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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctctaatgaatttttttttaccattttcttttcctaacttatatttattaggtggctctggtatgtcttccttttgtaatttgatttctattt...

Basic information

species Vitis vinifera
transcript Vv05s0029g01310.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os03g63090.2 (Oryza sativa), 5'ss of exon 7
GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctctaatgaatttttttttaccattttcttttcctaacttatatttattaggtggctctggtatgtcttccttttgtaatttgatttctattt
|||||||| || || || || ||||||||||| ||||||||||| ||||| || || ||||| || ||||| || || || |||||||||| |||      ||  |  ||||  ||  | ||  | ||| |||       ||| | |  |    ||  |||     | | || | |||||   | ||   
GGTTATGATATCAGTTTCCTGATAACAAACTACCACTGTGAGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaagg-----aaaaatgttttccttggctttcccatttgctaca----gtttgtgactttatactcatat---cacatattctgatttgtgctgtag--

upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G118586_T01 (Zea mays), 5'ss of exon 7
GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctctaatgaatttttttttaccattttcttttcctaacttatatttattaggtggctctggtatgtcttccttttgtaatttgatttc-tattt---------------------------
|| ||||| || || || || ||||||||||| || |||||||| ||||| || |||||||| || ||||| ||||||||||||||||||| ||||||        |    |    |    |||   ||  |  ||| |  |  || ||| | |  | |    | |  ||| |||  |||    | || |                            
GGCTATGATATCAGTTTCCTGATAACAAACTACCATTGTGAGGACATGCATAAGCACAAGCTCATAGATTTCATCGTGCAATTTATGGAGgtaagttcatacgcataagcataggcatggctttgagtttgtcgcttgttctcttttggtcgata-gatgcaacgttgttt-gtatgttggcagcgtactcacactattctgcttacatgaaccccag

upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G112015_T01 (Zea mays), 5'ss of exon 6
----------GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctctaatgaatttttttttaccattttcttttcctaacttatatttattaggtggctctggtatgtcttccttttgtaatttgatttc-tattt---------------------------
          || ||||| || || || || ||||||||||| || |||||||| ||||| || |||||||| || ||||| ||||||||||||||||||| ||||||        |    |    |    |||   ||  |  ||| |  |  || ||| | |  | |    | |  ||| |||  |||    | || |                            
TATGTTTCAGGGCTATGATATCAGTTTCCTGATAACAAACTACCATTGTGAGGACATGCATAAGCACAAGCTCATAGATTTCATCGTGCAATTTATGGAGgtaagttcatacgcataagcataggcatggctttgagtttgtcgcttgttctcttttggtcgata-gatgcaacgttgttt-gtatgttggcagcgtactcacactattctgcttacatgaaccccag

upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA05G28650.1 (Glycine max), 5'ss of exon 7
GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctctaatgaatttttttttaccattt-----tcttttcctaacttatatttattaggtggctctggtatgtcttccttttgtaatttgatttctattt
|| |||||||||||||| ||||||||||| || ||||||||||| ||||| || ||||| |||||||| ||||| ||||||||||||||||||||   | |  |||   | ||  |   ||||     |  |||     ||| || | ||||  |   |   | ||    |    |    ||    ||||||   
GGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTTATTGACTTTATTGTGCAATTTATGGAGgcaagaattttgttgaccctattacttggatttgcattttattttgcggcttgtagtaattatctaaattaaggatactgtatgatct--atggagtttcta---

upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA08G11740.1 (Glycine max), 5'ss of exon 7
GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctctaatgaatttttttttaccattt-----tcttttcctaacttatatttattaggtggctctggtatgtcttccttttgtaatttgatttctattt
|| |||||||||||||| ||||||||||| || ||||||||||| ||||| || ||||| || ||||| ||||| ||||||||||||||||||||   | |  |||   | |   |   ||||     |  |||  |  ||| || | ||||  |   |  |  ||    |   | || | |  || |       
GGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTCATTGACTTTATTGTGCAATTTATGGAGgcaagaattttgttgaccctataacttggatttgcattttattttgtggcttgtagtaattatctaaattagagatactgtatctatggagt--gactatgg---

upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT4G14147.2 (Arabidopsis thaliana), 5'ss of exon 8
GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctctaatgaatttttttttaccattttcttttcctaacttatatttattaggtg-gctctggtatgtcttccttttgtaatttgatttctattt----
|| |||||||| |||||||||||||||||||| ||||| || || ||||| ||||| ||||| |||||||| ||  | || |||||||||||||||         ||  |  | ||   ||| | |   | |   ||      |||||  |    ||   |     |   | | |   |||  |   |  |    
GGCTATGACATAAGCTTTCTTATAACAAACTACCACTGCGAAGAGATGCAGAAACAGAAGCTAATTGATTTCATTATTCAGTTTATGGAGGCAAgtctctctcgaaacctaatctttttattctatgaccttgg-ttgctcccattagtagcatcctaacaatcaatatatgtcttggttgcatcaaacctaatg

upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT4G14147.1 (Arabidopsis thaliana), 5'ss of exon 8
GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctctaatgaatttttttttaccattttcttttcctaacttatatttattaggtg-gctctggtatgtcttccttttgtaatttgatttctattt
|| |||||||| |||||||||||||||||||| ||||| || || ||||| ||||| ||||| |||||||| ||  | || |||||||||||||||         ||  |  | ||   ||| | |   | |   ||      |||||  |    ||   |     |   | | |   |||  |   |  |
GGCTATGACATAAGCTTTCTTATAACAAACTACCACTGCGAAGAGATGCAGAAACAGAAGCTAATTGATTTCATTATTCAGTTTATGGAGgcaagtctctctcgaaacctaatctttttattctatgaccttgg-ttgctcccattagtagcatcctaacaatcaatatatgtcttggttgcatcaaacct

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|29785136|gb|CB341880.2|CB341880
EST:     AGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG                         GATATCGATAAAGAGATAAGCGAATTGAAATTGTCGGTGAACACACGTGGG
genomic: AGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctc ... catattgcagGATATCGATAAAGAGATAAGCGAATTGAAATTGTCGGTGAACACACGTGGG
EST: gi|351046852|gb|FQ454462.1|FQ454462
EST:     AGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAA                         GATATCGATAAAGAGATAAGCGAATTGAAATTGTCGGTGAACACACGTGGG
genomic: AGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctc ... catattgcagGATATCGATAAAGAGATAAGCGAATTGAAATTGTCGGTGAACACACGTGGG
EST: gi|71857830|gb|DT006885.1|DT006885
EST:     AGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG                         GATATCGATAAAGAGATAAGCGAATTGAAATTGTCGGTGAACAC
genomic: AGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctc ... catattgcagGATATCGATAAAGAGATAAGCGAATTGAAATTGTCGGTGAACAC
EST: gi|110693326|gb|EE069458.1|EE069458
EST:     AGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG                         GATATCGATAAAGAGATAAGCGAATTGAAATTGTCGGTGAACACACGTGGG
genomic: AGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctc ... catattgcagGATATCGATAAAGAGATAAGCGAATTGAAATTGTCGGTGAACACACGTGGG
EST: gi|349826081|gb|FQ415886.1|FQ415886
EST:     AGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG                         GATATCGATAAAGAGATAAGCGAATTGAAATTGTCGGTGAACACACGTGGG
genomic: AGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctc ... catattgcagGATATCGATAAAGAGATAAGCGAATTGAAATTGTCGGTGAACACACGTGGG
EST: gi|33405119|gb|CF210746.1|CF210746
EST:     AGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG                         GATATCGATAAAGAGATAAGCGAATTGAAATTGTCGGTGAACACACGTGGG
genomic: AGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctc ... catattgcagGATATCGATAAAGAGATAAGCGAATTGAAATTGTCGGTGAACACACGTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctctaatgaatttttttttaccattttcttttcctaacttatatttattaggtggctctggtatgtcttccttttgtaatttgatttctattt

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