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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtttggaggtggtgcactgggctggttaatgcacaggtatatttgacaatgtgactgcaaaggggctaattttgttttgctcacataaattcgtgcagGTTCATGAAGGGAGAAATCATGAAGTTCGGGAGCTTGTGAAAAGTGCTGGACTTCAG

Basic information

species Vitis vinifera
transcript Vv13s0019g04740.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04740.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os03g05806.1 (Oryza sativa), 3'ss of exon 7
atgtttggaggtggtgcactgggctggttaatgcacaggtatatttgacaatgtgactgcaaaggggctaattt-tgttttgctcacataaat-tcgtgcagGTTCATGAAGGGAGAAATCATGAAGTTCGGGAGCTTGTGAAAAGTGCTGGACTTCAG-------------------------------------------
 | ||   |  |   ||| |    | |   ||| | |  |  |   | ||  |    ||   |    || |||  | |  |  |    | ||| ||  ||||||||||||||| ||||||||||||||||| || || ||| | | ||| || ||  ||                                           
gtattcttaactaaagcaattctataga-gatgtaaacttgcaaa-ggcatagcatttggtcatctactcattggtatgctattttttttaatgtctggcagGTTCATGAAGGAAGAAATCATGAAGTTCGTGAACTCGTGCAGAATGCAGGCCTAGAGGTTTGTTTGTATGCTCAATATTTTTTTTCTCAAGTTTTCCCTT
















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|34543504|gb|CF511736.1|CF511736
EST:     AGCTACTACCACCACAGCCAAATATATCGAAACCTAGACTTCGTGTTGTG                         GTTCATGAAGGGAGAAATCATGAAGTTCGGGAGCTTGTGAAAAGTGCTGGA
genomic: AGCTACTACCACCACAGCCAAATATATCGAAACCTAGACTTCGTGTTGTGgtactatttt ... attcgtgcagGTTCATGAAGGGAGAAATCATGAAGTTCGGGAGCTTGTGAAAAGTGCTGGA
EST: gi|30256420|gb|CB972263.1|CB972263
EST:     AGCTACTACCACCACAGCCAAATATATCGAAACCTAGACTTCGTGTTATG                         GTTCATGAAGGGAGAAATCATGAAGTTCGGGAACTTGTGAAAAGTGCTGGA
genomic: AGCTACTACCACCACAGCCAAATATATCGAAACCTAGACTTCGTGTTGTGgtactatttt ... attcgtgcagGTTCATGAAGGGAGAAATCATGAAGTTCGGGAGCTTGTGAAAAGTGCTGGA
EST: gi|110701324|gb|EE078768.1|EE078768
EST:     AGCTACTACCACCACAGCCAAATATATCGAAACCTANACTTCGTGTTGTG                         GTTCATGAAGGGAGAAATCATGAAGTTCGGGAAACTTGTGAAA-GTGCTGG
genomic: AGCTACTACCACCACAGCCAAATATATCGAAACCTAGACTTCGTGTTGTGgtactatttt ... attcgtgcagGTTCATGAAGGGAGAAATCATGAAGTTCGGGAG-CTTGTGAAAAGTGCTGG
EST: gi|161715781|gb|FC065148.1|FC065148
EST:     AGCTACTAC-ACCACAGCCAA-TATATCGAAAC-TAGACTTC-TGT-GTG                         GT-CATGAAGG-AGAA-TCATGA-GTTCGG-AGCT-GTGAA
genomic: AGCTACTACCACCACAGCCAAATATATCGAAACCTAGACTTCGTGTTGTGgtactatttt ... attcgtgcagGTTCATGAAGGGAGAAATCATGAAGTTCGGGAGCTTGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacaatgtgactgcaaaggggctaattttgttttgctcacataaattcgtgcagGTTCATGAAGGGAGAAATCATGAAGTTCGGGAGCTTGTGAAAAGTGCTGGACTTCAG
                                  tgctcac  putative branch site (score: 2)
                       taattttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtttggaggtggtgcactgggctggttaatgcacaggtatatttgacaatgtgactgcaaaggggctaattttgttttgctcacataaattcgtgcagGTTCATGAAGGGAGAAATCATGAAGTTCGGGAGCTTGTGAAAAGTGCTGGACTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
-tgtttgg
- - - - -ggtggtg
- - - - - - - - - - gggctgg
- - - - - - - - - - - - - - -aatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgactgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctcaca