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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaacttgtattctttgtttttctttttcaactaaacctgtgtctcttattcgctatacctctgttaatttgttttctttttctttcaatgtctcttcagCTGGCCCCTAGGCAGGAGCCTGTTCTTGATTCTTCCAAGTACACTGCTGCTGATGTGCGCATT

Basic information

species Vitis vinifera
transcript Vv04s0023g00800.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaacttgtattctttgtttttctttttcaactaaacctgtgtctcttattcgcta-tacctctgttaatttgttttctttttctttcaatgtct-cttcagCTGGCCCCTAGGCAGGAGCCTGTTCTTGATTCTTCCAAGTACACTGCTGCTGATGTGCGCATT
      || ||  |   | | ||| |  | ||| |     ||| |  ||||  |   ||| | | ||| ||  |     | || |  |  |   |  |||||||  |  |||| || || |||||  | |||||  ||||||||||||||||||| |||||||||
--gttctgcatgttccttatgtctctccctactcacttattgtataatattttcccctacttttattagttcctaagagtgttgtgcctgtacatgtttcagCTTACTGCTAGACAAGAACCTGTAGTGGATTCAACCAAGTACACTGCTGCTGACGTGCGCATT
















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|33403422|gb|CF209049.1|CF209049
EST:     TGATAGACGAGGCACAGAAAGCATTGGAAGAGGCTGAAGCACTTAAGAAG                         CTGGCCCCTAGGCAGGAGCCTGTTCTTGATTCTTCCAAGTACACTGCTGCT
genomic: TGATAGACGAGGCACAGAAAGCATTGGAAGAGGCTGAAGCACTTAAGAAGgtttgtgttt ... gtctcttcagCTGGCCCCTAGGCAGGAGCCTGTTCTTGATTCTTCCAAGTACACTGCTGCT
EST: gi|110698321|gb|EE075705.1|EE075705
EST:     TGATAGACGAGGCACAGAAAGCATTGGGAGAGGCTGAAGCACTTAAGAAG                         CTGGCCCCTAGGCAGGAGCCTGTTCTTGATTCTTCCA
genomic: TGATAGACGAGGCACAGAAAGCATTGGAAGAGGCTGAAGCACTTAAGAAGgtttgtgttt ... gtctcttcagCTGGCCCCTAGGCAGGAGCCTGTTCTTGATTCTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattcgctatacctctgttaatttgttttctttttctttcaatgtctcttcagCTGGCCCCTAGGCAGGAGCCTGTTCTTGATTCTTCCAAGTACACTGCTGCTGATGTGCGCATT
                 tgttaat  putative branch site (score: 3)
                       tttgttttctttttct  CT-rich tract
                   ttaatttgttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttgtattctttgtttttctttttcaactaaacctgtgtctcttattcgctatacctctgttaatttgttttctttttctttcaatgtctcttcagCTGGCCCCTAGGCAGGAGCCTGTTCTTGATTCTTCCAAGTACACTGCTGCTGATGTGCGCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - -ctaaacc
- - - - - - - - - - - - - - - - - - - - tgtctct