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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTATGATGCCACAACACATTTTGAGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaactaattattttgccattatgattttgtcattgttgaggttgtgacccactcattgctttagtattgttattgtctgctgctataatctttttt...

Basic information

species Vitis vinifera
transcript Vv05s0094g01550.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0094g01550.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA08G13300.1 (Glycine max), 5'ss of exon 12
AGTTATGATGCCACAACACATTTTGAGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaactaattattttgccattatgattttgtcattgttgaggttgtgacccactcattgctttagtattgttattgt-ctgctgctataatctttttt-
||||||||||| || || || |||||||| || ||    ||||| ||||||||||||||  ||||||||||||||||||    || |   || |  |  |    |||    || ||||  |  |     |  ||  | |   | | ||  ||||| || | |  ||| | | |||| 
AGTTATGATGCTACTACTCACTTTGAGTCGACCGTGGATGATGTTCTCAACATGTATACATTGATAACTGGAAAGgtaagtgtta-tgccttggttaccacttgtttccacttcttgaattaatttttgagccacagatagtg-actgagattgttctacagtaatactgtatttta

upper sequence: Vv05s0094g01550.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA05G30140.1 (Glycine max), 5'ss of exon 12
AGTTATGATGCCACAACACATTTTGAGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaactaattatt--ttgcca-ttatgattttgtcattgttgaggttgtgacccactcattgct-ttagtattgttattgtctgctgctataatctttttt
||||||||||| || || || |||||||| |||||    || || ||||||||||||||  ||||||||||||||||||    ||    ||  || ||| || |     | || |   | |  |||| | ||||  || |    |   ||||||      |  | || || | |     
AGTTATGATGCTACTACTCACTTTGAGTCGACTGTGGATGACGTTCTCAACATGTATACATTGATAACTGGAAAGgtaagtgttatgccttggttaccacttgtttccatttcttgaattaatttgtaagccacaaatagtgactgagattgttccacaatagtactgtatttta----
















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|22007169|gb|BQ792203.1|BQ792203
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGCCCTCAGTGTGGATTTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|33406671|gb|CF212298.1|CF212298
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATTTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|352777878|gb|FQ466931.1|FQ466931
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCCTGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATTTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|352782310|gb|FQ470212.1|FQ470212
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|71873773|gb|DT022828.1|DT022828
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|110692608|gb|EE072046.1|EE072046
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|110728096|gb|EE103364.1|EE103364
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|110731100|gb|EE108936.1|EE108936
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|37188887|gb|CF608236.1|CF608236
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|30323326|gb|CD006588.1|CD006588
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|30137389|gb|CB922727.1|CB922727
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|110386791|gb|EC951416.1|EC951416
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|32245877|gb|CD711696.1|CD711696
EST:     GTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: GTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|33406756|gb|CF212383.1|CF212383
EST:     GTCAACTGTCATGGATGTGGATCA-CATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGC
genomic: GTCAACTGTCATGGATGTGC-TCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGC
EST: gi|110371769|gb|EC935892.1|EC935892
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|352768234|gb|FQ469409.1|FQ469409
EST:     AGTCAACTGTCATGGATGTGCTCAATATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|71888788|gb|DT037843.1|DT037843
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAAAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|110692538|gb|EE071896.1|EE071896
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
EST: gi|110418003|gb|EC984109.1|EC984109
EST:     AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAG                         GTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA
genomic: AGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaacta ... ttttgtgcagGTTCTGGACCTCAGTGTGGATCTAAGTGCTGCCAGCGCTGCAGAAGAATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTATGATGCCACAACACATTTTGAGTCAACTGTCATGGATGTGCTCAACATGTATACCATGATAACTGGAAAGgtaaaaactaattattttgccattatgattttgtcattgttgaggttgtgacccactcattgctttagtattgttattgtctgctgctataatctttttt

- - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccactc