Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAAgtaagtttagaacacattttccctttatcttgtgcatattctcaggatatatattttttcccctgcaaatcagctttcatgaagtagtcccactatcttctatgcagccttatcacctcctgctattttgcag

Basic information

species Vitis vinifera
transcript Vv04s0023g02940.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA01G37420.1 (Glycine max), 5'ss of exon 12
CTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAAgtaagtttagaacacattttccctttatcttgtgcatattctcaggatatatattttttcccctgcaaatcagctttcatgaagtagtcccactatcttctatgcagccttatcacctcctgctattttgcag
||||||| || || ||||||||||||||||||||||||||| |  |||  || ||||| ||||||| ||||||||| ||       ||    |||||| | | |       | |||  || ||    | || | |     || ||||    ||| || || || |   |    ||  ||| | |                          
CTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGGACGAGAATTGGGAAGCTGCTAGAAAGgtggaagaggatttaattttctcatgaat-----cgtatcttctggtctcacatgtatga---tggaaatatagttttattaattactatgagatcctggtattctgtag-----------------------

upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA02G05680.1 (Glycine max), 5'ss of exon 12
CTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAAgtaagtttagaacacattttccctttatcttgtgcatattctcaggatatatattttttcccctgcaaatcagctttcatgaagtagtcccactatcttctatgcagccttatcacctcctgctattttgcag
|||||||||| |||| |||||| |||||||||||||||||  |  |||  ||||||||||||||||   ||||||| ||  ||   | |     |||   ||||   |    |  || |    ||||     |||     || |||| |   ||    || |  |||   |||    ||| | |                          
CTGAACTTGTAGAAAAAGTTGTACTTCTTGGAGCACCCATCCCAATCATGGATGAGAACTGGGAAGCAACTAGAAAGgtttgtggggga-----tttaattttactcttaataggtttttctcatat-----tttatttatgaaaatgaatcttttctaact--tcctggtattcggtattctgtag-----------------------

upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA11G07870.1 (Glycine max), 5'ss of exon 11
CTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAAgtaagtttagaacacattttccctttatcttgtgcatattctcaggatatatattttttcccctgcaaatcagctttcatgaagtagtcccactatcttctatgcagccttatcacctcctgctattttgcag
||||||| || || ||||||||||||||||||  ||||||| |  |||  |||||||| ||||||| ||||||||| ||      |||    ||||| |   ||  | ||  || ||||              | || | || |    ||        |  ||||   | ||  | |||||             ||||| |||| || ||
CTGAACTGGTCGAGAGAGTTGTTCTTCTTGGATTACCCATTGCAATCAAGGATGAGAATTGGGAAGCTGCTAGAAAGgtggaagaagatttaatttttctcataaatagt--atcttcttga-----------tctcacatgtatggtaga------aatatagttttattaattactatgaga----------tcctggtattctgtag

upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA16G24310.1 (Glycine max), 5'ss of exon 12
CTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAAgtaagtttagaacacattttccctttatcttgtgcatattctcaggatatatattttttcccctgcaaatcagctttcatgaagtagtcccactatcttctatgcagccttatcacctcctgctattttgcag
||||||| || |||| |||||| |||||||||||||||||  |  |||  ||||||||||||||||  |||||||| || ||   || |   | |||  ||     | |   || | ||||          | |||    || |||| |   ||   |||    |||    ||  | ||                               
CTGAACTAGTAGAAAAAGTTGTGCTTCTTGGAGCACCCATCCCAATCAAGGATGAGAACTGGGAAGCAGCTAGAAAGgttagcggaggatttaatttttctcctgataga--atttcctca----------tctttttaatgaaaatgaatcttttcgaac--atcctggcattctgtag------------------------------

upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT4G36210.1 (Arabidopsis thaliana), 5'ss of exon 11
CTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAAgtaagtttagaacacattttccctttatcttgtgcatattctcaggatatatattttttcccctgcaaatcagctttcatgaagtagtcccactatcttctatgcagccttatcacctcctgctattttgcag
|||||||||| || |||||||||||||||||||||||||||||  |||    ||| ||||||  ||  |  || || ||||  |||    |   | |     ||        | |||  ||  |||||  |    ||    |  |||||  | | |      | |  ||  |      ||  |    ||||  ||  | || |||   ||
CTGAACTTGTGGAGAGAGTTGTTCTTCTTGGAGCACCCATTTCAATCAATAGTGAAAACTGGCGAGACGTAAGGAAGgtaa--tta----attctctgatagtacaaacactacattaccaaaatataggtcacatctatgg--aatcaaatcttaaatgagattttcaaaagagaaaattaa----tatc-tctggtcctgtttgatag

upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT2G18100.1 (Arabidopsis thaliana), 5'ss of exon 12
CTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAAgtaagtttagaacacattttccctttatcttgtgcatattctcaggatatatattttttcccctgcaaatcagctttcatgaagtagtcc-cactatcttctatgcagccttatcacctcctgctattttgcag
||||| |||| |||||||||||||||||||||||||| |||||  |||   ||||||| |||  ||  |  ||||| ||||      |||    ||        |    | |   |    ||  |   | |      |   | ||   | |  || |   ||  ||   |  ||||| || | ||  || | |     | | |        
CTGAAATTGTGGAAAGAGTTGTTCTTCTTGGAGCACCAATTTCAATCAAGAATGAGAATTGGCGAGACGTAAGAAAGgtaat----aaaccttcttgatgagagttccctaccattaacaagagttggtgtcacagtctaggaaacagatccgtcttttggtgttctgtatcatcttatacg-agtttttttatgggttaccag-------

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|110360866|gb|EC924300.1|EC924300
EST:     TTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA                         ATGGTGGCTGGAAGATTTGTGAATGCATTCTCTACAAATGATTGGACACTT
genomic: TTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAAgtaagtttag ... tattttgcagATGGTGGCTGGAAGATTTGTGAATGCATTCTCTACAAATGATTGGACACTT
EST: gi|33401930|gb|CF207557.1|CF207557
EST:     TTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA                         ATGGTGGCTGGAAGATTTGTGAATGCATTCTCTACAAATGATTGGACACTT
genomic: TTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAAgtaagtttag ... tattttgcagATGGTGGCTGGAAGATTTGTGAATGCATTCTCTACAAATGATTGGACACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAAgtaagtttagaacacattttccctttatcttgtgcatattctcaggatatatattttttcccctgcaaatcagctttcatgaagtagtcccactatcttctatgcagccttatcacctcctgctattttgcag

- - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - GAGATG