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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagtatgagtgttttggtgggggttgctgaaaatgacttatgcctcgataacctttgattttggtagcatattgatttaaagcttttcttcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATCAACAAGAGGTTGTCAAGAAAGCTCGACCGGCAGTGGAAGAAAAGCATTG

Basic information

species Vitis vinifera
transcript Vv12s0121g00010.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0121g00010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g51790.1 (Oryza sativa), 3'ss of exon 1
--tgagtatgagtgttttggtgggggttgctgaaaatgacttatgcctcgataacctttgattttggtagcatattgatttaaagcttttcttcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATCAACAAGAGGTTGTCAAGAAAGCTCGACCGGCAGTGGAAGAAAAGCATTG
  |   |     ||||||  |      |||| |   ||  | |     |      ||   || |   |     ||||| ||      |    |    |  || ||||||| ||||| ||||||||| | ||| |||| || ||  | |||||||||||||| ||||| || ||||| ||| || | |||||| ||||||| |
tttttttcctgttgtttttctcacc-ctgctcatcttgcttca-atagcagctttctactatctaaatttagcattgacttgggttgtcatcttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATCAACAAGAGATTGTCTAGGAAGCTTGACAGGAAATGGAAGCAAAGCATCG

upper sequence: Vv12s0121g00010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G31160.1 (Glycine max), 3'ss of exon 1
------tgagtatgagtgttttggtgggggttgctgaaaatgacttatgcctcgat--aacctttgattttggtagcatattgatttaaagcttttcttcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATCAACAAGAGGTTGTCAAGAAAGCTCGACCGGCAGTGGAAGAAAAGCATTG
        | || | || |||   | | |  |||  ||        ||  || |    ||  ||   ||||||  | ||  |  |  |||  | | | |     | || ||||||||||||| ||||| || |||||||| || || |||||||| ||||| ||||||||||| |||||||| ||     | ||||||||||||||||
tactaacaaataag-gtctttctctagagtctgcataatgccgtgcatttcttgtctgaatgttaatttttgggtgaatgatactgcaaa--tatccat-----acagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATCAATAAGAGGTTGTCCAGAAAGCTTGATAAAAAATGGAAGAAAAGCATTG

upper sequence: Vv12s0121g00010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G14350.1 (Glycine max), 3'ss of exon 1
tgagtatgagtgttttggtgggggttgctgaaaatgacttatgcctcgata--acctttgattttggtagcatattgatttaaagcttttcttcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATCAACAAGAGGTTGTCAAGAAAGCTCGACCGGCAGTGGAAGAAAAGCATTG
  | || |     | |  ||| |  |||  ||        ||   | |     |  ||   ||||||  | ||  | || | |         || |||  || ||||||||||||| ||||| || |||||||| || || |||||||| ||||| ||||||||||| |||||||| ||     | ||||||||||||||||
caaataaggtcagtctc-tggagtctgcataatgctttgcatttattgtctctatgttactttttgggtgaatgataatgtgactgcaaatatccata-cagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATCAATAAGAGGTTGTCTAGAAAGCTTGATAAAAAATGGAAGAAAAGCATTG

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|71865444|gb|DT014499.1|DT014499
EST:     CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGG                         GTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
genomic: CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGGgtattgtctc ... tcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
EST: gi|110693758|gb|EE070268.1|EE070268
EST:     CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGG                         GTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
genomic: CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGGgtattgtctc ... tcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
EST: gi|77587277|gb|DV222772.1|DV222772
EST:     CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGG                         GTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
genomic: CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGGgtattgtctc ... tcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
EST: gi|18459747|gb|BM438025.1|BM438025
EST:     CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGG                         GTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
genomic: CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGGgtattgtctc ... tcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
EST: gi|37187465|gb|CF606818.1|CF606818
EST:     CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGG                         GTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
genomic: CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGGgtattgtctc ... tcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
EST: gi|110700957|gb|EE078076.1|EE078076
EST:     CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGG                         GTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
genomic: CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGGgtattgtctc ... tcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
EST: gi|110384675|gb|EC949132.1|EC949132
EST:     CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGG                         GTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
genomic: CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGGgtattgtctc ... tcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
EST: gi|110416722|gb|EC982721.1|EC982721
EST:     CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGG                         GTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
genomic: CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGGgtattgtctc ... tcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
EST: gi|110384118|gb|EC948534.1|EC948534
EST:     CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGG                         GTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
genomic: CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGGgtattgtctc ... tcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
EST: gi|71870226|gb|DT019281.1|DT019281
EST:     CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGG                         GTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
genomic: CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGGgtattgtctc ... tcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
EST: gi|110367977|gb|EC931935.1|EC931935
EST:     CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGG                         GTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
genomic: CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGGgtattgtctc ... tcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
EST: gi|110408291|gb|EC973924.1|EC973924
EST:     CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGG                         GTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC
genomic: CGGTCAGGAACGAGTTCAAGCCCAGCGAGTTTGGCCGAATGCGCAAAAGGgtattgtctc ... tcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgataacctttgattttggtagcatattgatttaaagcttttcttcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATCAACAAGAGGTTGTCAAGAAAGCTCGACCGGCAGTGGAAGAAAAGCATTG
                         tattgat  putative branch site (score: 3)
                                      cttttcttc  putative PPT
                                       ttttcttcaataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagtatgagtgttttggtgggggttgctgaaaatgacttatgcctcgataacctttgattttggtagcatattgatttaaagcttttcttcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATCAACAAGAGGTTGTCAAGAAAGCTCGACCGGCAGTGGAAGAAAAGCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - tgagtgt
- - - - - - - - ggtgggg
- - - - - - - - - - - -gttgctg
- - - - - - - - - - - - - - - aaaatga
- - - - - - - - - - - - - - - - - - - -tatgcct