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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcatactttgatggcatgcttggcactcccaactccatgtatggaggaatctctattttccaattttttattgtgcttgtaattgtgtttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACAGCAACTGAGAGGACCATCTGCTGCATCCTTGAGAACTACCAGAAGGAAG

Basic information

species Vitis vinifera
transcript Vv14s0128g00370.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0128g00370.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA10G29600.1 (Glycine max), 3'ss of exon 8
aatcatactttgatggcatgcttggc-actcccaactccatgtatggaggaatctctat---tttccaattttttattgtgcttgtaattgtgtttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACAGCAACTGAGAGGACCATCTGCTGCATCCTTGAGAACTACCAGAAGGAAG
 || | ||||| ||       |   | | |   ||| |||||||          |  ||   |||  | | ||  | | ||| |||  ||   |||    |||||||||||||||||| |||||||||||||||||||| |||||||| || || || |||||||||||||| |||||||| || |||||| ||||||||||||
-attaaacttttattttggcttcaactaattttaaccccatgtacatgaatgctttcataagttttaactgttggactatgcatgtttttaacttt---cgcagAGCAATGAGCAGATGAAGCAATATGTTCACTTGTTAAACTCTACTCTAACGGCTACTGAGAGGACCATTTGCTGCATACTGGAGAACAACCAGAAGGAAG

upper sequence: Vv14s0128g00370.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA20G37700.1 (Glycine max), 3'ss of exon 8
aatcatacttt-gatggcatgcttggcactcccaactccatgtatggaggaatctctattttccaattt--tttattgtgcttgtaattgtgtttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACAGCAACTGAGAGGACCATCTGCTGCATCCTTGAGAACTACCAGAAGGAAG
 || | |||||  || ||       |   |          ||    ||| ||| | |  ||     ||    | | | ||| |||  ||    ||  |  |||||||||||||| || ||||||||||||||||||||||||||||| || || || |||||||||||||| |||||||| || |||||| ||||||||||||
-attaaacttttaatagctcaaagtgtgttgttgggattttgccgtgagtaatattttattctggcttcaactaactttgcatgttttttaactt--tcacagAGCAATGAGCAAATGAAGCAATATGTTCACTTGTTGAACTCTACTCTAACGGCTACTGAGAGGACCATTTGCTGCATACTAGAGAACAACCAGAAGGAAG
















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|27582221|gb|CB004916.1|CB004916
EST:     GTACTGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAG                         AGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
genomic: GTACCGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAGgttagtcctg ... ttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
EST: gi|110723248|gb|EE100342.1|EE100342
EST:     GTACTGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAG                         AGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
genomic: GTACCGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAGgttagtcctg ... ttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
EST: gi|30132449|gb|CB917788.1|CB917788
EST:     GTACTGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAG                         AGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
genomic: GTACCGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAGgttagtcctg ... ttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
EST: gi|110366356|gb|EC930222.1|EC930222
EST:     GTACCGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAG                         AGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
genomic: GTACCGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAGgttagtcctg ... ttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
EST: gi|30325038|gb|CD008300.1|CD008300
EST:     GTACTGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAG                         AGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
genomic: GTACCGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAGgttagtcctg ... ttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
EST: gi|110427592|gb|EC994039.1|EC994039
EST:     GTACTGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAG                         AGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
genomic: GTACCGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAGgttagtcctg ... ttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
EST: gi|87584849|gb|DY473852.1|DY473852
EST:     GTACTGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAG                         AGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
genomic: GTACCGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAGgttagtcctg ... ttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
EST: gi|29784787|gb|CB341220.2|CB341220
EST:     GTACTGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAG                         AGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
genomic: GTACCGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAGgttagtcctg ... ttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
EST: gi|110375281|gb|EC940255.1|EC940255
EST:     GTACTGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAG                         AGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
genomic: GTACCGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAGgttagtcctg ... ttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
EST: gi|32267603|gb|CD716566.1|CD716566
EST:     GTACTGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAG                         AGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA
genomic: GTACCGACTACCAGTCCAGAAGATTAGAAATTCGATATGGACAGAAAAAGgttagtcctg ... ttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggaatctctattttccaattttttattgtgcttgtaattgtgtttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACAGCAACTGAGAGGACCATCTGCTGCATCCTTGAGAACTACCAGAAGGAAG
        tctattttccaatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcatactttgatggcatgcttggcactcccaactccatgtatggaggaatctctattttccaattttttattgtgcttgtaattgtgtttggttgcagAGCAATGAGCAGATAAAGCAATATGTTCACTTGTTGAACTCTACCCTCACAGCAACTGAGAGGACCATCTGCTGCATCCTTGAGAACTACCAGAAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - -gcatgct
- - - - - - - - - - - - -cactccc
- - - - - - - - - - - - - - - - - - ccatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcttg