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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcatataagaaagcagtagctatacactatgctgatttttccatgatttgcaaaattctcttttgtttgttagaactgatatattgaactgggttcagGTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGG

Basic information

species Vitis vinifera
transcript Vv06s0004g03140.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g03140.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G07570.1 (Glycine max), 3'ss of exon 7
-----------tctcatataagaaagcagtagctatacactatgctgatttttccatgatttgcaaaattctcttttgtttgttagaactgatatattgaactgggttcagGTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGG
            ||||| ||| | |     | |||||   |||  |  ||    |||    ||  ||  |   |      | || ||     | | ||||| ||  | |||||||| ||||| ||||| || || || |||   |||||||| ||||| ||||| ||||| |||||||||||||||||
agaaacaggatgctcatgtaatataa----aactatattttattatagttcagacatatgctgagaa--tgcataacacgtatttgat----tgtgttgaattgaat-cagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCATTCATCATTGAGAAGGGAATGCCTGG

upper sequence: Vv06s0004g03140.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 7
tctcatataagaaagcagtagctatacactatgctgatttttccatgatttgcaaaattctcttttgtttgttagaac-----tgat-atattgaactgggttcagGTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGG
      |  || | ||    |  ||| |  |   |||||||   ||  ||    | ||   ||     |   ||| ||     ||||  | ||||| ||  | |||||||| ||||| ||||| || || || |||   |||||||| ||||| ||||| ||||| |||||||||||||||||
---agaaacaggatgctcatgtaatataaaac-ttgattttattatagttca-gacatatgctgagaatgcatagcacgtatttgattgtgttgaattgaat-cagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCATTCATCATTGAGAAGGGAATGCCTGG
















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|352772844|gb|FQ470459.1|FQ470459
EST:     TAAATGGAAACAAGATGTGGTGCACCAATGGTCCAATTGCTCAGACACTG                         GTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCA
genomic: TAAATGGAAACAAGATGTGGTGCACCAATGGTCCAATTGCTCAGACACTGgtatcttcat ... ctgggttcagGTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCA
EST: gi|352764155|gb|FQ467725.1|FQ467725
EST:     TAAATGGAAACAAGATGTGGTGCACCAATGGTCCAATTGCTCAGACACTG                         GTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCA
genomic: TAAATGGAAACAAGATGTGGTGCACCAATGGTCCAATTGCTCAGACACTGgtatcttcat ... ctgggttcagGTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCA
EST: gi|22010794|gb|BQ795828.1|BQ795828
EST:     TAAATGGAAACAAGATGTGGTGCACCAATGGTCCAATTGCTCAGACACTG                         GTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCA
genomic: TAAATGGAAACAAGATGTGGTGCACCAATGGTCCAATTGCTCAGACACTGgtatcttcat ... ctgggttcagGTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCA
EST: gi|352781928|gb|FQ469225.1|FQ469225
EST:     TAAATGGAAACAAGATGTGGTGCACCAATGGTCCAATTGCTCAGACACTG                         GTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCA
genomic: TAAATGGAAACAAGATGTGGTGCACCAATGGTCCAATTGCTCAGACACTGgtatcttcat ... ctgggttcagGTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCA
EST: gi|352772398|gb|FQ469923.1|FQ469923
EST:     TAAATGGAAACAAGATGTGGTGCACCAATGGTCCAATTGCTCAGACACTG                         GTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAGGGAATTACAGCA
genomic: TAAATGGAAACAAGATGTGGTGCACCAATGGTCCAATTGCTCAGACACTGgtatcttcat ... ctgggttcagGTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCA
EST: gi|110729869|gb|EE106297.1|EE106297
EST:     TAAATGGAAACAAGATGTGGTGCACCAATGGTCCAATTGCTCAGACACTG                         GTTGTTTATGCGAAAACAGATATTACAGCTCATTCAAAAGGAATTACAGCA
genomic: TAAATGGAAACAAGATGTGGTGCACCAATGGTCCAATTGCTCAGACACTGgtatcttcat ... ctgggttcagGTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCA
EST: gi|352778090|gb|FQ467143.1|FQ467143
EST:     TAAATGGAAACAAGATGTGGTGCACCAATGGTCCCATTGCTCAGACACTG                         GTTGTTTATGCCAAAACGGATATTACAGCTCA
genomic: TAAATGGAAACAAGATGTGGTGCACCAATGGTCCAATTGCTCAGACACTGgtatcttcat ... ctgggttcagGTTGTTTATGCGAAAACGGATATTACAGCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttgcaaaattctcttttgtttgttagaactgatatattgaactgggttcagGTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGG
                              aactgat  putative branch site (score: 3)
                                   atatattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcatataagaaagcagtagctatacactatgctgatttttccatgatttgcaaaattctcttttgtttgttagaactgatatattgaactgggttcagGTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - gaaagca
- - - - - - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - - - - - ccatgat