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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattaaggaattaaaaattttaggaattatttggacaaagcctacgtaacctgtatcaggtttcttatcaatcttattttaccaatttgattgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGAATTGATAGAGCCCACTCTTCGTGAACTACAAGGAAAGATGAGAGAAG

Basic information

species Vitis vinifera
transcript Vv05s0020g01520.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G28440.2 (Glycine max), 3'ss of exon 2
----------tattaaggaattaaaaattttaggaattatttggacaaagcctacgt-aacctgtatcaggtttcttatcaatcttattttaccaatttgattgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGAATTGATAGAGCCCACTCTTCGTGAACTACAAGGAAAGATGAGAGAAG
          |  |||    |   ||||  || | |  |||   | |  || |  |  ||  | |   |  |  ||  |  ||   || |   |   ||||       || || |||||| || || |||||||| ||||| || ||||||||||||||||||||||| ||||| || || |||||||| |||| ||||||||| ||  
tatgcttacttgataacttgtaccaaataatatgtaccatt---atattgcttgggagaatgtatggaaattgactctttgatgccatgtattc--cttgaaca--gATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCTGGGAATTGATTGAGCCTACACTCCGTGAACTTCAAGCAAAGATGAGGGA--

upper sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G11450.1 (Glycine max), 3'ss of exon 2
---------tattaaggaattaaaaattttaggaattatttggacaaagcctacgt-aacctgtatcaggtttcttatcaatcttattttaccaatttgattgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGAATTGATAGAGCCCACTCTTCGTGAACTACAAGGAAAGATGAGAGAAG
         |  |||    |   ||||  || | |  ||||  | |  || |  |  ||  | |   |  |  ||  |  ||   || ||  |   ||||       || || |||||| || || |||||||| ||||| || |||||||||||||||||||| || ||||| || || |||||||| |||| ||||||||| ||  
atgcttacttcataacttgtaccaaataatatgtaccattt--atattgcttgggagaatgtatggaaattgactctttgatgccatgttttc--cttgaaca--gATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCTGGGAATTAATTGAGCCTACACTCCGTGAACTTCAAGCAAAGATGAGGGA--

upper sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G15700.1 (Glycine max), 3'ss of exon 1
--------tattaaggaattaaaaattttaggaattatttggacaaagcctacgtaacctgtatcaggtttcttatcaatcttattttaccaatttgattgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGAATTGATAGAGCCCACTCTTCGTGAACTACAAGGAAAGATGAGAGAAG
        |  |    || | | ||||   |   ||  ||   ||| ||     |||  ||    |  |  |   |  || | || |   |  ||| |  |  |  |    |||||| || || |||||||||||||| |  |||||||||||||||||||| || ||||| ||||| | |||||| |||| ||||||||| ||| 
tggttaattcatgtttaacttataattcatgttctttcttttccaatgctagtataatgtgggggaattgacccttagatgtcatatcttcc-tttaacagATACAA----AATGCCAAAAGTAAAGACAAACCGTGTTACATACCCAGAGGGCTGGGAATTAATTGAGCCTACTCTCCATGAACTTCAAGCAAAGATGAGGGAA-

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|110388722|gb|EC953500.1|EC953500
EST:     CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|77588197|gb|DV223308.1|DV223308
EST:     CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|110390257|gb|EC955158.1|EC955158
EST:     CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|71873094|gb|DT022149.1|DT022149
EST:     CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|110703965|gb|EE081360.1|EE081360
EST:     CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|161712823|gb|FC062346.1|FC062346
EST:     CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|110411061|gb|EC976761.1|EC976761
EST:     GCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: GCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|110384284|gb|EC948712.1|EC948712
EST:     CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|71868362|gb|DT017417.1|DT017417
EST:     CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|110694079|gb|EE070869.1|EE070869
EST:     CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|110390488|gb|EC955400.1|EC955400
EST:     CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|110684956|gb|EE062823.1|EE062823
EST:     CGCGTAGCTTCTATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|34319429|gb|CF372183.1|CF372183
EST:     ATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCT-GGA
genomic: ATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|71873619|gb|DT022674.1|DT022674
EST:     CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|77577432|gb|DV217443.1|DV217443
EST:     CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
EST: gi|30297281|gb|CB974075.1|CB974075
EST:     CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAG                         AATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA
genomic: CGCGTAGCTTCGATCGCGCCGAGTCTCGATTTTGATTTTCTCTCGCATAGgtatgcaaca ... ttgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaacctgtatcaggtttcttatcaatcttattttaccaatttgattgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGAATTGATAGAGCCCACTCTTCGTGAACTACAAGGAAAGATGAGAGAAG
               tttcttatcaatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattaaggaattaaaaattttaggaattatttggacaaagcctacgtaacctgtatcaggtttcttatcaatcttattttaccaatttgattgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGAATTGATAGAGCCCACTCTTCGTGAACTACAAGGAAAGATGAGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - aattaaa
- - - - - - - - - - - - - - - - ggacaaa
- - - - - - - - - - - - - - - - - - - - - - - - acctgta