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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTGTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAGgtactgtatggccaaaaactaaagcaaatctacatttcgaaaatatggtacataggaacacatgggagccatagacaatggtaggcattagacaagagtt...

Basic information

species Vitis vinifera
transcript Vv01s0011g00620.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA01G07070.1 (Glycine max), 5'ss of exon 5
GACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTGTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAGgtactgtatggccaaaaactaaagcaaatctacatttcgaaaatatggtacataggaacacatgggagccatagacaatggtaggcattagacaagagtt-----
|||||| |||| || ||||||||||||||||||||| |||| ||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||   | |||    | |  | |   ||   | |||||    | | | | | |  | ||   ||         |    ||| |    | ||   | |   |     
GACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTGTTGAGAGACAACCTGACTCTCTGGACCTCTGATTTGCCTGAGGATGGAGgtga-gaatgattgacacttgatataaga-tgcattt---gagttttgcatagggaaagcaataaatattgcaccatatgttgctgaataatgatgtcctagaga

upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA20G03120.1 (Glycine max), 5'ss of exon 5
GACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTGTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAGgtactgt-atggccaaaaactaaagcaaatctacatttcgaaaatatggtacataggaacacatgggagccatagacaatggtaggcattagacaagagtt----
||||||||||| || ||||||||||||||||||||| |||| ||||||||| |||||||||| ||||||||||||||||||||||| ||||| ||||||||||   | |||    | |  | |   ||   | ||||| ||   | ||   | ||  |  ||     |  |||||  | |  |     | | | |    ||    
GACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTGCTGAGAGACAATCTCACTCTCTGGACCTCTGATTTACCTGAGGATGGAGgtatgatcatgattgagacttgacataaga-tgcatttggat--tctgcctcttaatattacc--ataagcatagcaacttttttctctaacatactctttgtta

upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA07G35240.1 (Glycine max), 5'ss of exon 5
GACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTGTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAGgtactgt-atggccaaaaactaaagcaaatctacatttcgaaaatatggtacataggaacacatgggagccatagacaatggtaggcattagacaagagtt-----
||||||||||| || ||||||||||||||||||||| |||| ||||||||| |||||||||| ||||||||||||||||| ||| | ||||| ||||||||||   | |||    | |  |     ||   | || || ||   | ||   | ||  |  ||     |  ||||| |||  || | |  || |||| |  |     
GACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTGCTGAGAGACAATCTCACTCTCTGGACCTCCGATCTACCTGAGGATGGAGgtatgatcatgattgagacttggcataaga-tgcacttggac--tctgcctcgtaatattac-cataaaacatag-caactgtcgtctcta-acaaaatctgttat

upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA02G12930.1 (Glycine max), 5'ss of exon 5
GACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTGTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAGgtactgtatggccaaaaactaaagcaaatctacatttcgaaaatatggtacataggaacacatgggagccatagacaatggtaggcattagacaagagtt---
|||||| |||| || ||||||||||||||||||||| |||| ||||||||||||||||||||||| ||||||||||| || ||||| || || ||||||||||    |  |    |||||  |    |  | |||||    | | | | | |  | ||   ||         |    ||| |    | ||   | |  ||   
GACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTGTTGAGAGACAACCTTACTCTCTGGACTTCCGATTTACCAGAGGATGGAGgtatgagaatgattgaaacttgatattagatgcattt---gagttttgcatagggaaagcaataaatattgcaccgtatgttgctgaataatgatgtcttaga

upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S348_15V6.1 (Physcomitrella patens), 5'ss of exon 5
GACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTGTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAGgtactgtatggccaaaaactaaagcaa--atctacatttcgaaaatatggtacataggaacacatgggagccatagacaatggtaggcattagacaagagtt
|| || |||||||||||||| ||||||||||||||  |||| ||||||||  | || |||||||| ||||| ||||| || ||| |||  || || ||||||   |||               |||    | | |   | ||    || |      ||       |     | | |      ||  | |   | |  | | |
GATACGTTGAGCGAGGAGTCGTACAAGGACAGCACGTTGATCATGCAGCTACTAAGGGACAACCTGACTCTGTGGACGTCGGATCTGCAGGAGGAGGGAGgtgg-gtagacgtgtggcgcggtgcagtggtttgcgggtggatgg-atagggagagggggtgtgggttgtgcgttggtgggagtgtgtagcgggcgtgtgat

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|349830763|gb|FQ417061.1|FQ417061
EST:     GTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGAAGGAG                         GTGAAGACAACTTCAAAGG
genomic: GTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAGgtactgtatg ... tccattgcagGTGAAGACAACTTCAAAGG
EST: gi|351012160|gb|FQ426882.1|FQ426882
EST:     GTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAG                         GTGAAGACAACTTCAAAGGTGA
genomic: GTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAGgtactgtatg ... tccattgcagGTGAAGACAACTTCAAAGGTGA
EST: gi|110373768|gb|EC938103.1|EC938103
EST:     GTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAG                         GTGAAGACAACTTCAAAGGTGAAGAACCCAAGGCTGCTGAACCTACTGAG
genomic: GTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAGgtactgtatg ... tccattgcagGTGAAGACAACTTCAAAGGTGAAGAACCCAAGGCTGCTGAACCTACTGAG
EST: gi|351033251|gb|FQ462023.1|FQ462023
EST:     GTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAA                         GTGAAGACAACTTCAAAGGTGAA
genomic: GTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAGgtactgtatg ... tccattgcagGTGAAGACAACTTCAAAGGTGAA
EST: gi|352789764|gb|FQ478579.1|FQ478579
EST:     GTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAG                         GTGAAGACAACTT
genomic: GTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAGgtactgtatg ... tccattgcagGTGAAGACAACTT
EST: gi|351055188|gb|FQ440527.1|FQ440527
EST:     GTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAG                         GTGAAGACAACTTCAAAGGTGAAGAACCCAAGGCT
genomic: GTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAGgtactgtatg ... tccattgcagGTGAAGACAACTTCAAAGGTGAAGAACCCAAGGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTGTTGAGAGACAACCTCACTCTCTGGACCTCTGATTTGCCTGAAGATGGAGgtactgtatggccaaaaactaaagcaaatctacatttcgaaaatatggtacataggaacacatgggagccatagacaatggtaggcattagacaagagtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atagacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacaaga