | |||  || ||||    ||   ||     | ||| || | | |||  ||   ||||||||| || ||||||||||||||||||||||| |||||||||||||| ||||| |||||||| |||    ||||| |||| |||  |  |  |       
gtgcttaa--tgtattatagtgc-----tatactttatcttgccctgtaatgcaatttgactaagcctcaa--tgttggta-tatatttccat---ttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCTCATATAAAGGCGGATTTAGGGGGC

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 10
gtgttta-tcttat-atgctagtatatgtgtgtatttgaactttacttgtttgta-attctgatagatctttggttattgataat-ctgtttttataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAGTTAGAGAAGAGGAAGAGTGAGGGCACATACAAATACAAAGGTCACTTTA
|||  || | || | ||  |  ||| |   ||| |||  | ||  ||  | | |  | | |||     |     |  || ||  | ||  | ||     ||||||||| || ||||||||||||||||||||||| |||||||||||||| ||||| |||||||| |||   || |||| ||||||   | ||  | |     
gtgcctaatgttgttatagtgctatcttgctgtgttt--atttggctcctctatccaatttgaagcggcaccaat-gttaatcttgcttgtattgccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAAGAAGGCAAATACAATGGCGAATTTAAAGGGC

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 10
----gtgtttatcttatat--gctagtatatgtgtgtatttgaactttacttgtttgtaattctga--tagatctttggttattgataatct------gtttttataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAGTTAGAGAAGAGGAAGAGTGAGGGCACATACAAATACAAAGGTCACTTTA-
    |  | ||||    |    ||  |  |      |       ||  |       | ||    ||  |  |    || |||||   || ||      |  |||   | | ||||||| |||||||| |||||||||||| | || |||||||||||||||||| ||||||| | |||||  ||||| |||||  ||  | | | |||      
gtctgcttctatccaccactaactgattcaaacaaattaaaaggctaaaacctcaagcaaactcgaactgaaaacctgtttattttgaacctttatatgaattttctcttcagGTTGCTAAAATAGAGACAGAGAAAATGTTGATTCAAATGGTTGAAACCGAGCTAGAGAAAAAGAAGACAGAGGGTACATATGAACGCGA-GTTCATGGGGA

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|161710861|gb|FC058565.1|FC058565
EST:     CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAG                         GTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACC
genomic: CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAGgtgtttatct ... tataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACC
EST: gi|87583926|gb|DY473286.1|DY473286
EST:     CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAG                         GTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
genomic: CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAGgtgtttatct ... tataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
EST: gi|161717766|gb|FC066590.1|FC066590
EST:     CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAG                         GTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
genomic: CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAGgtgtttatct ... tataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
EST: gi|110699977|gb|EE077493.1|EE077493
EST:     CAATTCAAGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAG                         GTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
genomic: CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAGgtgtttatct ... tataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
EST: gi|110730531|gb|EE107719.1|EE107719
EST:     AATTCAGGAACAATTGATGCTTGAAAGAAATCCACATGGGGAATGTCCAG                         GTTGCCAAAATAGAAACAGAGAAAATGCTTATACAAATGGGTTGAAACCGA
genomic: AATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGG-AATGTCCAGgtgtttatct ... tataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGG-TTGAAACCGA
EST: gi|110730571|gb|EE107799.1|EE107799
EST:     CAATTCAAGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAG                         GTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
genomic: CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAGgtgtttatct ... tataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
EST: gi|77584856|gb|DV221506.1|DV221506
EST:     CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAG                         GTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
genomic: CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAGgtgtttatct ... tataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
EST: gi|161714537|gb|FC062987.1|FC062987
EST:     CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAG                         GTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
genomic: CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAGgtgtttatct ... tataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
EST: gi|71857501|gb|DT006556.1|DT006556
EST:     CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAG                         GTTGCAAAAATAGGAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
genomic: CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAGgtgtttatct ... tataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
EST: gi|161719694|gb|FC067068.1|FC067068
EST:     CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAG                         GTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
genomic: CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAGgtgtttatct ... tataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
EST: gi|110720557|gb|EE096583.1|EE096583
EST:     CAATTCAAGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAG                         GTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
genomic: CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAGgtgtttatct ... tataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
EST: gi|27581975|gb|CB004670.1|CB004670
EST:     CAATTCAAGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAG                         GTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG
genomic: CAATTCAGGAACAATTGATGCTTGAAAGAGATCCACATGGGAATGTCCAGgtgtttatct ... tataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttgtaattctgatagatctttggttattgataatctgtttttataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAGTTAGAGAAGAGGAAGAGTGAGGGCACATACAAATACAAAGGTCACTTTA
                            tattgat  putative branch site (score: 3)
                                     tctgttttt  putative PPT
                           ttattgataatctgtt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtttatcttatatgctagtatatgtgtgtatttgaactttacttgtttgtaattctgatagatctttggttattgataatctgtttttataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAGTTAGAGAAGAGGAAGAGTGAGGGCACATACAAATACAAAGGTCACTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA