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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacaactaatcaaatgtcttccaggccataagttcaccaatgtttaactgaagacctcatattaattaattagttgatgttttgtgatgattgtcctagGGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCTGGAGGCACTGGCATCACTCCAATGTTCCAG

Basic information

species Vitis vinifera
transcript Vv06s0009g01710.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g01710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G05640.1 (Glycine max), 3'ss of exon 4
ctacaactaatcaaatgtcttccaggccataagttcaccaatgtttaa--ctgaagacctcatattaattaattagttg--atgt-tttgtgatgattgtcctagGGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCTGGAGGCACTGGCATCACTCCAATGTTCCAG
   |||| ||| | || ||||         || |||    || || ||     |  | |   || |   || ||| |||  ||||  ||    | ||    | |||| || || ||||| |||||   |||||| | |||||| || ||| ||||||| |||||||||||||| |||||||| || 
---caac-aataatat-tctttggcataggaaattcttatattttaaaaatatataatcatctaatgcatagttatttgcaatgtacttactcttatatctccagGGACGTTTTAAGTACCAGCCCAACCAAGTAAGAGCTTTGGGTATGATTGCTGGTGGCACTGGCATCACCCCAATGTTTCAA
















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|110720681|gb|EE096826.1|EE096826
EST:     ATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAG                         GGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
genomic: ATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAGgtaaaaactc ... attgtcctagGGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
EST: gi|110388734|gb|EC953513.1|EC953513
EST:     AAGGTGATTACCTGGCTGTGAAGGGACCTAAG                         GGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
genomic: AAGGTGATTACCTGGCTGTGAAGGGACCTAAGgtaaaaactc ... attgtcctagGGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
EST: gi|110401612|gb|EC968227.1|EC968227
EST:     ATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAG                         GGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
genomic: ATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAGgtaaaaactc ... attgtcctagGGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
EST: gi|33406066|gb|CF211693.1|CF211693
EST:     ATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAG                         GGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
genomic: ATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAGgtaaaaactc ... attgtcctagGGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
EST: gi|33405978|gb|CF211605.1|CF211605
EST:     ATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAG                         GGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
genomic: ATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAGgtaaaaactc ... attgtcctagGGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
EST: gi|71864812|gb|DT013867.1|DT013867
EST:     ATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAG                         GGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
genomic: ATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAGgtaaaaactc ... attgtcctagGGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
EST: gi|110688836|gb|EE067844.1|EE067844
EST:     ATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAG                         GGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
genomic: ATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAGgtaaaaactc ... attgtcctagGGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
EST: gi|110718332|gb|EE095045.1|EE095045
EST:     ATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAG                         GGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT
genomic: ATTTTCGGGAGATGTGTGAAGGTGATTACCTGGCTGTGAAGGGACCTAAGgtaaaaactc ... attgtcctagGGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactgaagacctcatattaattaattagttgatgttttgtgatgattgtcctagGGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCTGGAGGCACTGGCATCACTCCAATGTTCCAG
                                              ttgtcct  CT-rich tract
            tcatattaattaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacaactaatcaaatgtcttccaggccataagttcaccaatgtttaactgaagacctcatattaattaattagttgatgttttgtgatgattgtcctagGGGCGCTTCAAGTATCAGCCTGGCCAAGTTATAGCTTTTGGGATGCTTGCTGGAGGCACTGGCATCACTCCAATGTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
ctacaac
- - - - aatcaaa
- - - - - - - -tgtcttc
- - - - - - - - - - - caggcca
- - - - - - - - - - - - - - - - - tcaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - acctcat