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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcctatgtcaaaatattgatagtgttattgtttagggctccattcatgaagcaattgtgtttttatcattttgattggaaatgcaattcaatttacagATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCCAATTCTACCCAACCAGATGGCAATAGTCAAGCCTCAGCTCCTTCTAATG

Basic information

species Vitis vinifera
transcript Vv05s0077g02310.t01
intron # 2
splice site 3'
intron type U2

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|71863616|gb|DT012671.1|DT012671
EST:     TAAGAAGATACGGCTGAGCCATAAG                         ATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
genomic: TAAGAAGATACGGCTGAGCCATAAGgtggtgaata ... caatttacagATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
EST: gi|352773658|gb|FQ472440.1|FQ472440
EST:     TAAGAAGATACGGCTGAGCCATAAG                         ATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
genomic: TAAGAAGATACGGCTGAGCCATAAGgtggtgaata ... caatttacagATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
EST: gi|30125771|gb|CB911110.1|CB911110
EST:     TAAGAAGATACGGCTGAGCCATAAG                         ATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
genomic: TAAGAAGATACGGCTGAGCCATAAGgtggtgaata ... caatttacagATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
EST: gi|352785394|gb|FQ477608.1|FQ477608
EST:     TAAGAAGATACGGCTGAGCCATAAG                         ATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
genomic: TAAGAAGATACGGCTGAGCCATAAGgtggtgaata ... caatttacagATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
EST: gi|110688178|gb|EE066434.1|EE066434
EST:     TAAGAAGATACGGCTGAGCCATAAG                         ATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
genomic: TAAGAAGATACGGCTGAGCCATAAGgtggtgaata ... caatttacagATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
EST: gi|22010813|gb|BQ795847.1|BQ795847
EST:     TAAGAAGATACGGCTGAGCCATAAG                         ATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
genomic: TAAGAAGATACGGCTGAGCCATAAGgtggtgaata ... caatttacagATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
EST: gi|71858909|gb|DT007964.1|DT007964
EST:     TAAGAAGATACGGCTGAGCCATAAG                         ATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
genomic: TAAGAAGATACGGCTGAGCCATAAGgtggtgaata ... caatttacagATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
EST: gi|110728878|gb|EE104832.1|EE104832
EST:     CCCGAAAGTAAGAAGATACGGCTGAGCCATAAG                         ATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
genomic: CCCGAAAGTAAGAAGATACGGCTGAGCCATAAGgtggtgaata ... caatttacagATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
EST: gi|110711785|gb|EE088658.1|EE088658
EST:     TAAGAAGATACGGCTGAGCCATAAG                         ATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC
genomic: TAAGAAGATACGGCTGAGCCATAAGgtggtgaata ... caatttacagATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgaagcaattgtgtttttatcattttgattggaaatgcaattcaatttacagATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCCAATTCTACCCAACCAGATGGCAATAGTCAAGCCTCAGCTCCTTCTAATG
                         ttttgat  putative branch site (score: 4)
                tttttatcattttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcctatgtcaaaatattgatagtgttattgtttagggctccattcatgaagcaattgtgtttttatcattttgattggaaatgcaattcaatttacagATTCAGCTAGAATATGGAGGCATCAAAAGTGCTACGAACCCTAATCAAGCCAATTCTACCCAACCAGATGGCAATAGTCAAGCCTCAGCTCCTTCTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- -cctatgt
- - - - - caaaata
- - - - - - - - - - - - - - - - - - - - -ccattca
- - - - - - - - - - - - - - - - - - - - - - - - -gaagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcaa