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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGACAACCACCGGTGTGAAGAGGCTGTACCAGATGCAGGCAAATGGAACTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatctagatttttcactctttttagctcgttatatactgaattttgtgctattatttcaaatttcgatggttttgtgctattatttcaagtttg...

Basic information

species Vitis vinifera
transcript Vv17s0000g09840.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09840.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os11g26850.2 (Oryza sativa), 5'ss of exon 1
AGAGACAACCACCGGTGTGAAGAGGCTGTACCAGATGCAGGCAAATGGAACTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatctagatttttcactctttttag-ctcgttatatactgaattttgtgctattatttcaaatttcgatggttttgtgctattatttcaagtttg---
 ||||| ||||||||||| |||||||| |||||||||||||  |  ||  | ||  | ||  | || ||||| |||||||| || || |||||||||||||| | | |||      |  | | |||| ||  | | ||||||     || |   ||| ||      |   | |   | |   || || | ||   |  ||    
GGAGACCACCACCGGTGTCAAGAGGCTCTACCAGATGCAGGAGACCGGCGCCCTCCTCTTCCCCGCCATCAACGTCAACGACTCCGTCACCAAGAGCAAGgtgaagcatcc---cctccctccctttctaatcccattatatttcagatctgaagctgtttgcgttagcctagcctgctgcttg-tactgttcttaccttagta

upper sequence: Vv17s0000g09840.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA05G28480.1 (Glycine max), 5'ss of exon 1
AGAGACAACCACCGGTGTGAAGAGGCTGTACCAGATGCAGGCAAATGGAACTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatctagatttttcactctttttagctcgttatatactgaattttgtgctattatttcaaatttcgatggttttgtgctattatttcaagtttg---
 || || ||||| ||||| |||||||| || ||||||||||| ||||| |||||  | ||  ||||||| |||||||| || ||||||||||||||||||||||||  |||   | |  ||    |  | |||  ||||||  | || | |  | | | | |||| || | | || | |||      | ||      |||   
GGAAACCACCACTGGTGTTAAGAGGCTATATCAGATGCAGGCGAATGGGACTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAGgtaatgtctcttcttctcccagatctggt-gctttttatatgtttaaatgtaggtt-tgagttcagatct-gttgttcttggatgggttttgtggcgttggtg

upper sequence: Vv17s0000g09840.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA08G11480.1 (Glycine max), 5'ss of exon 1
AGAGACAACCACCGGTGTGAAGAGGCTGTACCAGATGCAGGCAAATGGAACTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatctagatttttcactctttttagctcgttatatactgaattttgtgctattatttcaaatttcgatggttttgtgctattatttcaagtttg---
 || || ||||| || || |||||||| || ||||||||||| ||||| |||||| | ||  ||||||| |||||||| || ||||| ||||||||||||||||||  |||   |    ||    |  |  ||  || | |  | || | |  | | | | |||  || | | || |||||      | ||      |||   
GGAAACCACCACTGGAGTTAAGAGGCTCTATCAGATGCAGGCGAATGGGACTCTTCTCTTCCCTGCTATTAATGTCAATGACTCTGTCACCAAGAGCAAGgtaatgtctctttttcccccagatctagtgtcttttt-tgtgttaaaatgtaggat-tgagttcggatct-gttgtttttggatgggttttgtgccattggtg

upper sequence: Vv17s0000g09840.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA11G36620.1 (Glycine max), 5'ss of exon 1
AGAGACAACCACCGGTGTGAAGAGGCTGTACCAGATGCAGGCAAATGGAACTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatctagatttttcactctttttagctcgttatatactgaattttgtgctattatttcaaatttcgatggttttgtgctattatttcaagtttg
||| || ||||||||||| |||||||| |||||||||||||| |||||  | || |||||  |||| ||||| ||||| || || || |||||||||||||||       || ||||||      |||  | | ||       ||||     |   |   | |   ||     | |||                      
AGAAACCACCACCGGTGTCAAGAGGCTCTACCAGATGCAGGCCAATGGCTCCCTCTTGTTCCCTGCCATCAACGTCAATGACTCGGTCACCAAGAGCAAGgtacgtaccatacattttttgtctgttt--gtttgtctgtcggtgaaagaaatataaaagtgtttgatgcaatttgttgcag------------------

upper sequence: Vv17s0000g09840.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT4G13940.1 (Arabidopsis thaliana), 5'ss of exon 1
AGAGACAACCACCGGTGTGAAGAGGCTGTACCAGATGCAGGCAAATGGAACTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatgga-tctagatttttcactctttttagctcgtt--atatactgaatttt--gtgctattatttcaaatttcgatggttttgtgctattatttcaagtttg
 || || ||||| ||||| |||||||| ||||||||||||  ||||||||||||||||||  |||| || || || ||||| ||||| ||||||||||||||| ||   |  |||||| |  || |  |      | |  || | ||   | ||  |  || |  |||   ||      || ||      |  ||    |     
GGAAACTACCACTGGTGTTAAGAGGCTTTACCAGATGCAGCAAAATGGAACTCTTTTGTTCCCTGCCATTAACGTTAACGACTCTGTCACCAAGAGCAAGgtattgatcttcagatttgtttctttactagtgatgataaatctgctaggtctttagctctgtagtttttgatgcgataggcttaacaacaacataatca-----

upper sequence: Vv17s0000g09840.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT3G23810.1 (Arabidopsis thaliana), 5'ss of exon 1
AGAGACAACCACCGGTGTGAAGAGGCTGTACCAGATGCAGGCAAATGGAACTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatctagatttttcactctttttagctcgttat-atactgaattttgtgctattatttcaaatttcgatggttttgtgctattatttcaagtttg-
 ||||| || || ||||| |||||||| || ||||||||||  | |||| |||| |||||  |||| || || ||||| || ||||| ||||||||||||||||||   |    | |  |  |        || | | | ||| ||  |||||    |||  |  | | | | ||| |||      |  |    | |  || 
GGAGACTACTACTGGTGTTAAGAGGCTTTATCAGATGCAGGAGACTGGAGCTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAGgtaatgtggcacattatagctttagaagacactagatctgatattg--ttttgcctaatttgtggataatacaatgttttgaaatcaccaaaatatgaatga

upper sequence: Vv17s0000g09840.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S20_291V6.1 (Physcomitrella patens), 5'ss of exon 2
AGAGACAACCACCGGTGTGAAGAGGCTGTACCAGATGCAGGCAAATGGAACTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatg-gatc--tagatttttcactctttttagctcgttatatac---tgaattttgtgctattatttcaaatttcgatggttttgtgctattatttcaagtttg----------------------------
 ||||| || || || |||||| ||||||||||||||  ||  || ||||  || |||||  |||| |||||||| ||||| ||||| || ||||||||||||||| || |  | | |     | ||  |     | ||| |  ||   ||  |   | |         |      || | |    | |      | |   || |                             
GGAGACGACGACGGGAGTGAAGCGGCTGTACCAGATGATGGACAACGGAAGCCTGTTGTTCCCTGCCATCAATGTGAACGACTCTGTGACGAAGAGCAAGgtaatgtgacccgtgggtggcagattccgtaagtgttgttgtggacgcgtgtgtggggggtgggggggccgtggaacggtaggagggagggggagtgtgtggtgtcgggtgctgacgtttgggtcgctgtgcag

upper sequence: Vv17s0000g09840.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ11220 (Selaginella moellendorffii), 5'ss of exon 1
AGAGACAACCACCGGTGTGAAGAGGCTGTACCAGATGCAGGCAAATGGAACTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatg--gatctagatttttcactctttttagctcgttatatactgaatttt-gtgctattatttcaaatttcgatggttttgtgctattatttcaagtttg
 ||||| ||||| ||||| |||||||| |||||||||||| | |||||| | ||  | ||  | |||||||||||||||||||| || ||||||||||||||| |   ||  |   || || | | | || |    ||||  | || |   |  ||||| || ||| | |                                 
GGAGACCACCACTGGTGTCAAGAGGCTCTACCAGATGCAGTCGAATGGATCGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgtactcacgacttcttttgtttattgtcttgaaaa-gtta-gtgctcatcgtgagtgcttttcttttacag--------------------------------

upper sequence: Vv17s0000g09840.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ11444 (Selaginella moellendorffii), 5'ss of exon 1
AGAGACAACCACCGGTGTGAAGAGGCTGTACCAGATGCAGGCAAATGGAACTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatctagatttttcactctttttagctcgttatatactgaattttgtgctattatttcaaatttcgatggttttgtgctattatttcaagtttg
 ||||| ||||| ||||| |||||||| |||||||||||| | |||||| | ||  | ||  | |||||||||||||||||||| || |||||||||||||||             |  |    | ||| | |  || | |    || || |||||   ||    | |     |  ||||                    
GGAGACCACCACTGGTGTCAAGAGGCTCTACCAGATGCAGTCGAATGGATCGCTGCTCTTCCCGGCTATCAATGTCAACGATTCAGTCACCAAGAGCAAGgta------------ctcacgacttcttttgtttattctcttgaaaagttagtgct--catcgtgagtgcttttctttttacag----------------

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|349830115|gb|FQ420375.1|FQ420375
EST:     CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAG                         ATTGACAACTCGTATGGATGCCGACACT
genomic: CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTTGTATGGATGCCGACACT
EST: gi|110720368|gb|EE096227.1|EE096227
EST:     CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
genomic: CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
EST: gi|351016966|gb|FQ424393.1|FQ424393
EST:     CAACGATTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
genomic: CAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
EST: gi|87586766|gb|DY474908.1|DY474908
EST:     CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
genomic: CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
EST: gi|351028017|gb|FQ425918.1|FQ425918
EST:     CAACGATTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
genomic: CAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
EST: gi|33403493|gb|CF209120.1|CF209120
EST:     CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
genomic: CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
EST: gi|110372240|gb|EC936393.1|EC936393
EST:     CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
genomic: CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
EST: gi|349826992|gb|FQ419083.1|FQ419083
EST:     TCTTT-GTTTGCTGCTATNCA-TGTCAACGATTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
genomic: TCTTTTGTTTGCTGCTAT-CAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
EST: gi|161718457|gb|FC066325.1|FC066325
EST:     CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
genomic: CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
EST: gi|351049007|gb|FQ431551.1|FQ431551
EST:     CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
genomic: CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
EST: gi|351022325|gb|FQ445100.1|FQ445100
EST:     CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAG                         TTTGACAACTT
genomic: CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTT
EST: gi|110685971|gb|EE063157.1|EE063157
EST:     CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
genomic: CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
EST: gi|110356833|gb|EC919944.1|EC919944
EST:     CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
genomic: CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
EST: gi|110685963|gb|EE063142.1|EE063142
EST:     CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
genomic: CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
EST: gi|351033327|gb|FQ446559.1|FQ446559
EST:     CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA
genomic: CTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatc ... ttcaatgcagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGACAACCACCGGTGTGAAGAGGCTGTACCAGATGCAGGCAAATGGAACTCTTTTGTTTGCTGCTATCAATGTCAACGATTCTGTTACCAAGAGCAAGgtaatggatctagatttttcactctttttagctcgttatatactgaattttgtgctattatttcaaatttcgatggttttgtgctattatttcaagtttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG