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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttgggttggtgtgcctgccatctcctgtatgagctgatatctacttttatgtattttcatttaaatttgatggtttgaaagctcatgagttcttccagGTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCAGCCCCTGGTCACACAACAGCAGCCAGAGCTCTGGTAGACTGTGCTGTTCGAG

Basic information

species Vitis vinifera
transcript Vv19s0015g01920.t01
intron # 4
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|349812064|gb|FQ410861.1|FQ410861
EST:     ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGG                         GTTTGGGATGTTCTCTCAAATAAGGAAGCTGTCGATATCGTAGCTTCAGCC
genomic: ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGGgtatctttct ... gttcttccagGTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCAGCC
EST: gi|349816839|gb|FQ399707.1|FQ399707
EST:     ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGG                         GTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCAGCC
genomic: ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGGgtatctttct ... gttcttccagGTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCAGCC
EST: gi|349808493|gb|FQ405637.1|FQ405637
EST:     ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGGTGGG                         GTTTGGGATGTTCTCTCAAATAAAGGA-GCTGTTGATATCGTAGCTTCAGC
genomic: ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGGgtatctttct ... gttcttccagGTTTGGGATGTTCTCTCAAATAA-GGAAGCTGTTGATATCGTAGCTTCAGC
EST: gi|349823148|gb|FQ400127.1|FQ400127
EST:     ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGG                         GTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCAACC
genomic: ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGGgtatctttct ... gttcttccagGTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCAGCC
EST: gi|349819638|gb|FQ413522.1|FQ413522
EST:     ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGG                         GTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTGCAGCC
genomic: ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGGgtatctttct ... gttcttccagGTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCAGCC
EST: gi|349813219|gb|FQ411459.1|FQ411459
EST:     ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGG                         GTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCCGCC
genomic: ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGGgtatctttct ... gttcttccagGTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCAGCC
EST: gi|349810260|gb|FQ401706.1|FQ401706
EST:     ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGG                         GTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCAGCC
genomic: ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGGgtatctttct ... gttcttccagGTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCAGCC
EST: gi|349819685|gb|FQ402622.1|FQ402622
EST:     ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGG                         GTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCAGCC
genomic: ATCGCCATCTCACTGAGAGGGATGAGTTCATTATTCTTGCCACTGATGGGgtatctttct ... gttcttccagGTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttatgtattttcatttaaatttgatggtttgaaagctcatgagttcttccagGTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCAGCCCCTGGTCACACAACAGCAGCCAGAGCTCTGGTAGACTGTGCTGTTCGAG
                     atttgat  putative branch site (score: 5)
                                              ttcttcc  putative PPT
     atgtattttcatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttgggttggtgtgcctgccatctcctgtatgagctgatatctacttttatgtattttcatttaaatttgatggtttgaaagctcatgagttcttccagGTTTGGGATGTTCTCTCAAATAAGGAAGCTGTTGATATCGTAGCTTCAGCCCCTGGTCACACAACAGCAGCCAGAGCTCTGGTAGACTGTGCTGTTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - gggttgg
- - - - - - gtgcctg
- - - - - - - - - -ccatctc
- - - - - - - - - - - - - ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcatga