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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgaacttgaactaccatcatttctattcctttttctttacatttatacattgtttagcatgttctttctttgtaccatagtaatctttttttcaatttggttatatattttttgagtaaatcatgagatttcttgatgcagGTAGTTTCCTATCATTGACAAGAAACTGGAGCCCTGGTGATAAATTGACCCTTCAGCTGCCCATTAGACTAAGAACAGAGGCTATTAAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g01770.t01
intron # 10
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|349825269|gb|FQ417990.1|FQ417990
EST:     TGGTGCCAAAGCCTCAATTAATGCTCAGGATCTGCCTGTACCAGCTCCAA                         GTAGTTTCCTATCATTGACAAGAAACTGGAGCCCTGGTGATAAATTGACCC
genomic: TGGTGCCAAAGCCTCAATTAATGCTCAGGATCTGCCTGTACCAGCTCCAAgtgtgaactt ... cttgatgcagGTAGTTTCCTATCATTGACAAGAAACTGGAGCCCTGGTGATAAATTGACCC
EST: gi|351054198|gb|FQ450280.1|FQ450280
EST:     TGGTGCCAAAGCCTCAATTAATGCTCAGGATCTGCCTGTACCAGCTCCAA                         GTAGTTTCCTATCATTGACAAGAAACTGGAGCCCTGGTGATAAATTGACCC
genomic: TGGTGCCAAAGCCTCAATTAATGCTCAGGATCTGCCTGTACCAGCTCCAAgtgtgaactt ... cttgatgcagGTAGTTTCCTATCATTGACAAGAAACTGGAGCCCTGGTGATAAATTGACCC
EST: gi|110699440|gb|EE076439.1|EE076439
EST:     TGGTGCCAAAGCCTCAATTAATGCTCAGGATCTGCCTGTACCAGCTCCAA                         GTAGTTTCCTATCATTGACAAGAAACTGGAGCCCTGGTGATAAATTGACCC
genomic: TGGTGCCAAAGCCTCAATTAATGCTCAGGATCTGCCTGTACCAGCTCCAAgtgtgaactt ... cttgatgcagGTAGTTTCCTATCATTGACAAGAAACTGGAGCCCTGGTGATAAATTGACCC
EST: gi|351022487|gb|FQ447009.1|FQ447009
EST:     TGGTGCCAAAGCCTCAATTAATGCTCAGGATCTGCCTGTACCAGCTCCAA                         GTAGTTTCCTATCATTGACAAGAAACTGGAGCCCTGGTGATAAATTGACCC
genomic: TGGTGCCAAAGCCTCAATTAATGCTCAGGATCTGCCTGTACCAGCTCCAAgtgtgaactt ... cttgatgcagGTAGTTTCCTATCATTGACAAGAAACTGGAGCCCTGGTGATAAATTGACCC
EST: gi|110723755|gb|EE101433.1|EE101433
EST:     ATTAATGCTCAGGATCTGCCTGTACCAGCTCCAA                         GTAGTTTCCTATCATTGACAAGAAACTGGAGCCCTGGTGATAAATTGACCC
genomic: ATTAATGCTCAGGATCTGCCTGTACCAGCTCCAAgtgtgaactt ... cttgatgcagGTAGTTTCCTATCATTGACAAGAAACTGGAGCCCTGGTGATAAATTGACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttcaatttggttatatattttttgagtaaatcatgagatttcttgatgcagGTAGTTTCCTATCATTGACAAGAAACTGGAGCCCTGGTGATAAATTGACCCTTCAGCTGCCCATTAGACTAAGAACAGAGGCTATTAAAG
                                            tcttgat  putative branch site (score: 4)
                                          tttctt  CT-rich tract
       aatttggttatatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgaacttgaactaccatcatttctattcctttttctttacatttatacattgtttagcatgttctttctttgtaccatagtaatctttttttcaatttggttatatattttttgagtaaatcatgagatttcttgatgcagGTAGTTTCCTATCATTGACAAGAAACTGGAGCCCTGGTGATAAATTGACCCTTCAGCTGCCCATTAGACTAAGAACAGAGGCTATTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC