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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttgtagagttttgctgattttgagaacttatgaagatgtctcctttcatccagttcttttttgtgaaagtcctcacattaaattattctgctttgcagTTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAG

Basic information

species Vitis vinifera
transcript Vv16s0039g02270.t01
intron # 6
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|161721212|gb|FC070718.1|FC070718
EST:     TTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAG                         TTCTTCATAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTG
genomic: TTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAGgtatccccag ... tgctttgcagTTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTG
EST: gi|110719175|gb|EE096848.1|EE096848
EST:     TTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAG                         TTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTG
genomic: TTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAGgtatccccag ... tgctttgcagTTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTG
EST: gi|27584835|gb|CB007530.1|CB007530
EST:     TTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAG                         TTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTG
genomic: TTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAGgtatccccag ... tgctttgcagTTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTG
EST: gi|30125898|gb|CB911237.1|CB911237
EST:     TTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAG                         TTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTG
genomic: TTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAGgtatccccag ... tgctttgcagTTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTG
EST: gi|110686390|gb|EE063974.1|EE063974
EST:     TTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAG                         TTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTG
genomic: TTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAGgtatccccag ... tgctttgcagTTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTG
EST: gi|110698756|gb|EE076614.1|EE076614
EST:     TTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAG                         TTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTG
genomic: TTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAGgtatccccag ... tgctttgcagTTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTG
EST: gi|161718060|gb|FC067589.1|FC067589
EST:     TTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAG                         TTCTTCATAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTG
genomic: TTCATCATTAGGAGAGACCTACCTGGATTTGGTGAAAAGGTTGGATGAAGgtatccccag ... tgctttgcagTTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatccagttcttttttgtgaaagtcctcacattaaattattctgctttgcagTTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAG
                          tcctcac  putative branch site (score: 2)
                                          ttctgcttt  putative PPT
                             tcacattaaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttgtagagttttgctgattttgagaacttatgaagatgtctcctttcatccagttcttttttgtgaaagtcctcacattaaattattctgctttgcagTTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - -tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcaca