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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGGTGATCTGCACCATGTCTGGGGTTCATTTCAGGAGTCACAACCTTTTGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAGgtacgtgtgagatgcgtattagacaagagaaaggggaggataattttttgtcatgaatgaagacataaagtagtctgaatattaatggaaatacatacat...

Basic information

species Vitis vinifera
transcript Vv02s0033g00260.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0033g00260.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os12g16220.3 (Oryza sativa), 5'ss of exon 1
TGTGGTGATCTGCACCATGTCTGGGGTTCATTTCAGGAGTCACAACCTTTTGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAGgta---cgtgtgagatgcgtattagacaagagaaaggggaggataattttttgtcatgaatgaagacataaagtagtctgaatattaa-tggaaatacatacat
 || ||  ||| | ||||||| || || ||  || | || ||||||||  || | |||||||| ||||| |||||||||||||||||||||||  | ||||||     | |   |  |   |     ||     |    |  | ||    |||   ||  ||   | ||    |  ||||   ||||  | |||| | | |   
CGTCGTCGTCTCCGCCATGTCCGGCGTCCACCTCCGCAGCCACAACCTCATGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatttttcaatcagctccacaaattagtacataattaaaagaacttgatttggctgtgtatatcttatt-tctgtccattatcttgaaaaataaa---

upper sequence: Vv02s0033g00260.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA16G17680.3 (Glycine max), 5'ss of exon 1
TGTGGTGATCTGCACCATGTCTGGGGTTCATTTCAGGAGTCACAACCTTTTGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAGgtacgtgtgagatgcgtattagacaagagaaaggggaggataattttttgtcatgaatgaagacataaagtagtctgaatattaatggaaatacatacat---
||| || ||| |  |||| ||||| |||||  ||||||| |||| | |     |||| |||||||||||||||||||||||||||||||| ||| |||||||  |  |   |  | | ||   |  |           | || || ||    ||||||  | |   ||   |     |||   | |   || | |||  |   
TGTTGTCATCAGTGCCATCTCTGGTGTTCACATCAGGAGCCACAGCATCACTCTGCAACTCAAACTTGTTGAGGCCATCAAAGAAGCTGGGAACGTTAAGgttagctttgaac-cttctttttcttgctttttcttttgttatttcttaa--atgaatagatattaaagccacagacaattagactattaaaatataatttgt

upper sequence: Vv02s0033g00260.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA09G34470.1 (Glycine max), 5'ss of exon 1
TGTGGTGATCTGCACCATGTCTGGGGTTCATTTCAGGAGTCACAACCTTTTGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAGgtacgtgtgagatgcgtat-------tagacaagagaaaggggaggataatttt-ttgtcatgaatgaagacataaagtagtctgaatattaatggaaatacatacat
||| ||||| |||||||||||||| ||||||||  |   ||||||| | ||| |||||||||||||||| ||||||||||| |  || || ||| |||||||| ||   | || | |||       ||   |  | |    | || || |||   |  |  | | | || |  | | ||||  |||    || |  |||         
TGTTGTGATTTGCACCATGTCTGGTGTTCATTTTCGCTCTCACAACTTGTTGGTGCAGCTCAAACTTGTGGAGGCCATCAAGGCTGCAGGGAACGTTAAGgtatgttgtatatccctatacctatatatgtataatatgttgtagcattattcaatctttttaagtaaaaaattgaggtagaatgatagatagttaaaag--------

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|33407732|gb|CF213359.1|CF213359
EST:     TGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAG                         CGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGAAGATGCA
genomic: TGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAGgtacgtgtga ... attatttcagCGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGGAGATGCA
EST: gi|33409205|gb|CF214832.1|CF214832
EST:     TGATGCATCTCACACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAG                         CGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGAAGATGCA
genomic: TGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAGgtacgtgtga ... attatttcagCGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGGAGATGCA
EST: gi|351035792|gb|FQ463637.1|FQ463637
EST:     TGATGCAGCTCAAGCTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAG                         CGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGAAGATGCA
genomic: TGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAGgtacgtgtga ... attatttcagCGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGGAGATGCA
EST: gi|33408357|gb|CF213984.1|CF213984
EST:     TGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAG                         CGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGAAGATGCA
genomic: TGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAGgtacgtgtga ... attatttcagCGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGGAGATGCA
EST: gi|33409691|gb|CF215318.1|CF215318
EST:     TGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAG                         CGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGAAGATGCA
genomic: TGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAGgtacgtgtga ... attatttcagCGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGGAGATGCA
EST: gi|33408614|gb|CF214241.1|CF214241
EST:     ATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAG                         CGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGAAGATGCA
genomic: ATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAGgtacgtgtga ... attatttcagCGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGGAGATGCA
EST: gi|351016398|gb|FQ423825.1|FQ423825
EST:     TGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAG                         CGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGAAGATGCA
genomic: TGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAGgtacgtgtga ... attatttcagCGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGGAGATGCA
EST: gi|33409802|gb|CF215429.1|CF215429
EST:     TGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAG                         CGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGAAGATGCA
genomic: TGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAGgtacgtgtga ... attatttcagCGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGGAGATGCA
EST: gi|33410413|gb|CF216040.1|CF216040
EST:     CCATCAAAGAAGCTGGAAACATTAGG                         CGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGAAGATGCA
genomic: CCATCAAAGAAGCTGGAAACATTAAGgtacgtgtga ... attatttcagCGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGGAGATGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGGTGATCTGCACCATGTCTGGGGTTCATTTCAGGAGTCACAACCTTTTGATGCAGCTCAAACTTGTTGAGGCCATCAAAGAAGCTGGAAACATTAAGgtacgtgtgagatgcgtattagacaagagaaaggggaggataattttttgtcatgaatgaagacataaagtagtctgaatattaatggaaatacatacat

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaata