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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCATCAGAGGCTGAAACAGCAACAGCAAGCCTTGATGCAGCAAGCTCTTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAGgtgcgagtcttttttggtttctggttctatttttttccctgggatttgtttttgggtgatcgatgtccttgcgattagatgtttggatttggctcgtttg...

Basic information

species Vitis vinifera
transcript Vv09s0002g00880.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 1
GCAGCATCAGAGGCTGAAACAGCAACAGCAAGCCTTGATGCAGCAAGCTCTTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAGgtgcgagtcttttttggtttctggttctatttttttccctgggatttgtttttgggtgatcg-atgtccttgcgattagatgtttggatttggctcgtttg---
|||| |||| |||||||| ||||| || |||||  ||||||||||||||||||| || || ||||| ||||||||||| || ||| | ||||||||||||||  |   |        | |||  | |  ||    || |||   || | | ||   | ||||  |  ||| |   || |    | | |||| |||  || |   
GCAGAATCACAGGCTGAAGCAGCAGCAACAAGCTCTGATGCAGCAAGCTCTTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAGgt-tggaccccacacactctctc-tccgtttccgatcactgc--ttcgatcttatcttatcgtgttgcctcgatcttcgtgtctcgcattttgctatttcgggg

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA07G04640.1 (Glycine max), 5'ss of exon 1
GCAGCATCAGAGGCTGAAACAGCAACAGCAAGCCTTGATGCAGCAAGCTCTTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAGgtgcgagtcttttttggtttctggttctatttttttccctgggatttgtttttgggtgatcgatgtccttgcgat-tagatgt-ttggatttggctcgtttg-
|| | | |||  || | | |||||||| |||||  | ||||||||||||||||| || || ||||| ||||||||||| |||||| | |||||||||||||| ||   |  |  |    |||   ||| |   |||||  |    | | ||     | |||| ||| ||  |||| |   ||| |   |||| ||   || | 
GCTGAAGCAGCAGCAGCAGCAGCAACAACAAGCTCTTATGCAGCAAGCTCTTCTCCAACAACAGTCTCTCTACCACCCTGGCCTCCTTGCTCCTCCTCAGgttcggacccctcatatactctctctctctccatttcc--gatcatagcttcgatcttatcg-tgttctatcgatcttcgtgtctcccattttgccatttcgg
















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|161716028|gb|FC065534.1|FC065534
EST:     TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAG                         ATAGAGCCAATACCAAGTGGAAATCTGCCTCCTTGTTTTGATTCAAGTACA
genomic: TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAGgtgcgagtct ... tattttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA
EST: gi|349811318|gb|FQ407544.1|FQ407544
EST:     TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAG                         ATAGAGCCCATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA
genomic: TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAGgtgcgagtct ... tattttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA
EST: gi|161721264|gb|FC069684.1|FC069684
EST:     TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAG                         ATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA
genomic: TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAGgtgcgagtct ... tattttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA
EST: gi|110694202|gb|EE071104.1|EE071104
EST:     TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAG                         ATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA
genomic: TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAGgtgcgagtct ... tattttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA
EST: gi|351031018|gb|FQ439054.1|FQ439054
EST:     TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAG                         ATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA
genomic: TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAGgtgcgagtct ... tattttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA
EST: gi|27755123|gb|CB035878.1|CB035878
EST:     TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAG                         ATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA
genomic: TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAGgtgcgagtct ... tattttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA
EST: gi|77582239|gb|DV220083.1|DV220083
EST:     TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAG                         ATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA
genomic: TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAGgtgcgagtct ... tattttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA
EST: gi|110357183|gb|EC920553.1|EC920553
EST:     TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAG                         ATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA
genomic: TTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAGgtgcgagtct ... tattttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGCATCAGAGGCTGAAACAGCAACAGCAAGCCTTGATGCAGCAAGCTCTTCTTCAGCAGCAGTCGCTCTACCACCCCGGCCTCTTGGCTCCTCCTCAGgtgcgagtcttttttggtttctggttctatttttttccctgggatttgtttttgggtgatcgatgtccttgcgattagatgtttggatttggctcgtttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC