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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtggcagttgcaaaatacataaactgcaaggtattaagacgttatatctgttgtacactttcttgttaaccatattgaattatacctttattctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATACTCATGCTGATCTGAATTTGTACACTAAACATCAAGCTTGAAAAAATTTG

Basic information

species Vitis vinifera
transcript Vv11s0016g03200.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G147882_T01 (Zea mays), 3'ss of exon 9
--------------------------------------ggtggcagttgcaaaata-----cataaactgcaaggtattaagacgttatatctgttgtacactt-----tcttgttaaccatattgaattatacctttattctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATACTCATGCTGATCTGAATTTGTACACTAAACATCAAGCTTGAAAAAATTTG
                                         ||||| ||| |   |     |||  |     |   ||  | |  |||| |    |||  | ||     ||||   | |    ||| || ||| ||  | |   |||| || |||||  |||  ||     | |||||| |||||||||||||||| ||||| || |||||||| |  |||    |     | || |||  | |    
gtaagctctatcaggcatcctcgatcggatggctggagccaggcagatgctagccatctgccattcatcaggatacatatatatattatgttctctgtcaaattccgaatctttacagctgcgttgtat-atatctccactgc-ccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACACTCACGCGGATCTGAAATCCTACGACGACAGCAAGGCCTGATCAGAGGAC

upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA01G01170.2 (Glycine max), 3'ss of exon 10
-----ggtggcagttgcaaaatac-ataaactgcaaggtattaa-gacgttatatctgttgtacactttcttgttaaccatattgaattatacctttattctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATACTCATGCTGATCTGAATTTGTACACTAAACATCAAGCTTGAAAAAATTTG
      |   ||||   ||||| |  ||||  | ||  ||  || ||  ||     | |||||    |||||   | ||   ||| |||     | | || | |||||| ||||||  ||  |||       ||| |||| |||||||||||||| |||||||||||| ||||| | || |  ||||| |||||||||  |      
gaggcagctacagtattaaaattctgtaaatagaaacttaaaaatgaaattgggctttttgtagtggttcttaacatcc---ttgcatt----ttctcttgttccagATATCCTCCCATCTTATGCCATGACTACATGACTCAGCGCTACAAGGACACTCATGCTGATTTGAATATTTATAAGAAACAGCAAGCTTGAGTAGTCAAC
















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|32459007|gb|CD800181.1|CD800181
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAA                         ACTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|110727031|gb|EE103356.1|EE103356
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|45771236|gb|CN007088.1|CN007088
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|83275538|gb|DV939546.1|DV939546
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCGGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|110428851|gb|EC995334.1|EC995334
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|83276122|gb|DV940130.1|DV940130
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCGGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|110390246|gb|EC955146.1|EC955146
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|77588241|gb|DV223328.1|DV223328
EST:     GCAAGTCAGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: GCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|30253347|gb|CB970898.1|CB970898
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|71887181|gb|DT036236.1|DT036236
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCGGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACA
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACA
EST: gi|77589174|gb|DV223847.1|DV223847
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCGGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|83275983|gb|DV939991.1|DV939991
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCACTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|71884795|gb|DT033850.1|DT033850
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCGGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|46910495|gb|CN545870.1|CN545870
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|30253270|gb|CB970821.1|CB970821
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|110421097|gb|EC987385.1|EC987385
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
EST: gi|71884047|gb|DT033102.1|DT033102
EST:     TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCGGATAAAAACCCTCCCAA                         ATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC
genomic: TGTCTTGTTGAATGCTTGCCAACCTGCAAGTCAGATAAAAACCCTCCCAAgtaagtagcc ... attctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctgttgtacactttcttgttaaccatattgaattatacctttattctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATACTCATGCTGATCTGAATTTGTACACTAAACATCAAGCTTGAAAAAATTTG
                   tgttaac  putative branch site (score: 2)
                                        cctttattct  putative PPT
                           atattgaattatacct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtggcagttgcaaaatacataaactgcaaggtattaagacgttatatctgttgtacactttcttgttaaccatattgaattatacctttattctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATACTCATGCTGATCTGAATTTGTACACTAAACATCAAGCTTGAAAAAATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - -caaaata
- - - - - - - - - cataaac
- - - - - - - - - - - - - - - - - - - - - - - - ctgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccata