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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactgacctaaaactcagtagcttcatatcccgaatcccattttaattaggatataaacattgggcctcttaactttgttctaatgaaaaaatcttgcagATCCAAACCGCCCAGGCATGCATATGAAGCTGATTAAATTTCTTCTAAAGCTCAAGGCGCCACGCATTGTTTACGTCTCATGTAATCCTGCCACATGTGC

Basic information

species Vitis vinifera
transcript Vv09s0002g02670.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02670.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA15G02550.1 (Glycine max), 3'ss of exon 7
-----------aactgacctaaaactcagtagcttcatatcccgaatcccattttaattaggatataaacattgggcctcttaactttgttctaatgaaaaaatcttgcagATCCAAACCGCCCAGGCATGCATATGAAGCTGATTAAATTTCTTCTAAAGCTCAAGGCGCCACGCATTGTTTACGTCTCATGTAATCCTGCCACATGTGC
            |||| |  || | |   ||  |    ||   |  |  | ||||   |     | |  ||||   | ||| | | ||||        |||  |  ||||||||| || |||||||| ||||| |||||| ||||||| || |||||||| || | ||| || ||||| || || ||||| ||||||||||||||||||||
tatgttgttcacactggctgaagatt--ataattcacaatattggttgtcgttttgtgtgaccca-atgcattacacttctcaccattgt--------aaacttaatgcagATCCCAATCGCCCAGGAATGCACATGAAGTTGATTAAGTTCCTTCTAAATCTTAGGGCACCTCGCATAGTGTATGTCTCTTGTAATCCTGCCACATGTGC

upper sequence: Vv09s0002g02670.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G42890.1 (Glycine max), 3'ss of exon 8
--aactgacctaaaactcagtagcttcatatcccgaatcccattttaattaggatataaacattgggcctcttaactttgttctaatgaaaaaatcttgcagATCCAAACCGCCCAGGCATGCATATGAAGCTGATTAAATTTCTTCTAAAGCTCAAGGCGCCACGCATTGTTTACGTCTCATGTAATCCTGCCACATGTGC
  |  |    || |   | | || ||   || |  |||     ||   ||    | | | |       |  |  ||||    | | || |||  |  ||||||||| || |||||||| ||||| || ||| |||||||||| || ||||| || | ||| || ||||| || || ||||| || |||||||||||||||||
ttattttgtttacactgctgaagattttaattcacaatattggttgtctttttgtgtcacc--caatgcattacacttctcaccattgtaaacttaatgcagATCCCAATCGCCCAGGAATGCACATTAAGTTGATTAAATTCCTGCTAAATCTTAGGGCACCTCGCATAGTGTATGTCTCTTGCAATCCTGCCACATGTGC
















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|110360458|gb|EC923573.1|EC923573
EST:     TGGTGAAAACTTTGGCAAGGATTTCCCTAAGCCTGATGTGGTCATTTCAG                         ATCCAAACCGCCCAGGCATGCACATGAAGCTGATTAAATTTCTTCTAAAGC
genomic: TGGTGAAAACTTTGGCAAGGATTTCCCTAAGCCTGATGTGGTCATTTCAGgtgatcttct ... aatcttgcagATCCAAACCGCCCAGGCATGCATATGAAGCTGATTAAATTTCTTCTAAAGC
EST: gi|30325919|gb|CD009181.1|CD009181
EST:     TGGTGAAAACTTTGGCAAGGATTTCCCTAAGCCTGATGTGGTCATTTCAG                         ATCCAAACCGCCCAGGCATGCATATGAAGCTGATTAAATTTCT
genomic: TGGTGAAAACTTTGGCAAGGATTTCCCTAAGCCTGATGTGGTCATTTCAGgtgatcttct ... aatcttgcagATCCAAACCGCCCAGGCATGCATATGAAGCTGATTAAATTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaggatataaacattgggcctcttaactttgttctaatgaaaaaatcttgcagATCCAAACCGCCCAGGCATGCATATGAAGCTGATTAAATTTCTTCTAAAGCTCAAGGCGCCACGCATTGTTTACGTCTCATGTAATCCTGCCACATGTGC
                                 ttctaat  putative branch site (score: 2)
                                 ttctaatgaaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactgacctaaaactcagtagcttcatatcccgaatcccattttaattaggatataaacattgggcctcttaactttgttctaatgaaaaaatcttgcagATCCAAACCGCCCAGGCATGCATATGAAGCTGATTAAATTTCTTCTAAAGCTCAAGGCGCCACGCATTGTTTACGTCTCATGTAATCCTGCCACATGTGC

- - - -ctaaaac
- - - - - - - - - - - - catatcc
- - - - - - - - - - - - - - - - -aatccca
- - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcctctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgaaaa