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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttgctcttctatttcctcttatagcaaggaaggaaatttcattgtctaatgattgtgtatgtgtgagcactgcatgcatgtatgatttttttc...

Basic information

species Vitis vinifera
transcript Vv07s0005g05160.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 5'ss of exon 4
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtg-aggcttgctcttctatttcctcttatagcaaggaaggaaatt-tcattgtctaatgattgtgtatgtgtgagcactg-catgcatgtatgatttttttc
|||||| ||||| ||||| |||||||||||||| || |||||||| || |||||||| |||||||||||  | |||||||| |||||||| || ||||||||    |    |  || | | ||   ||  |  ||  ||     || | |  | | |||  ||       | ||   |||| | |  ||     |   | |  
GGAAGAGTTTGTCATGACCAAGGATGAGTTTTCCGGTGCTGATATCAAAGCAATATGTACTGAAGCTGGACTTCTTGCTTTGAGAGAACGCCGAATGAAGgtatgagtgaacctttttgtctctaattgaaataatcaaaccttttatgagagcccaat--ttagaccgttttgtctactgacctatataccaaacaatgtc-

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 5'ss of exon 5
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtg----aggcttgctcttctatttcctcttatagcaaggaaggaaatttcattgtctaatgattgtgtatg-tgtgagc-actgcatgcatgtatgatttttttc---------------------------------------------------------------------------------
 ||||| ||||| ||||| ||||||||||||||||| ||||| || || |||||||| || || || || ||||| |||||||| || ||  | ||||||||     ||  ||| | |   |      ||  | ||     || |   || ||  |  ||   | | | ||  |  | || | | | | ||  | ||| |||   |                                                                                 
AGAAGAGTTTGTGATGACCAAGGATGAGTTTTCTGGTGCTGACATCAAAGCAATATGTACGGAGGCCGGATTGCTCGCTTTAAGGGAGCGCAGAATGAAGgtaactcagctttgttttctcaaccagactccttgctctctagtactgttaatgttaaaactttcgagcatactaagtgccaatcctttcagatctgagtttgagctgcgctcagaacatatttgcatggaatgcaagtctttgttgcacttctctttttacatttgctgttcttctgttgctttag

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G095593_T01 (Zea mays), 5'ss of exon 4
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttgctcttctatttcctcttatagcaaggaaggaaatttcattgtctaatg--attgtgtatgtgtgagcactgcatgcatgtatgatttttttc
|||||| ||||||||||| || || |||||||| || |||||||| |||||||| ||||| || ||||| |||||||| |||||||||||  | |||||||| || | ||  ||| ||| |  |  || |   ||      |||||  | |   |||   | |||  |  |      |||   |   | |  |||     | 
GGAAGAGTTTGTTATGACCAAAGACGAGTTTTCGGGTGCTGATATTAAGGCAATCTGCACAGAGGCTGGATTGCTTGCCTTAAGAGAACGCAGAATGAAGgt-agacgtgaacttttatcttttgctaaaaatagattcagaattttctgggtgaatataactgttcaaataactcaactattttgctattggataggaat-

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 5
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgag---gcttgctcttcta--tttcctcttatagcaaggaaggaaatttcattgtctaatgattgtgtatgtgtgagcactgcatgcatgtatgatttttttc-
 ||||| ||| ||||| | || ||||||||||| || ||||| || ||||| || || ||||||||||| ||||||||||| ||||| ||||| |||||||| ||   |||   |   | |  |  || ||| |             | |    |   |   ||||     |||  |     | | || |    | | ||||||  
AGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagctcagtacaccaaatacccccttctgttttttcccatgaatctgctactttg-gattaaccttgttgg-----tacctgaaaccgtcactttttttg

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G056569_T01 (Zea mays), 5'ss of exon 4
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttgctcttctatttcctcttatagcaaggaaggaaatttcattgtctaatgattgtgtatgtgtgagcactgcatgcatgtatgatttttttc---
|||||| ||||||||||| || |||||||| || || |||||||| ||||| || ||||| || ||||| ||||| || |||||||||||  | ||||| ||||| | ||  ||| |||  |  | |  |     | |  || ||   | |   |||    || |  |  | |      | |  || |   ||    |     
GGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAAgtgag-cctgaacttgtatccctacatcaattc--gtataaacttgtctgggtgaatagaagtattcgaataactcgaccttttatttgctatcgaataggga

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA19G35510.1 (Glycine max), 5'ss of exon 5
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttgctcttctatttcctcttatagcaaggaaggaaatttcattgtctaatgattgtgtatgtgtg-agcactgcatgcatgtatgatttttttc
 ||||||||||||||||||||||||||||| ||||||||||||||||| |||||||| ||||||||||| || ||||||||| ||||||| || |||||||| ||   |  |||||||| |  |  || ||  | |    ||||    |  ||   ||    | |||   || |    |||    | | || |     || 
AGAAGAATTTGTTATGACTAAGGATGAGTTCTCTGGAGCTGATATAAAAGCAATATGTACTGAAGCTGGCTTACTTGCTTTACGAGAACGCCGGATGAAGgttagtagta-tcttctatatatttgtagagttatggcctaaataatgtgatcctgtggaaatatattattgtactgttgctgttaggaattacaaagtta

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 5
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttgctcttctatttcctcttatagcaaggaaggaaatttcattg-tctaatgattgtgtatgtgtgagcactgcatgcatgtatgatttttttc--
 ||||||||||||||||| ||||||||||| ||||||||||||||||| |||||||| ||||||||||| || ||||||||| ||||||| || |||||||| ||   |  |||||||| |  |  || ||  |      |||     ||| ||   ||    |  || | ||     |   ||| |||| |   ||      
AGAAGAATTTGTTATGACCAAGGATGAGTTCTCTGGAGCTGATATAAAAGCAATATGTACTGAAGCTGGCTTACTTGCTTTACGAGAACGCCGAATGAAGgttagaagta-tcttctatatgtttgtacagttatagcctaaacaatgttgatcctgtggaaataaat-tatggaacttagttgc-tgtaaggaattacaaag

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G04920.1 (Glycine max), 5'ss of exon 5
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttgctcttctatttcctcttatagcaaggaaggaaatttcattgtctaatgattgtgtatgtgtgagcactgcatgcatgtatgatttttttc----
||||||||||||||||||||| ||||| || |||||||||||||||||||||||||| |||||||| ||||| |||||| || ||||||| || |||||||| ||   | ||||  | |||  | | |||   |  ||    | | ||||||   | |   ||   |   |    ||  |    ||  || |            
GGAAGAATTTGTTATGACTAAAGATGAATTCTCTGGAGCTGATATAAAGGCAATATGTACTGAAGCCGGTTTACTTGCTCTACGAGAACGCCGAATGAAGgtaagaaat-ctctcttgttta-tatgatat--aataatagtactccattgttgtacggaagttgctagttttttacaactcatattgataaagccaaaatata

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 5
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttgctcttctatttcctcttatagcaaggaaggaaatttcattgtctaatgattgtgtatgtgtgagcactgcatgcatgtatgatttttttc-----
||||||||||||||||||||| || || || || ||||||||||||||||||||||| |||||||||||||| |||||| || ||||||| || |||||||| ||   |    || |   ||   |  |   |   ||   |||   | |     ||  |||| |    ||     || | |   |  | | | || ||      
GGAAGAATTTGTTATGACTAAAGACGAATTCTCCGGAGCTGATATAAAGGCAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatctctttgtggctcaattgtttatat--aatataataatagtactccattgttgtatggaagt---tgctacttttttacaagctcttattgataaa

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 5'ss of exon 5
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgagg-cttgctcttctatttcctcttatagcaaggaaggaaatttcattgtctaatgattgtgtatgtgtgagcactgcatgcatgtatgatttttttc-
 ||||| ||||| ||||| || || ||||| || |||||||||||||||||||||||||| ||||||||| |||||||| | ||||| || || ||||| || |||  |  ||    | |  || |||    ||  ||| | ||| |     |  ||| ||| |   |   | | |  ||  ||  | |   |||  |||  
AGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCACAGAAGCTGGTCTGCTTGCTCTTAGAGAGCGTCGGATGAAAgtaaggattctctggcttctcaccacttgattcatcgaacgcaatct-----ttgaataattttactt---taacctttgtttg-gtcttctattggtttag

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 5
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgagg---cttgctcttctatttc---ctcttatag-caaggaaggaaatttca-ttgtctaatgattgtgtatgtgtgagcactgcatgcatgtatgatttttttc-
 ||||| ||||| ||||| || || ||||| || ||||||||||||||||| ||||||||||| |||||| | || ||| | || || || |||||||||||   |   |||   | | || |||   | | || |  ||   |   | |   || |||   ||| | |    |  ||     | ||  |  |  |  ||||| ||   
CGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCACTGAGGCTGGTCTACTAGCTCTCAGGGAGCGTCGTATGAAGgtagagactcttaaccatttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccac-tgacgctaatgtgtttaaattggatttgttcag

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 5
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttgctcttctatttcctcttatagcaaggaaggaaatttcattgtctaatgattgtgtatgtgtgagcactg-catgcatgtatgatttttttc-------------------------------------------------------------
||| ||||| || ||||| |||||||| || ||||| ||||| || || || || ||||| ||||||||| | ||||| ||||| || || ||||||||||||||  |  |  |||| | |  |||| ||           |||     |    |  | ||     | | |     |   ||||  ||||| |||     |                                                             
GGAGGAATTCGTGATGACCAAGGATGAATTCTCTGGTGCTGACATTAAAGCTATCTGCACGGAAGCTGGTCTTCTTGCATTAAGGGAGCGCCGTATGAAGgtgagcttgccatttctttgtattcttttatatgtatttttaatgcgtctcgtcagaggttacacttttttagttgccctcatggctgtataattgcaggctttgaattggcttgttttgattctgtgactaagtattgactgtggattcttaatgccacag

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ32659 (Selaginella moellendorffii), 5'ss of exon 5
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttgctcttctatttcctcttatagcaaggaaggaaatttcattgtctaatgattgtgtatgtgtgagcactgcatgcatgtatgatttttttc
 ||||| ||||| ||||| |||||||| || ||||||||||| || |||||||| ||||||||||||||  | || ||  ||||||||||||| ||||||||     || |||     ||| | |   |  |  | || ||  |||| |  |||   |                                          
TGAAGAGTTTGTGATGACGAAGGATGAATTCTCTGGAGCTGACATCAAGGCAATGTGCACTGAAGCTGGGCTTCTGGCACTAAGAGAACGGCGGATGAAGgtag---tttctcaatgcttttcacaactttcttgtaacgat-tttcttcttctccag------------------------------------------

upper sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 5
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttgctcttctatttcctcttatagcaaggaaggaaatttcattgtctaatgattgtgtatgtgtgagcactgcatgcatgtatgatttttttc
 ||||| ||||| ||||| ||||| || |||||||||||||| || |||||||| ||||||||||||||  | || ||  ||||||||||||| ||||||||     || |||     ||| | |   |  |  | || ||  |||| |  |||   |                                          
TGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCACTGAAGCTGGGCTTCTGGCACTAAGAGAACGGCGGATGAAGgtag---tttctcgatgcttttcacaactttcttgtaacgat-tttcttcttctccag------------------------------------------

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|229418620|gb|GO652857.1|GO652857
EST:     CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAG                         GTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAG
genomic: CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttg ... tgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAG
EST: gi|110703456|gb|EE080320.1|EE080320
EST:     CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAG                         GTGACACATGTAGACTTCAAGAAAGCAAAGGAGAAAGTGATGTTCAAGAAG
genomic: CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttg ... tgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAG
EST: gi|110392599|gb|EC958132.1|EC958132
EST:     CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAG                         GTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAG
genomic: CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttg ... tgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAG
EST: gi|71881961|gb|DT031016.1|DT031016
EST:     CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAG                         GTGACTCATGTAGACTTCAAGAA
genomic: CAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttg ... tgtgcttcagGTGACTCATGTAGACTTCAAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCACTGAAGCTGGTTTGCTTGCTTTAAGAGAACGGCGTATGAAGgtgaggcttgctcttctatttcctcttatagcaaggaaggaaatttcattgtctaatgattgtgtatgtgtgagcactgcatgcatgtatgatttttttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaaat