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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttggatttgttatctttttctttgtatatattttgcttccagttttttctattgataagctacctaaaggcctatagccttattttgttttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGTGATG

Basic information

species Vitis vinifera
transcript Vv13s0067g02900.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g02900.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G062391_T01 (Zea mays), 3'ss of exon 2
ttttggatttgttatctttttct-ttgtatatatt--ttgcttccagtttt-ttctattgataagctacctaaaggcctata-gccttattttgttttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGTGATG
    |  || ||| | ||   || ||||| |  ||  | | |  || |  | || |||| || || |   | |   | |||| |     ||    | ||||  |||| ||||| || || ||  |||| |||||  ||||||||||| | |||||||| || ||||| |||||||||||||| |||||||
----gtgttcgtttttttgaactattgtacactttactggttcacaatcctgttgtattaattagttggatgacc-cttatatgttgctttacaatctcttgcagAGGGACACGACCGGACTTTCTACAGAAAATGCAGAGCTTAAGATAAGGTTACAGGCCATGGAGCAACAAGCTCAACTCCGTGATG

upper sequence: Vv13s0067g02900.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G40010.1 (Glycine max), 3'ss of exon 2
--------ttttggatttgttatctttttctttgtatatattttgcttccagttttttctattgataagctacctaaaggcctatagccttattttgttttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGTGATG
        |||   |||  |||  ||  |  ||| |||||| |  |  |  |   ||  ||||   | ||||||| | | | |||    |        | | ||  ||||||| |||||||| |||||||||||||| |||||| | ||||||||||||||||| ||||||||||||||| |  || ||||||
gcactttgtttccaattcattaagttgat--ttggatatatgtaacagc--ggcattcatatt---atgctacctga-gacttattctttctgaaacatctttttcagAGAGATACAACTGGTCTGACTACTGAAAATACAGAGTTGAAGCTTAGGTTACAAGCCATGGAACAACAAGCTAACTTATGTGATG
















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|351047307|gb|FQ454918.1|FQ454918
EST:     CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAG                         AGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA
genomic: CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAGgtttttgttt ... tttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA
EST: gi|352786028|gb|FQ481823.1|FQ481823
EST:     CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAG                         AGAGACACAACTGGCCTGACTACTGAAAACACAGAGCT
genomic: CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAGgtttttgttt ... tttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCT
EST: gi|110390594|gb|EC955513.1|EC955513
EST:     CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAG                         AGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA
genomic: CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAGgtttttgttt ... tttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA
EST: gi|351034403|gb|FQ463216.1|FQ463216
EST:     CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAG                         AGAGACACAACTGGGCCTGACTACTGAAAACACAGAGCTTAAGC
genomic: CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAGgtttttgttt ... tttcttatagAGAGACACAACTGG-CCTGACTACTGAAAACACAGAGCTTAAGC
EST: gi|351013711|gb|FQ433863.1|FQ433863
EST:     CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAG                         AGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAA
genomic: CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAGgtttttgttt ... tttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAA
EST: gi|351030452|gb|FQ432390.1|FQ432390
EST:     CCCTTCAA-CAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAG                         AGAGACACAACTGGCCTGACTACTGAAAACACAAAGCTTAAGCTTAGGTTA
genomic: CC-TTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAGgtttttgttt ... tttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA
EST: gi|349807440|gb|FQ401405.1|FQ401405
EST:     CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAG                         AGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA
genomic: CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAGgtttttgttt ... tttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA
EST: gi|161716290|gb|FC068082.1|FC068082
EST:     CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAG                         AGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTT
genomic: CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAGgtttttgttt ... tttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTT
EST: gi|351031577|gb|FQ459834.1|FQ459834
EST:     CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAG                         AGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA
genomic: CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAGgtttttgttt ... tttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA
EST: gi|351052001|gb|FQ450692.1|FQ450692
EST:     CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAG                         AGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA
genomic: CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAGgtttttgttt ... tttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA
EST: gi|349826371|gb|FQ417868.1|FQ417868
EST:     CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAG                         AGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA
genomic: CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAGgtttttgttt ... tttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA
EST: gi|351046408|gb|FQ453024.1|FQ453024
EST:     CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAG                         AGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCT
genomic: CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAGgtttttgttt ... tttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCT
EST: gi|110388249|gb|EC952981.1|EC952981
EST:     CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAG                         AGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA
genomic: CCCTTCAAACAGAAGCAACCACTCTTTCTGCACAACTCACGCTTTTCCAGgtttttgttt ... tttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctattgataagctacctaaaggcctatagccttattttgttttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGTGATG
                  acctaaa  putative branch site (score: 3)
                                  ccttattttgttttct  putative PPT
                                    ttattttgttttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttggatttgttatctttttctttgtatatattttgcttccagttttttctattgataagctacctaaaggcctatagccttattttgttttcttatagAGAGACACAACTGGCCTGACTACTGAAAACACAGAGCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - gcttcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctaaa