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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGATGGTTTGTTGGGTCCCTACTGGAAAGCAATGGGATTGGCCTTCAACTGTACTTTCCTCCTTTTTGGATCCGTCATACAGCTGATTGCTTGTGCAAGgtcagtttcattttcattaagaatggtaaaaatcagaaatctggggtggtggggaggattaatctgaggtggtgatgaactggtgggatgtttacag

Basic information

species Vitis vinifera
transcript Vv13s0067g00330.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g00330.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA18G03280.1 (Glycine max), 5'ss of exon 4
TGGATGGTTTGTTGGGTCCCTACTGGAAAGCAATGGGATTGGCCTTCAACTGTACTTTCCTCCTTTTTGGATCCGTCATACAGCTGATTGCTTGTGCAAGgtcagtttcattttcattaagaat--ggtaaaaatcagaaatctggggtggtggggaggattaatctgaggtggtgat--gaactggtgggatgtttacag---
 ||| || ||| ||||||| ||||||||||| || ||||||||||||||||| ||||| ||||| |||||||| ||||| ||||| || ||||||||||||||   |  |||| |  | | |||    |   |        | |    ||||   ||  |||| |   | ||   |||  ||     |   ||  | |      
-GGAAGGCTTGCTGGGTCCATACTGGAAAGCTATTGGATTGGCCTTCAACTGCACTTTTCTCCTCTTTGGATCTGTCATCCAGCTCATAGCTTGTGCAAGGtc---tcaatttcctcttataatcaaattgtatcttctttttttaattggtacagactattactgccatgtttggattagattcaattttatcataatcaatt

upper sequence: Vv13s0067g00330.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G35080.1 (Glycine max), 5'ss of exon 4
TGGATGGTTTGTTGGGTCCCTACTGGAAAGCAATGGGATTGGCCTTCAACTGTACTTTCCTCCTTTTTGGATCCGTCATACAGCTGATTGCTTGTGCAAGgtc--agtttcattttcattaagaatggtaaaaa---tcagaaatctggggtggtggggaggattaatctgaggtggtgatgaactggtgggatgtttacag
|||| || ||  ||||||| ||||||||||| || || |||||||||||||| ||||| ||||| |||||||| ||||| ||||| || ||||||||||||||  | |||| | ||     | ||| |||       |    |||  |    |      |     |   |  | |  |  | || |  |      | ||   
TGGAAGGCTTACTGGGTCCATACTGGAAAGCTATTGGGTTGGCCTTCAACTGCACTTTTCTCCTCTTTGGATCTGTCATCCAGCTCATAGCTTGTGCAAGgtctcaatttcctcttataacataattgtatgttctttttttaattcgaaccgactataacttgcatgtttggattatattcaatttttccataatctat--

upper sequence: Vv13s0067g00330.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA14G06600.1 (Glycine max), 5'ss of exon 3
TGGATGGTTTGTTGGGTCCCTACTGGAAAGCAATGGGATTGGCCTTCAACTGTACTTTCCTCCTTTTTGGATCCGTCATACAGCTGATTGCTTGTGCAAGgtcagtttcattttcattaagaatggtaaaaatcagaaatctggggtggtggggaggatt---aatctgaggtggtgatgaactggtgggatgtttacag-----
|||| |||||  ||||||| ||||||||||| || || ||||||||||| || ||||||||||| ||||| ||||| || ||||| ||||||||||||||||  |  |  |   ||||| |  | || ||  |   |||| || |||  | ||||  ||    | | ||  |   |  |  |      |||   ||| |      
TGGAAGGTTTACTGGGTCCATACTGGAAAGCCATTGGCTTGGCCTTCAATTGCACTTTCCTCCTCTTTGGGTCCGTTATCCAGCTTATTGCTTGTGCAAGgtatgaat--tccccattatg--tagtcaaggttttaaat-tgcggttatagggacaatcgtgattttgttgccatctttgatattatggaaaattataaacaaa

upper sequence: Vv13s0067g00330.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G42290.1 (Glycine max), 5'ss of exon 3
TGGATGGTTTGTTGGGTCCCTACTGGAAAGCAATGGGATTGGCCTTCAACTGTACTTTCCTCCTTTTTGGATCCGTCATACAGCTGATTGCTTGTGCAAGgtcagtttcattttcattaagaatggtaaaaatcagaaat--ctggggtggtggggaggattaatctgaggtggtgatgaac-tggtgggatgtttacag---
|||| |||||  ||||||| ||||||||||| || || ||||||||||| || ||||| ||||| ||||||||||| || ||||| ||||||||||||||||  |    | || ||| |    | || ||| |   ||||  | |   | ||||  |  || | | ||  ||  |  | ||  |  ||| |  ||   |    
TGGAAGGTTTACTGGGTCCATACTGGAAAGCCATTGGCTTGGCCTTCAATTGCACTTTTCTCCTCTTTGGATCCGTTATCCAGCTTATTGCTTGTGCAAGgtatga---aattccatcagttgtagtcaaagttttaaattgcagttattgtggtaatcatgattttgtcgtcatccttaatattatggaaaattatgaacaa

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|29781566|gb|CB346109.2|CB346109
EST:     TGTACTTTCCTCCTTTTTGGATCCGTCATACAGCTGATTGCTTGTGCAAG                         CAATATATACTACATAAATGATCGACTGGAGATGAGGACATGGACCTACAT
genomic: TGTACTTTCCTCCTTTTTGGATCCGTCATACAGCTGATTGCTTGTGCAAGgtcagtttca ... atgtttacagCAATATATACTACATAAATGATCGACTGGACAAGAGGACATGGACCTACAT
EST: gi|37189068|gb|CF608417.1|CF608417
EST:     TGTACTTTCCTCCTTTTTGGATCCGTCATACAGCTGATTGCTTGTGCAAG                         CAATATATACTACATAAATGATCGACTGGACAAGAGGACATG
genomic: TGTACTTTCCTCCTTTTTGGATCCGTCATACAGCTGATTGCTTGTGCAAGgtcagtttca ... atgtttacagCAATATATACTACATAAATGATCGACTGGACAAGAGGACATG
EST: gi|110402117|gb|EC968752.1|EC968752
EST:     TGTACTTTCCTCCTTTTTGGATCCGTCATACAGCTGATTGCTTGTGCAAG                         CAATATATACTACATAAATGATCGACTGGACAAGAGGACATGGACCTACAT
genomic: TGTACTTTCCTCCTTTTTGGATCCGTCATACAGCTGATTGCTTGTGCAAGgtcagtttca ... atgtttacagCAATATATACTACATAAATGATCGACTGGACAAGAGGACATGGACCTACAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGATGGTTTGTTGGGTCCCTACTGGAAAGCAATGGGATTGGCCTTCAACTGTACTTTCCTCCTTTTTGGATCCGTCATACAGCTGATTGCTTGTGCAAGgtcagtttcattttcattaagaatggtaaaaatcagaaatctggggtggtggggaggattaatctgaggtggtgatgaactggtgggatgtttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT