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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACAAGAGGTTTGCTGGATTCAGCAGGGATGGTAAGCAACTTGATGCTGATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagatctaagtctgcttggatgttaggggggaaaaattgtgattctgaatcctgcattattagcggtacttgattagagactccaatccctctatctcatgcacataatttcttacattgttgagaactatgcag

Basic information

species Vitis vinifera
transcript Vv00s0174g00190.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0174g00190.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os01g67134.1 (Oryza sativa), 5'ss of exon 7
TGACAAGAGGTTTGCTGGATTCAGCAGGGATGGTAAGCAACTTGATGCTGATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagat-------ctaagtctgct-tggatgttaggggggaaaaattgtg------attctgaatcctgcattattagcggtacttg-attagagactccaatccctctatctcatgcacataatttcttacattgttgagaactatgcag-------------------------------------------------
|||||||||||||||||| ||||  | ||| |  ||||| |||||| ||||| ||||||||||||| ||||  ||||| || || ||||  || |||| |||||| |        ||  ||   | |   || ||    |  |    ||||      |||  || |  || |        | | |||| | ||  ||||  || |  | ||          | ||||| ||||  | | |   | | |||                                                   
TGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggcactattagatcaattgttcgtgctattttgacattgctgtgtgttgtattaggagttatgtagctgccttgatgcttgtaatattgactaaaa-cattataagcaggctggaaaatttgttactgtttagctcagtctgcttgatttttattctcatcagtttaaaatttctacttatgtacttcttgcag

upper sequence: Vv00s0174g00190.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 7
TGACAAGAGGTTTGCTGGATTCAGCAGGGATGGTAAGCAACTTGATGCTGATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagatctaa--gtctgcttggatgttaggggggaaaaattgtgattctgaatcctgcattattagcggtacttgattagagactccaatccctctatctcatgcacataatttcttacattgttgagaactatgcag-------------------------------------------------
|||||||||||||||||| ||||  | ||| |  ||||| |||||| ||||| ||||||||||||| ||||  ||||| || || ||||  || |||| |||||| |   |   |  | |    |||| | |  |     |||| |||  ||||  || |        | |  ||     |       || |  | |||    |    || |||| ||||  | | |   | | |||                                                   
TGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggcactattagatcaattgttcgtgctgtggg-ttgt-attaggaattatgtagctgccttgatgtttataacgttgactaaagcattatataaagtttggattatttgttactgtttagctcagtctgctttattttgattgtcatcaggataaattttcttcttatgtacttgttgcag

upper sequence: Vv00s0174g00190.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G090738_T01 (Zea mays), 5'ss of exon 7
TGACAAGAGGTTTGCTGGATTCAGCAGGGATGGTAAGCAACTTGATGCTGATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagatctaagtctgcttggatgttaggggggaaaaattgtgattctgaatcctgcattattagcggtacttgattagagactccaatccctctatctcatgcacataatt-tcttacattgttgagaactatgcag
 || |||||||||||||| ||||  | ||||| |||||| || ||||||||| | ||||||||||| |||| ||||  |||||||||||  ||||||| ||| ||  ||  |  || |||  ||  ||         ||| |  || |   |||  | || | |  | |  |||  ||   | |   |    | | ||  |   |  ||| | ||  |                    
CGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGTACATCTATGGTCTCCATGTTGCTGAGTATATGAAGgtaag--ctgtgcatg-ttgcttgccag---------attatagtttt---tccccccttgt-aatgat--ttggatatcaatttgtaagtttatttcataaatatgtaactgtccca--------------------

upper sequence: Vv00s0174g00190.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM5G815894_T03 (Zea mays), 5'ss of exon 7
TGACAAGAGGTTTGCTGGATTCAGCAGGGATGGTAAGCAACTTGATGCTGATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagatctaagtctgcttggatgttaggggggaaaaattgtgattctgaatcctgcattattagcggtacttgattagagactccaatccctctatctcatgcacataatttcttacattgttgagaactatgcag
 || |||||||||||||| ||||  | |||||  ||||| || ||||||||| | || |||||||| |||| |||||||||||||||||  || |||| ||| || | |  |  |||| | || | |          ||  |  |||  | | |    || ||   |  |  | ||  ||   |  | ||  |  || || |    ||  |    |  ||     ||          
CGAGAAGAGGTTTGCTGGTTTCAAGAAGGATGACAAGCAGCTGGATGCTGATATCCATCGCAAGTACATCTATGGTGGCCATGTTGCTGACTACATGAGGgttagttgt--gcttgct-gcatatcac---------atcatatttc--atttcctttttgtttttgtaaactaatctgat-ttatactcaattgatttcgttgttattttgatctttatctcccag----------

upper sequence: Vv00s0174g00190.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA07G06580.1 (Glycine max), 5'ss of exon 7
TGACAAGAGGTTTGCTGGATTCAGCAGGGATGGTAAGCAACTTGATGCTGATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagatctaag-tctgcttggatgttaggggggaaaaattgtgattctgaatcctgcattattagcggtacttgattagagactccaatccctctatctcatgcacataatttcttacattgttgagaactatgcag
||| |||||||||||||| ||    | |||    ||| | ||||||||||| ||||| ||||| ||| | |||||||| ||||||||||| ||||||| ||   |    ||| | |  ||   | | ||    |     || | || |   ||  || ||| |||||  || ||| ||||| |  |  ||   | ||| |  ||||                                
TGATAAGAGGTTTGCTGGGTTTGATAAGGAAAAGAAGGAGCTTGATGCTGAGGTTCATCGCAAATATGTTTTTGGTGGACATGTTGCTGCCTATATGAAGgcatgcgagaagattttattttgtatcagtcttgtgttgtt-taatgcaatatt-tggatttttagc--tagttg-ttagacaaccttattt-tatattttctgcag-------------------------------

upper sequence: Vv00s0174g00190.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA13G35580.2 (Glycine max), 5'ss of exon 7
TGACAAGAGGTTTGCTGGATTCAGCAGGGATGGTAAGCAACTTGATGCTGATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagatctaagtctgcttggatgttaggggggaaaaattgtg--attctgaatcctgcattattagcggtacttgattagagactccaatccctctatctcatgcacataatttcttacattgttgagaactatgcag
 ||||||||||||||||| ||    | |||    ||| | ||||||||||| ||||| ||||| ||| | |||||||| ||||||||||| ||||||| ||   ||  ||||  ||  |       | |        ||| |   || ||  ||   |  || | |||   | ||| ||||| |  | | |   | ||| |  ||||                                
CGACAAGAGGTTTGCTGGGTTTGATAAGGAGAAGAAGGAGCTTGATGCTGAGGTTCATCGCAAATATGTTTTTGGTGGACATGTTGCTGCCTATATGAAGgcatgagataagattgtatattgtacaagtcttctttattatataatgctatatttggatttttcagc--catttg-ttagacaaccta-tttttttattttctgcag-------------------------------

upper sequence: Vv00s0174g00190.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA16G03170.1 (Glycine max), 5'ss of exon 7
TGACAAGAGGTTTGCTGGATTCAGCAGGGATGGTAAGCAACTTGATGCTGATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagatctaagtctgcttggatgttaggggggaaaaattgtgattctgaatcctgcattattagcggtacttgattagagactcca-atccctctatctcatgcacataatttcttacattgttgagaactatgcag
|||||||||||||||||| ||    | |||    ||| | ||||||||||| || || ||||| ||| | |||||||| ||||||||||| ||||||| ||   ||   |||  |      || ||    |    |  ||    |  ||  |  || | |||| |   |  |    |||    |  | | || | | | || ||||                                
TGACAAGAGGTTTGCTGGGTTTGATAAGGAGAAGAAGGAGCTTGATGCTGAGGTGCATCGCAAATATGTTTTTGGTGGACATGTTGCTGCCTATATGAAGgcatgagagaagatttt----atttt----gtaccagttttctgtattgttttatggaatatttggatttttcagctagttgttagacaaccttttttttcctgcag-------------------------------

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|22011174|gb|BQ796208.1|BQ796208
EST:     ATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACG                         ACTTTAATGGAAGACGAGCCAGAGAAGTATCAGTCTCACTTTAGTGAGTAC
genomic: ATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagatcta ... aactatgcagACTTTAATGGAAGACGAGCCAGAGAAGTATCAGTCTCACTTTAGTGAGTAC
EST: gi|30137441|gb|CB922779.1|CB922779
EST:     ATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACG                         ACTTTAATGGAAGACGAGCCAGAGAAGTATCAGTCTCACTTTAGTGAGTAC
genomic: ATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagatcta ... aactatgcagACTTTAATGGAAGACGAGCCAGAGAAGTATCAGTCTCACTTTAGTGAGTAC
EST: gi|30301305|gb|CB978099.1|CB978099
EST:     ATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACG                         ACTTTAATGGAAGACGAGCCAGAGAAGTATCAGTCTCACTTTAGTGAGTAC
genomic: ATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagatcta ... aactatgcagACTTTAATGGAAGACGAGCCAGAGAAGTATCAGTCTCACTTTAGTGAGTAC
EST: gi|51050065|gb|CO818363.1|CO818363
EST:     ATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACG                         ACTTTAATGGAAGACGAGCCAGAGAAGTATCAGTCTCACTTTAGTGAGTAC
genomic: ATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagatcta ... aactatgcagACTTTAATGGAAGACGAGCCAGAGAAGTATCAGTCTCACTTTAGTGAGTAC
EST: gi|32458156|gb|CD799330.1|CD799330
EST:     ATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACG                         ACTTTAATGGAAGACGAGCCAGAGAAGTATCAGTCTCACTTTAGTGAGTAC
genomic: ATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagatcta ... aactatgcagACTTTAATGGAAGACGAGCCAGAGAAGTATCAGTCTCACTTTAGTGAGTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACAAGAGGTTTGCTGGATTCAGCAGGGATGGTAAGCAACTTGATGCTGATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagatctaagtctgcttggatgttaggggggaaaaattgtgattctgaatcctgcattattagcggtacttgattagagactccaatccctctatctcatgcacataatttcttacattgttgagaactatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC