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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattcatatgtgttatttgagattggcctttttatttttatttttttatttactaattatttctgtgtggtggtttttgaaatttggatcgtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAGTTGTGCGCTTCTCCTTCTTCTGTAAATGGGCTGCTTTCAGTCAACAGCA

Basic information

species Vitis vinifera
transcript Vv02s0236g00140.t01
intron # 1
splice site 3'
intron type U2

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|352789785|gb|FQ478600.1|FQ478600
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAG--C--TCG                         GTC-GGATGGTTTTGATGATGTATTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|349822445|gb|FQ412709.1|FQ412709
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAG--C--TCG                         GTC-GGATGGTTTTGATGATGTATTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|71873772|gb|DT022827.1|DT022827
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCG                         GTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|349820979|gb|FQ408687.1|FQ408687
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAG--C--TCG                         GTC-GGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|349819279|gb|FQ412173.1|FQ412173
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAG--C--TCG                         GTC-GGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|71872712|gb|DT021767.1|DT021767
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCG                         GTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|349826413|gb|FQ417910.1|FQ417910
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAG--C--TCG                         GTC-GGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|349832733|gb|FQ422257.1|FQ422257
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCG                         GTCAGGATGGTTTTGATGATGTATTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|161708395|gb|FC056127.1|FC056127
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCG                         GTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|351019013|gb|FQ426512.1|FQ426512
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCG                         GTCAGGATGGTTTTGATGATGTATTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|71863154|gb|DT012209.1|DT012209
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCG                         GTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|351055152|gb|FQ440491.1|FQ440491
EST:     CAAGAGTCTTCGCTTCTCTCCCTTCCTCTTTCGCCGGCCGAG--C--TCG                         GTC-GGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|71864022|gb|DT013077.1|DT013077
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCG                         GTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|71877098|gb|DT026153.1|DT026153
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCG                         GTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|351014198|gb|FQ434787.1|FQ434787
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCG                         GTCAGGATGGTTTTGATGATGTATTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|349815321|gb|FQ400476.1|FQ400476
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAG--C--TCG                         GTC-GGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|351038650|gb|FQ464516.1|FQ464516
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAG--C--TCG                         GTC-GGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|34549400|gb|CF517632.1|CF517632
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGT--                         -T--GGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
EST: gi|110699550|gb|EE076647.1|EE076647
EST:     CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCG                         GTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG
genomic: CAAGAGTCTTCGCTTCTTTCCCTTCCTCTTTCGCCGGCCGAGCTCGGTCGgtaagtgatt ... gtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttactaattatttctgtgtggtggtttttgaaatttggatcgtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAGTTGTGCGCTTCTCCTTCTTCTGTAAATGGGCTGCTTTCAGTCAACAGCA
     tactaat  putative branch site (score: 1)
     tactaattatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattcatatgtgttatttgagattggcctttttatttttatttttttatttactaattatttctgtgtggtggtttttgaaatttggatcgtactgtaagGTCAGGATGGTTTTGATGATGTACTGTAGTGAAGCCTAGGCGGTAGTCTAGTTGTGCGCTTCTCCTTCTTCTGTAAATGGGCTGCTTTCAGTCAACAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggtgg