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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttatagtttctcttatttgctcctttctctttaagcatgctatttcttttttagtcatgtattaatttattttcttccctttaatcctatccttttccattctttgctgaggaactgcagGGAGATGGTAGTTGTTCATCCAGACCAAGAATTTCTTGACGACATCGCTGGAAAGCTAAAAGAG

Basic information

species Vitis vinifera
transcript Vv05s0102g00100.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0102g00100.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os06g43760.1 (Oryza sativa), 3'ss of exon 17
gtatgcttatagtttctcttatttgctcctttctctttaagcatgctatttcttttttagtcatgtattaatttattttcttccctttaatcctatc-cttttccattctttgctgaggaactgcagGGAGATGGTAGTTGTTCATCCAGACCAAGAATTTCTTGACGACATCGCTGGAAAGCTAAAAGAG
   |   | | ||||||  ||||    |||||  ||| | | ||   |   ||| ||      |||||      ||| |||||  |||   | |||  |||  ||| |||        ||  | ||||||||||||  |||||||||| ||| | ||||||||||| |||||  | |||||||||||||||
---tatgtgttgtttctggtatt----ccttttgcttcatg-atataaaagcttgttc-----tgtat------attatcttcaattttgccatatggcttaaccaatct--------gagtttcagGGAGATGGTGATTGTTCATCCTGACAATGAATTTCTTGAAGACATAACGGGAAAGCTAAAAGAG

upper sequence: Vv05s0102g00100.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G158627_T02 (Zea mays), 3'ss of exon 4
gtatgcttatagtttctcttatttgctcctttctctttaagcatgctatttcttttttagtcatgtattaatttattttcttccctttaatcctatccttttccattctttgctgaggaactgcagGGAGATGGTAGTTGTTCATCCAGACCAAGAATTTCTTGACGACATCGCTGGAAAGCTAAAAGAG
                |   ||||  || |  |  |||||       ||     ||  |   |||||  | |  ||||  |  | || | |  | |||| |     |   ||||  | |  | |||||||||||| ||||| ||||||||| | || |||||||| |||||  |||| || |||||||||
---------------attaaattttttcataacattttaaa------ataaaagttggaaaaatgtac-attgcatttagtagcattcagttgtgtcctgt---ggtgactgctttg-agtttcagGGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAG
















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|71861509|gb|DT010564.1|DT010564
EST:     GCTCGCAATATTCGTGAGCGTCACAATAAGCCCGTGAAAACACCACTCAG                         GGAGATGGTAGTTGTTCATCCAGACCAAGAATTTCTTGACGACATCGCTGG
genomic: GCTCGCAATATTCGTGAGCGTCACAATAAGCCCGTGAAAACACCACTCAGgtatgcttat ... ggaactgcagGGAGATGGTAGTTGTTCATCCAGACCAAGAATTTCTTGACGACATCGCTGG
EST: gi|33403916|gb|CF209543.1|CF209543
EST:     GCTCGCAATATTCGTGAGCGTCACAATAAGCCCGTGAAAACACCACTCAG                         GGAGATGGTAGTTGTTCATCCAGACCAAGAATTTCTTGACGACATCGCTGG
genomic: GCTCGCAATATTCGTGAGCGTCACAATAAGCCCGTGAAAACACCACTCAGgtatgcttat ... ggaactgcagGGAGATGGTAGTTGTTCATCCAGACCAAGAATTTCTTGACGACATCGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattttcttccctttaatcctatccttttccattctttgctgaggaactgcagGGAGATGGTAGTTGTTCATCCAGACCAAGAATTTCTTGACGACATCGCTGGAAAGCTAAAAGAG
             ctttaat  putative branch site (score: 4)
              tttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttatagtttctcttatttgctcctttctctttaagcatgctatttcttttttagtcatgtattaatttattttcttccctttaatcctatccttttccattctttgctgaggaactgcagGGAGATGGTAGTTGTTCATCCAGACCAAGAATTTCTTGACGACATCGCTGGAAAGCTAAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA