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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattgttcgaaaacaccttcatggttgcctcattttcttattttgtttttatgttttatcattatcttttgaataaagaattgatattatgtttcaatcatgacatctttggtactcatgtgcagAAAAGAAGCTGCATTGCGTCAAAGAGAG

Basic information

species Vitis vinifera
transcript Vv01s0244g00070.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0244g00070.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G44630.1 (Glycine max), 3'ss of exon 6
gtatattgttcgaaaacaccttcatggttgcctcattttcttattttgtttttatgttttatcattatcttttgaataaagaattgatattatgttt--caatcatgacatctt--tggtactcatgtgcagAAAAGAAGCTGCATTGCGTCAAAGAGAG
                                               ||  ||   ||      | | || ||| | |  |  ||    | | || |       |||||| |    |  |||| |  |||||||| ||||| ||||||||||||||||||
-----------------------------------------------gtaattgaattaatgtttaaactgttgcaaatgggttttccttcacgtatagtgtgtatgacacccccatattactaaattgcagAAAGGAAGCAGCATTGCGTCAAAGAGAG

upper sequence: Vv01s0244g00070.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G13260.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatattgttcgaaaacaccttcatggttgcctcattttcttattttgtttttatgttttatcattatcttttgaataaagaattgatattatgtttcaatcatgacatctttggtactcatgtgcagAAAAGAAGCTGCATTGCGTCAAAGAGAG
                        | ||      ||      | ||||||   | |||||  | || | |||    |   | ||||| ||   | ||  || |    | ||||| | |   | |||||||||||||| || |||||||||||||||
-----------------------gtagtcaat--atcaatacaatttgttgcca-gtttt--cgttttttttctgtt---ggattgaaat---gcttacatgaatgta-ctttgtttcatgt-tgcagAAAAGAAGCAGCTTTGCGTCAAAGAGAG
















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|30256262|gb|CB972105.1|CB972105
EST:     TGCTGGANCTTGGAGAGGGTGTATCTGANGGAAGCTAAATTGCTGAGCAG                         AAAAGAAGCTGCATTGCGTCAAAGAGAG
genomic: TGCT-GCTCTTGGAGAGGGTGTATCT-CTGGAAGCTAAATTGCTGAGCAGgtatattgtt ... tcatgtgcagAAAAGAAGCTGCATTGCGTCAAAGAGAG
EST: gi|161717169|gb|FC066567.1|FC066567
EST:     GTTGCTTCTCTTGGAGAGGGTGTATCTCTGGGAGCTAAATTGCTGAGCAG                         AAAAGAAGCTGCATTTGCGTCAA-GAGAG
genomic: GTTGCTGCTCTTGGAGAGGGTGTATCTCTGGAAGCTAAATTGCTGAGCAGgtatattgtt ... tcatgtgcagAAAAGAAGCTGCATT-GCGTCAAAGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaataaagaattgatattatgtttcaatcatgacatctttggtactcatgtgcagAAAAGAAGCTGCATTGCGTCAAAGAGAG
        aattgat  putative branch site (score: 4)
        aattgatattatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattgttcgaaaacaccttcatggttgcctcattttcttattttgtttttatgttttatcattatcttttgaataaagaattgatattatgtttcaatcatgacatctttggtactcatgtgcagAAAAGAAGCTGCATTGCGTCAAAGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA