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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatttgagtgataaaaacccttgattcaccacaagtcagtatttatctgttctgactttccatattttcctgatgaccacatcctctttctcatgacagATTCTTGGCATTCTTGATTTTGGTCGTGATGCTTGGATACATAGGGAGGACTGGATTCGCAGGGGGATTCATGTTGGAAGTGGCAGAAAGTATAAGGACT

Basic information

species Vitis vinifera
transcript Vv05s0049g00190.t01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g00190.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: LOC_Os04g09860.2 (Oryza sativa), 3'ss of exon 19
-------ctatttgagtgataaaaacccttgattcaccacaagtcagtatttatctgttctgactttccatattttcctgatgaccacatcctctttctcatgacagATTCTTGGCATTCTTGATTTTGGTCGTGATGCTTGGATACATAGGGAGGACTGGATTCGCAGGGGGATTCATGTTGGAAGTGGCAGAAAGTATAAGGACT
         ||   | || |    |   ||| ||  |  |   | | | |    || ||    || |   ||| || |  ||   || |  | ||  ||  | ||||||| | ||| | |||||| ||||||||||||||||||||||||| || || |||  |   |  ||  | ||  | || ||||| ||||| |||| ||| |
gtaaaaagcatgcaaatg-tgtgcagtgttgttttgctcctttttattttccccctttttgcgctct---tatatttcaaat--tcataagccctaacttgt-acagATTTTGGGCGTACTTGATATTGGTCGTGATGCTTGGATACATAGAGAAGATTGGGCTAAAAATGGTGTCCACATAGGGAGTGGGAGAAAATATAGGGATT
















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|71876443|gb|DT025498.1|DT025498
EST:     TTTTACAATCAAGAACAAATCCGACCTTTGTGTCATGGAAAGGTGGAGCA                         ATTCTTGGCATTCTTGATTTTGGTCGTGATGCTTGGATACATAGGGAGGAC
genomic: TTTTACAATCAAGAACAAATCCGACCTTTGTGTCATGGAAAGGTGGAGCTgtaagtcaag ... ctcatgacagATTCTTGGCATTCTTGATTTTGGTCGTGATGCTTGGATACATAGGGAGGAC
EST: gi|351014200|gb|FQ434789.1|FQ434789
EST:     TTTTACAATCAAGAACAAATCCGACCTTTGTGTCATGGAAAGGTGGAGCT                         ATTCTTGGCATTCTTGATTTTGGTCGTGATGCTTGGATACATAGGGAGGAC
genomic: TTTTACAATCAAGAACAAATCCGACCTTTGTGTCATGGAAAGGTGGAGCTgtaagtcaag ... ctcatgacagATTCTTGGCATTCTTGATTTTGGTCGTGATGCTTGGATACATAGGGAGGAC
EST: gi|351041158|gb|FQ444135.1|FQ444135
EST:     TTTTACAATCAAGAACAAATCCGACCTTTGTGTCATGGAAAGGTGGAGCT                         ATTCTTGGCATTCTTGATTTTGGTCGTGATGCTTGGATACATAGGGAGGAC
genomic: TTTTACAATCAAGAACAAATCCGACCTTTGTGTCATGGAAAGGTGGAGCTgtaagtcaag ... ctcatgacagATTCTTGGCATTCTTGATTTTGGTCGTGATGCTTGGATACATAGGGAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgttctgactttccatattttcctgatgaccacatcctctttctcatgacagATTCTTGGCATTCTTGATTTTGGTCGTGATGCTTGGATACATAGGGAGGACTGGATTCGCAGGGGGATTCATGTTGGAAGTGGCAGAAAGTATAAGGACT
                                ccacatcctctttctc  CT-rich tract
                 atatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatttgagtgataaaaacccttgattcaccacaagtcagtatttatctgttctgactttccatattttcctgatgaccacatcctctttctcatgacagATTCTTGGCATTCTTGATTTTGGTCGTGATGCTTGGATACATAGGGAGGACTGGATTCGCAGGGGGATTCATGTTGGAAGTGGCAGAAAGTATAAGGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - -ataaaaa
- - - - - - - - - cccttga
- - - - - - - - - - - - - -caccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcctc