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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCACCAGAGTTTGGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgcacttcatttctggaaagaatacttattatttgacataagtcttaaatcacctgatttaccttgcaatgtcag

Basic information

species Vitis vinifera
transcript Vv01s0011g05370.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 10
---CATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCACCAGAGTTTGGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgcacttcatttctggaaagaatacttattatttgacataagtcttaaatcacct--gatttaccttgcaatgtcag-
      | |||||  | || |||||     | ||   ||| || ||||| |||||||| ||  ||||||||||||| ||||| |||||||| || || |||||||| |  |   | |   |      |||  |   |||    | | |   |   | |   |  |  ||| |  | |      ||   
TTGACCGGATGGGCCTTGGAAAATC---CTCAAATGCTGAACCCCCAGAATTTGGTGCTGCAGCTGATGGTGATGCTGATCGCAACATGATTCTGGGTAAAAGgtattcttcagcctagatagcttgaagtttttgtatatactcataagtgctatgagaaatttatgatgtgtcctttgccttctag

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA03G05150.1 (Glycine max), 5'ss of exon 3
CATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCACCAGAGTTTGGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgcacttcatttctggaaagaatacttattatttgacataagtcttaaatcacctgatttaccttgcaatgtcag
|  ||||||||||||| ||||| ||  |  || ||||||| |||||||||||||| ||||||||||||||||||||||| |||||| | ||||| ||||||||||  ||  ||| |||| ||   |   ||  |||| | | || |   | |  |||  |    | | |||||   ||| ||
CTCGTATGGGATTGGGCAAATCTGAACCCCAAGATGAGCCCCCAGAGTTTGGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGGTTCTTGGTAAAAGgtagtgttgtccttaatttgtgatgaatttaaatattctctaacttttttgtgtaatatctgtgtatcccttgtt-tgttag

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA05G34790.1 (Glycine max), 5'ss of exon 10
CATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCACCAGAGTTTGGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgcacttcatttctggaaagaatacttattatttgacataagtcttaaatcacctgatttaccttgcaatgtcag
|  ||||||||||||| ||||| ||  |  || |||| || |||||||||||||| ||||||||||||||||||||||| |||||||| ||||| ||||||||||  ||| ||| |||| |||  |   ||  |||| |   || |      |  |  | |||  |  ||      ||| ||
CTCGTATGGGATTGGGCAAATCCGAACCACAAGATGATCCCCCAGAGTTTGGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGATACTTGGTAAAAGgtagtgttgcccttaatttgtggtgaatttaaatattctccaactttttgtgtgtaatatctgtgtatcccctgtttgttag

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA08G04890.1 (Glycine max), 5'ss of exon 10
CATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCACCAGAGTTTGGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgcacttcatttctggaaagaatacttattatttgacataagtcttaaatcacctgatttaccttgcaatgtcag
|  ||||||||||||| ||||| ||  |  || | ||||| |||||||||||||| ||||||||||||||||||||||| |||||| | ||||| ||||||||||  ||  ||| |||| ||   |   ||  |||| | | || |   | |  |||  |    | | || ||   ||| ||
CTCGTATGGGATTGGGCAAATCCGAACCCCAAGAAGAGCCCCCAGAGTTTGGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGGTTCTTGGTAAAAGgtagtgttgtccttaatttgtgatgaatttaaatattctctaacttttttgtgtaatatctgtgtatcccctgtt-tgttag

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 10
CATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCACCAGAGTTTGGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgcacttcatttctggaaaga-atacttatt-atttgacata---agtcttaaatcacctgatttacct-tgcaatgtcag
|| | |||||||| |||||||| ||  ||  |  ||| || ||||||||||| |||||| |||||||||||||||| ||||||||||||||||| |||||||||   | |      ||||  || ||| | |   ||  |  |   |||   |||  |     || | |  || || | || |   ||
CACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGTAACATGATCCTTGGTAAAAGgtagc-ttactgacgttttcaagagagatacatccatggaactagtataccaagtacttttaaacttaaagtatctcttcatttgtag

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 10
CATGTATGGGATTGGGTAAATCAGATG---CTAAAAATGAGCCACCAGAGTTTGGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactg--cacttcatttctggaaagaatacttattatttgacataagtcttaaatcacctgatttaccttgcaatgtcag----------
   | ||||||||| ||||| | ||||   ||      ||||| ||||||||||| |||||| |||||||||||||||| || ||||||||||| || ||||||||| |  |   | |||  || |       ||       || ||       | |   |    |    ||| |    ||| ||            
---GCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGCCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGAAACATGATCCTCGGTAAAAGgtagcagagactaattctcttttaagtgagatcacagagatgtggagcggatataccactctccccgttaaccaaaaatatctcttctccgcag

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|30133454|gb|CB918793.1|CB918793
EST:     GCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAG                         GTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
genomic: GCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgc ... gcaatgtcagGTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
EST: gi|30132705|gb|CB918044.1|CB918044
EST:     GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAG                         GTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
genomic: GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgc ... gcaatgtcagGTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
EST: gi|161709381|gb|FC059250.1|FC059250
EST:     GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAG                         GTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
genomic: GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgc ... gcaatgtcagGTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
EST: gi|30305224|gb|CB982018.1|CB982018
EST:     GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAG                         GTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
genomic: GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgc ... gcaatgtcagGTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
EST: gi|32270099|gb|CD719258.1|CD719258
EST:     GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAG                         GTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
genomic: GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgc ... gcaatgtcagGTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
EST: gi|30137874|gb|CB923212.1|CB923212
EST:     GCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAG                         GTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
genomic: GCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgc ... gcaatgtcagGTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
EST: gi|37183515|gb|CF602869.1|CF602869
EST:     GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAG                         GTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
genomic: GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgc ... gcaatgtcagGTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
EST: gi|351015349|gb|FQ445633.1|FQ445633
EST:     GTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCCTTGGCAAAAG                         GTTTTTTGTTACTCC
genomic: GTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCC-TTGGCAAAAGgtagtactgc ... gcaatgtcagGTTTTTTGTTACTCC
EST: gi|30125147|gb|CB910486.1|CB910486
EST:     GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAG                         GTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
genomic: GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgc ... gcaatgtcagGTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
EST: gi|30136409|gb|CB921747.1|CB921747
EST:     GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAG                         GTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
genomic: GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgc ... gcaatgtcagGTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
EST: gi|30305289|gb|CB982083.1|CB982083
EST:     GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAG                         GTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
genomic: GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgc ... gcaatgtcagGTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
EST: gi|349818554|gb|FQ403189.1|FQ403189
EST:     GTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAAG                         GTTTTT-GTTACT
genomic: GTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAA-Ggtagtactgc ... gcaatgtcagGTTTTTTGTTACT
EST: gi|349827300|gb|FQ421573.1|FQ421573
EST:     GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAG                         GTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
genomic: GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgc ... gcaatgtcagGTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
EST: gi|349810186|gb|FQ401632.1|FQ401632
EST:     GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAA                         GTTTTTTGTTACTCCATC
genomic: GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgc ... gcaatgtcagGTTTTTTGTTACTCCATC
EST: gi|161715091|gb|FC063627.1|FC063627
EST:     GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAG                         GTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT
genomic: GGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgc ... gcaatgtcagGTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCACCAGAGTTTGGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgcacttcatttctggaaagaatacttattatttgacataagtcttaaatcacctgatttaccttgcaatgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT