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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCATCAGAAAGTCGGAGTGTCCAAAAGAGCTTGAGCCTGCAGATAGGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctctatttttatatattgacttgttgcatttctcatgtccatgatcgtttgtcactacccatagcggtcagaaaatttacctgtatacctagt...

Basic information

species Vitis vinifera
transcript Vv10s0116g00210.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00210.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G01010.1 (Glycine max), 5'ss of exon 3
AGCATCAGAAAGTCGGAGTGTCCAAAAGAGCTTGAGCCTGCAGATAGGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctctatttttatatattgacttgttgcatttctcatgtccatgatcgtttg-tcactacccatagcggtcagaaaatttacctgtatacctagt
||||| | ||| || |||||||| |||||||||||||||| |||||||||||| |||||| |||| ||||||||| ||||| |||||||||  |  ||||||  ||| |||   |   |||  ||||  |  |||   |  | || |  |  || | | |    |    | |  || ||  |   ||||||   | |
AGCATAAAAAAATCTGAGTGTCCCAAAGAGCTTGAGCCTGAAGATAGGAGGTCATCTGTTAATGTTAACCTCATACGGAGGAATGAGAACTATCGTgtgagttttctgtttgagttatttggtttgtctctgttcaatttactattaaagcatgatgagtttagaccttgtttggataaact-tttgtataagcact

upper sequence: Vv10s0116g00210.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA15G11860.1 (Glycine max), 5'ss of exon 3
AGCATCAGAAAGTCGGAGTGTCCAAAAGAGCTTGAGCCTGCAGATAGGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctctatttttatatattgacttgttgcatttctcatgtccatgatcgtttgtcactacccatag---cggtcagaaaatttacctgtatacctagt
||||| | ||| || |||||||| |||||||||||||||| |||||||||||| |||||| |||| || |||||| ||||| |||||||||  |  ||||||  ||| |||   |   |||  ||||  |  |  |||  |  |  ||          |   | |||     ||  | | |      ||||||   |  
AGCATAAAAAAATCTGAGTGTCCCAAAGAGCTTGAGCCTGAAGATAGGAGGTCATCTGTTAATGTTAATCTCATACGGAGGAATGAGAACTATCGTgtgagttttctgtttgagttatttggtttgtctc--tgttcaattttacaattaaagcaggatgaacttagaccttgtttggacaaacttttgtataagcac-
















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|110712280|gb|EE089721.1|EE089721
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|110719390|gb|EE097311.1|EE097311
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|161718180|gb|FC066004.1|FC066004
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|28962956|gb|CB341989.1|CB341989
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|110691776|gb|EE070262.1|EE070262
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTANGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|161721150|gb|FC071025.1|FC071025
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|110404190|gb|EC970252.1|EC970252
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGAGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|30251570|gb|CB969303.1|CB969303
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|110685329|gb|EE063628.1|EE063628
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|30251625|gb|CB969358.1|CB969358
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|161721790|gb|FC070153.1|FC070153
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAAGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|33403502|gb|CF209129.1|CF209129
EST:     GGAGGTCCTCTGTTCATGCCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|110719961|gb|EE095536.1|EE095536
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCTTTTCAGGGGGGTGGGACGA-CTTTANG
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGG-TGGGACGAACTTTAGG
EST: gi|29785168|gb|CB341921.2|CB341921
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|110384599|gb|EC949049.1|EC949049
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|110362342|gb|EC925870.1|EC925870
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|161718887|gb|FC066370.1|FC066370
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|161713467|gb|FC063098.1|FC063098
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|33403419|gb|CF209046.1|CF209046
EST:     GGAGGTCCTCTGTTCATGCCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|110725917|gb|EE102878.1|EE102878
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|30255050|gb|CB971497.1|CB971497
EST:     AGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|110711891|gb|EE088884.1|EE088884
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAAAAAAGACCCGGGGTTC-ATTTCAGGGGGTGGGACGAACTTTAGG
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGG-TTCCATTTCAGGGGGTGGGACGAACTTTAGG
EST: gi|30305911|gb|CB982705.1|CB982705
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|110688136|gb|EE066344.1|EE066344
EST:     GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: GGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
EST: gi|110381091|gb|EC946406.1|EC946406
EST:     TGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCC                         GAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA
genomic: TGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctc ... tttcttgcagGAATCAGAAAAGACCCGGGTTCCATTTCAGGGGGTGGGACGAACTTTAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCATCAGAAAGTCGGAGTGTCCAAAAGAGCTTGAGCCTGCAGATAGGAGGTCCTCTGTTCATGTCAACCTCATAAGGAGGGATGAGAACTGCCCCgtgagtcctctatttttatatattgacttgttgcatttctcatgtccatgatcgtttgtcactacccatagcggtcagaaaatttacctgtatacctagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaat