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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataagcttatccagatactagcaaatagacatgcctctctctctctctctctctacacacacacatttgatctcactaaaaataaaaattgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGCATGACACAG

Basic information

species Vitis vinifera
transcript Vv07s0031g02190.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G031859_T04 (Zea mays), 3'ss of exon 13
aataagcttatccagatactagcaaatagacatgcctctct---ctctctctctctctacacacacacatttgatctcactaaaaataaaaattgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGCATGACACAG
 | |    |||| ||| |    ||||  | | |     |     |        | | |    | | |   |||| || |||  |       ||     || || |  |||| ||||||||||| ||||||||| ||||  | |||||||||||||||||||||
-acatatgtatctagaaaa-gccaaaacgtcttataatttggaacggagggagtatgtgataatagattcttgagctgactttattactgcatcacacgc-agAGCAATGACCCATACTTCAACAAGCTTATTAGAATTTTGGCGACTAGATGCATGACACAG

upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA04G39980.1 (Glycine max), 3'ss of exon 18
aataagcttatccagat-ac-tagcaaatagacatgcctctctctctctctctctctacacacacacatttgatctcactaaaaataaaaattgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGCATGACACAG
  |    || |  || | || |||| |    |    | | | |   |       | |     | ||   ||  |||| | | | || |||    | |  ||||||||||||||||||||||||||| | || || ||||| || ||||| |||||||| |||
gtttcctttttatagcttacatagctagcgtaagcacttattttcttagggtcttatttggtctcatgcttc-tctctc-atatatgaaacacttttttcagGGTGATGATCCATACTTCAATAAGTTAATCCGTATACTGGCAACTAGGTGCATGACTCAG

upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA06G14870.2 (Glycine max), 3'ss of exon 18
---aataagct-tatccagatactagcaaatagacatgcctctctctctctctctctctacacacacacatttgatctcactaaaaataaaaattgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGCATGACACAG
     |  ||| |  |    |||||||       | |     | | | | |       ||        ||| |  ||||  | |    ||||    | |  |||||||||||||| |||||||||||| | || || ||||| || ||||| |||||||| |||
tgattttggctgtggctctttactagcttgctagcttaagcatatttttttaaggtcttatttggtttcatgtt-tctctttta---caaaatacttttttcagGGTGATGATCCTTACTTCAATAAGTTAATCCGTATACTGGCAACTAGGTGCATGACTCAG

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|349815930|gb|FQ403547.1|FQ403547
EST:     TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTG                         GGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
genomic: TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTGgttagtttta ... tgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
EST: gi|351013790|gb|FQ433942.1|FQ433942
EST:     TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTG                         GGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
genomic: TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTGgttagtttta ... tgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
EST: gi|351054754|gb|FQ462784.1|FQ462784
EST:     TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTG                         GGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
genomic: TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTGgttagtttta ... tgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
EST: gi|351048032|gb|FQ441204.1|FQ441204
EST:     TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTG                         GGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
genomic: TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTGgttagtttta ... tgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
EST: gi|351055546|gb|FQ442342.1|FQ442342
EST:     TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTG                         GGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
genomic: TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTGgttagtttta ... tgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
EST: gi|351025060|gb|FQ433477.1|FQ433477
EST:     TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTG                         GGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
genomic: TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTGgttagtttta ... tgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
EST: gi|351036566|gb|FQ457279.1|FQ457279
EST:     TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTG                         GGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
genomic: TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTGgttagtttta ... tgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
EST: gi|351033178|gb|FQ461950.1|FQ461950
EST:     TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTG                         GGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
genomic: TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTGgttagtttta ... tgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
EST: gi|351054627|gb|FQ456824.1|FQ456824
EST:     TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTG                         GGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
genomic: TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTGgttagtttta ... tgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
EST: gi|349830463|gb|FQ416761.1|FQ416761
EST:     TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTG                         GGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
genomic: TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTGgttagtttta ... tgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
EST: gi|349810328|gb|FQ401774.1|FQ401774
EST:     TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTG                         GGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC
genomic: TGGATGTTTCATCATCAAAAGCACTGGCTGATTCACTTGATCATGCTGTGgttagtttta ... tgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctctctctacacacacacatttgatctcactaaaaataaaaattgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGCATGACACAG
                             cactaaa  putative branch site (score: 2)
                         atctcactaaaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataagcttatccagatactagcaaatagacatgcctctctctctctctctctctacacacacacatttgatctcactaaaaataaaaattgtctgccagGGTGATGATCCATACTTCAATAAGCTTATTCGAATACTAGCGACTAGATGCATGACACAG

aataagc
- - - - - - - - - - - -aaataga
- - - - - - - - - - - - - - - catgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa