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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgtatgtattttgttgtttaattgtattctttcttgctaatttaaatcagctatttggtcagttcacaagtgaaaatttctgaattttagtagagaatatt...

Basic information

species Vitis vinifera
transcript Vv13s0084g00660.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os03g20310.2 (Oryza sativa), 5'ss of exon 5
ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgta-------tgtattttgttgtttaattg--tattctttcttgctaatttaaatca-gctatttggtcagttcacaagtgaaaatttctgaattttagtagagaatatt
    | ||  ||||||||||||||||||| |||||| ||||||| ||  ||||||| || |||          |  || ||||   |||   | | |||| |||   | |  ||| | |   | |||||    ||| |   ||   | |  |    || |          
GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgtactataaccacaactttttgtcatattacctgtccttttttggacaatggaattatgacttctggtctccgcaccaactaaggatgcacatccatatt----------

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 3
ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgtatg-----tattttgttgtttaattgtattctttcttgctaatttaaatcagctatttggtcagttcacaagtgaaaatttctgaattttagtagagaatatt
||||| || ||||||||||| || |||||||||||  |||||||||| ||| |||||||||||||     || ||  || | |  ||   ||  |  ||  | |  ||||| ||     |     ||| ||  |      ||||  || |  | ||   ||    
ACTCTCCGCAGGCTTGCTCAGAACCGTGAAGCTGCCAGAAAAAGCCGCTTGCGAAAGAAAgtatgaatcataattacttatgtttttcagttaatatttattcacataaatgagtatactatcttgtttacctgcctttttttccaaaat--aataattaaa---

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA13G26280.1 (Glycine max), 5'ss of exon 7
ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgtatgtattttgttgtttaattgtattctttcttgctaat-ttaaatcagctatttggtcagttcacaagtgaaaatttctgaattttagtagagaatatt-------
||||| || ||||||||||| || |||||||||||  |||||||||| ||| ||||||||||||| ||  | ||   || || | || ||    | |||| || | |||  ||   | | |||  || |       |  |    ||||  |  | |||| |       
ACTCTCCGCAGGCTTGCTCAGAACCGTGAAGCTGCCAGAAAAAGCCGCTTGCGAAAGAAAgtatgaatcatatt---tacttatgtttttca--gttaatatttattcatata---gatgagtatactatcttgtttcccctcctttttttccaaaataataattaaa

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA20G39050.2 (Glycine max), 5'ss of exon 5
ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgta------tgtattt---tgttgtttaattgtattctttcttgctaatttaaatcagctatttggtcagttcacaagtgaaaatttctgaattttagtagagaatatt
||||| || ||||||||||| |||||||| || ||| ||||||| || |||||||||||||||      |||| ||   | || |||  |  ||||  || || | | | || ||||  | | || |   |||       | |  |  | ||| ||| ||         
ACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAAgtaggaatatgtacttacatattttttgttaatatttgttgttacaagtgtatatcatttttctgttttcttctttctccata--taataaatattactatg-------

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA10G44270.1 (Glycine max), 5'ss of exon 5
ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgtatgtattttgttgtttaattgtattctttcttgctaatttaaatcagctatttggtcagttcacaagtgaaaatttctgaattttagtagagaatatt---
| ||| || ||||||||||| ||||| || |||||| ||||||| || ||||||||||||||| | || | ||  ||  ||  | ||  ||  |  |  || | |  || | | |      ||      |     |||||  || | | || | | || |   
AGTCTCCGGAGGCTTGCTCAGAATCGCGAGGCTGCAAGAAAAAGTCGGTTGAGAAAGAAAgtaggaatat-gtacttacataatttttgttaatatttgttgatacaag-tgtatatcttttttctgttttcttctttctccatataatta-atattactatg

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT3G12250.5 (Arabidopsis thaliana), 5'ss of exon 5
ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgtatgta--ttttgttgtt----taattgtattctttcttgctaatttaaatcagctatttggtcagttcacaagtgaaaattt--ctgaattttagtagagaatatt----------------
|| |||||||||||||||||||||||||| || ||| |||||||| ||||||| ||||| |||||||  ||||| | ||    |  || |  | ||||||    |||    | |  |  |||     |    |   ||| || |  |||   ||   |  || || ||                
ACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAGgtatgtatattttgcttttgttcttgttttgatttttcttatatattcctcttatttccttgtaatatctctagaagaatatctatctgtcattaccttaagcatgttattgtttcctccatag

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT5G06960.2 (Arabidopsis thaliana), 5'ss of exon 4
ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgtatgt----attt-tgttgtttaattgtattctttcttgctaatttaaatca--gctatttggtcagttcacaag---tgaaaatttctgaattttagtagagaatatt
|| ||||||||||| |||||||| ||||| |||||| | |||||| ||||||| |||||||||||     |||| ||||  |   ||  |||||||  || |  ||  || ||  ||||||||   | |  |  |    ||    || ||| | |||  |||        
ACGCTTCGTAGGCTCGCTCAAAACCGTGAGGCTGCAAGGAAAAGCAGATTGAGGAAGAAAgtatgcttagatttatgttcatagtttcaattcttttatgttttttacaagcatagctatttgcaaactctaagatgtttgttggttactgcacttt--tag--------

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT5G06950.3 (Arabidopsis thaliana), 5'ss of exon 5
ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgtatgtattttgttgtttaattgtattctttcttgctaatttaaatcagct--atttggtcagtt--cacaagtgaaaatttctgaattttagtagagaatatt------------------
||||||||||||||||||||||| ||||| || ||| | |||||| ||||||| ||||| |||| |    |    ||   || |||  ||| || ||  ||    ||   |  | |||||   |    | |||   |  | | ||    |  ||  |     ||                  
ACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTGAGGAAGAAGgtatattaccttccatt-ggttttatctttttttactttttcttttctttttaaattggtgcatcgctagaagcatagctatttggtactacgttaattccttttaattgctccctccatag

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|26257000|gb|CA808063.1|CA808063
EST:     GGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA                         GCATATGTCCAACAGCTAGAAAGTAGCCGGATGAAGCTGACCCCAACTAGA
genomic: GGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgtatgtattt ... tttccattagGCATATGTCCAACAGCTAGAAAGTAGCCGGATGAAGCTGACCC-AACTAGA
EST: gi|156737550|gb|EV241663.1|EV241663
EST:     GGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA                         GCATATGTCCAACAGCTAGAAAGTAGCCGGATGAAGCTGACCCAACTAGAG
genomic: GGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgtatgtattt ... tttccattagGCATATGTCCAACAGCTAGAAAGTAGCCGGATGAAGCTGACCCAACTAGAG
EST: gi|110687850|gb|EE065730.1|EE065730
EST:     GGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA                         GCATATGTCCAACAGCTAGAAAGTAGCCGGATGAAGCTGACCCAACTAGAG
genomic: GGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgtatgtattt ... tttccattagGCATATGTCCAACAGCTAGAAAGTAGCCGGATGAAGCTGACCCAACTAGAG
EST: gi|30301282|gb|CB978076.1|CB978076
EST:     GGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAACCGATTGAGAAAGAAA                         GCATATGTCCAACAGCTAGAAAGTAGCCGGATGAAGCTGACCCAACTAGAG
genomic: GGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgtatgtattt ... tttccattagGCATATGTCCAACAGCTAGAAAGTAGCCGGATGAAGCTGACCCAACTAGAG
EST: gi|77583990|gb|DV221036.1|DV221036
EST:     GGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA                         GCATATGTCCAACAGCTAGAAAGTAGCCGGATGAAGCTGACCCAACTAGAG
genomic: GGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgtatgtattt ... tttccattagGCATATGTCCAACAGCTAGAAAGTAGCCGGATGAAGCTGACCCAACTAGAG
EST: gi|110428204|gb|EC994669.1|EC994669
EST:     GGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA                         GCATATGTCCAACAGCTAGAAAGTAGCCGGATGAAGCTGACCCAACTAGAG
genomic: GGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgtatgtattt ... tttccattagGCATATGTCCAACAGCTAGAAAGTAGCCGGATGAAGCTGACCCAACTAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgtatgtattttgttgtttaattgtattctttcttgctaatttaaatcagctatttggtcagttcacaagtgaaaatttctgaattttagtagagaatatt

- - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagaata