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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattggtacaaggtcgtgcctattttgttttctaaatactttggtgtttatttttcttaatttacctatttatcaatatcctcataccctactttttcagGTTTTGAGCATGAGTAGACTGGGAGGTGCTGGTGCAGTGGCACAACTCGTGGCTGACATCCCATTGCCAGCAGTTGAG

Basic information

species Vitis vinifera
transcript Vv05s0020g04620.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G004356_T01 (Zea mays), 3'ss of exon 5
cattggtacaaggtcgtgcctattttgttttctaaatactttggtgtttatttttc--ttaatttacctattt-atcaatatc----ctcataccctactttttcagGTTTTGAGCATGAGTAGACTGGGAGGTGCTGGTGCAGTGGCACAACTCGTGGCTGACATCCCATTGCCAGCAGTTGAG
            ||   ||  ||| || |  |   ||  ||   |  |||  |  |  || | |||| | ||| |||| |       |    |  ||      | ||||| | |||||||| || ||||| ||||||||||| |||||||| || || ||||| |||||| |  |||   || ||
------------gttcagctcattatgctaac---atctttgaatcattaactaccagttgagttacttgtttgatcactgatgggaccttgattctgtaacattagGTTCTAAGCATGAGCAGGCTGGGTGGTGCTGGTGCTGTGGCACAGCTGGTTGCTGATATCCCACTTTCAG---TTAAG
















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|349808681|gb|FQ405825.1|FQ405825
EST:     TGCTTGATGAAATTGTGGACTATGTGAAGTTCCTAAGGCTCCAAGTCAAG                         GTTTTGAGCATGA
genomic: TGCTTGATGAAATTGTGGACTATGTGAAGTTCCTAAGGCTCCAAGTCAAGgtaaatagtc ... actttttcagGTTTTGAGCATGA
EST: gi|110390144|gb|EC955038.1|EC955038
EST:     TGCTTGATGAAATTGTGGACTATGTGAAGTTCCTAAGGCTCCAAGTCAAG                         GTTTTGAGCATGAGTAGGCTGGGAGGTGCTGGTGCAGTGGCACAACTCGTG
genomic: TGCTTGATGAAATTGTGGACTATGTGAAGTTCCTAAGGCTCCAAGTCAAGgtaaatagtc ... actttttcagGTTTTGAGCATGAGTAGACTGGGAGGTGCTGGTGCAGTGGCACAACTCGTG
EST: gi|110701293|gb|EE078706.1|EE078706
EST:     TGCTTGATGAAATTGTGGACTATGTGAAGTTCCTAAGGCTCCAAGTCAAG                         GTTTTGAGCATGAGTAGACTGGGAGGTGCTGGTGCAGTGGCACAACTCGTG
genomic: TGCTTGATGAAATTGTGGACTATGTGAAGTTCCTAAGGCTCCAAGTCAAGgtaaatagtc ... actttttcagGTTTTGAGCATGAGTAGACTGGGAGGTGCTGGTGCAGTGGCACAACTCGTG
EST: gi|110387925|gb|EC952633.1|EC952633
EST:     TGCTTGATGAAATTGTGGACTATGTGAAGTTCCTAAGGCTCCAAGTCAAG                         GTTTTGAGCATGAGTAGACTGGGAGGTGCTGGTGCAGTGGCACAACTCGTG
genomic: TGCTTGATGAAATTGTGGACTATGTGAAGTTCCTAAGGCTCCAAGTCAAGgtaaatagtc ... actttttcagGTTTTGAGCATGAGTAGACTGGGAGGTGCTGGTGCAGTGGCACAACTCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttatttttcttaatttacctatttatcaatatcctcataccctactttttcagGTTTTGAGCATGAGTAGACTGGGAGGTGCTGGTGCAGTGGCACAACTCGTGGCTGACATCCCATTGCCAGCAGTTGAG
         tcttaat  putative branch site (score: 3)
                                       taccctactttttc  putative PPT
     tttttcttaatttacc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattggtacaaggtcgtgcctattttgttttctaaatactttggtgtttatttttcttaatttacctatttatcaatatcctcataccctactttttcagGTTTTGAGCATGAGTAGACTGGGAGGTGCTGGTGCAGTGGCACAACTCGTGGCTGACATCCCATTGCCAGCAGTTGAG

- - - - - - - - tgcctat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cataccc