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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCACTCAAATGAATGAAGAAAGTTCAAGATCTCATTTGATTCTTTCAATTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctttatcacttggagcatattctcttgggttaatttctttgacctcccctgagattttgcctaaatacacttagtttccattggtttgaaatt...

Basic information

species Vitis vinifera
transcript Vv04s0044g02020.t01
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 5'ss of exon 21
TGGCACTCAAATGAATGAAGAAAGTTCAAGATCTCATTTGATTCTTTCAATTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatct-ttatcacttggagc---atattctcttgggttaatttctt---tgacctcccctgagattttgccta-aatacacttagtttccattggtttgaaatt
||| ||  | |||||||  || || ||||| |||||||| ||||||||||| || |||||||||||||| || || || |||||   ||| |||||||||||||  |   || | ||| | | |   ||  |  | | | |   |  | |     |  |        |||||   || || | |  ||  ||  | |  |        
TGGAACAAATATGAATGTTGAGAGCTCAAGGTCTCATTTAATTCTTTCAATCATTATTGAAAGTACCAACCTCCAGACTCAATCTTATGCAAGAGGAAAGgtatggtgggttgtaactggaaacctcatgctagccttgctgtgtcgcataaccaatttgtttcacaattttttttataaaaaaactatatttgagtatt--------

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 20
TGGCACTCAAATGAATGAAGAAAGTTCAAGATCTCATTTGATTCTTTCAATTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctttatca--cttggagcata--ttctcttgggttaatttctttgacctcccctgagattttgcc--taaatacacttagtttccattggtttgaaatt
 || ||| | |||||||| || |||||||| |||||||| ||||||||| | || ||||||||||| ||||||||||||||||||  ||| ||||| |||||||   |   || |  ||  || ||||  | |  || |||| | |    || |    | |  || | |     | |||| |  || |   | ||   |       
CGGAACTAATATGAATGATGAGAGTTCAAGGTCTCATTTAATTCTTTCAGTCATTATTGAAAGTACAAATCTTCAAACCCAATCATATGCAAGAGGCAAGgtatggacagaatgaagctgcgaacataactccaatttggttgagtctactggcaatactttcgactataataatgaataaaaatattgaacgttctgtc------

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 20
TGGCACTCAAATGAATGAAGAAAGTTCAAGATCTCATTTGATTCTTTCAATTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctttatca--cttggagcatattctc--ttgggttaatttctttgacctcccctgagattttgcctaaatacacttagtttccattggtttgaaatt
||| ||  | |||||||| || |||||||| |||||||| ||||||||||| || ||||||||||| ||||| ||||| ||||||  ||| ||||| |||||||  ||   || |  ||  || | ||  | |  || |||  | |    ||||    | |     | |  | |   |     | | |  | || | ||     
TGGAACGAATATGAATGATGAGAGTTCAAGGTCTCATTTAATTCTTTCAATCATTATTGAAAGTACAAATCTCCAAACTCAATCATATGCAAGAGGCAAGgtat-gtcaggatgaagctgtgaacttaaccccaatttggtcgagtctagtgacaatactttcatctataacaatgaaataaaaatattgaatgttctgtc---

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GLYMA16G21340.1 (Glycine max), 5'ss of exon 25
TGGCACTCAAATGAATGAAGAAAGTTCAAGATCTCATTTGATTCTTTCAATTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctttatcacttggagcatattctcttgggttaatttctttgacctcccctgagattttgcctaaatacacttagtttccattggtttgaaatt----------
 || || ||||||||||| |||||||||||||||||| | ||||| |||||| | |||||||||||||| |||||||  || |||||||| | |||||||||||          | ||      | |||  ||      | |  | |  ||||   | ||| || | ||| | | | |      |   |||   || ||           
AGGAACCCAAATGAATGATGAAAGTTCAAGATCTCATCTCATTCTATCAATTGTAATTGAAAGTACCAACCTTCAAAGTCAGTCAGTTGCAAAAGGAAAGgtat----------attttagattttttcctttaacagcaataatatatcctcttttaagaattgggctagaaaaagtagaagacagatggaaagagatgaactttattc

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GLYMA11G09480.1 (Glycine max), 5'ss of exon 22
TGGCACTCAAATGAATGAAGAAAGTTCAAGATCTCATTTGATTCTTTCAATTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctt-tatcacttggagcatattctcttgggttaatttctttgacctcccctgagattttgcctaaatacacttagt--ttc----cattggtttgaaatt---------------------------------------------------------
 || || |||||||| || || ||||||||||||||| | || || |||||| |||||||||||||||| ||||||| |||||||  ||| || |||||||||||||  |  || ||||| |   ||   |      | | | |   ||          | ||| | |||  ||  |  |||   |||    |||  || |   ||                                                          
AGGGACACAAATGAACGACGAGAGTTCAAGATCTCATCTCATACTATCAATTGTCATTGAAAGTACCAACCTTCAAAGCCAATCAACTGCAAGGGGAAAGgtattattgtacattacttgtattttacctttgaatatcagtatgaatgttagtataccatattcttcctttat-tatgtagcaattcgaaacataagtattgtatgacctcgaggcaatgtggattttaactttttatgttggatttgtcatttgtcatacag

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GLYMA01G35950.1 (Glycine max), 5'ss of exon 22
TGGCACTCAAATGAATGAAGAAAGTTCAAGATCTCATTTGATTCTTTCAATTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtatta-tctttatcacttgga----------gcatattctcttgg--gttaat-ttctttgacctcccctgagattttgcc---taaatacacttagtttccattggtttgaaatt-------------------------------------------------
 || || || |||||||| |||||||||||||||||| | || || |||||| ||||||||||||| || ||||||| |||||||  ||| || |||||||||||  | |  || ||||  |          | ||||     ||   |||||| | |  |   || || | |  || || |   |  | ||||     ||  ||    | ||                                                     
AGGGACACAGATGAATGATGAAAGTTCAAGATCTCATCTCATACTATCAATTGTCATTGAAAGTACTAACCTTCAAAGCCAATCAACTGCAAGGGGAAAGgtattggtgtacattacttcaattttacctttgaatatcagtatgaatgttaatataccatattcttcctttattttgtggcaatttgaaacacaagtattttatgacctcgaggcattgcagtttttttaacttttttatgctggatttgtcatttgtcatacag

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GLYMA09G32740.1 (Glycine max), 5'ss of exon 22
TGGCACTCAAATGAATGAAGAAAGTTCAAGATCTCATTTGATTCTTTCAATTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctttatcacttggagcatattctcttgggttaatttctttgacctcccctgagattttgcctaaatacacttagtttccattggtttgaaatt--------
||| || |||||||| || |||||||||||||||||| | ||||| || ||| | |||||||||||||| |||||||  || |||||||| || ||||||||||  | |  ||  |||        | || |       | |  | |  | ||   |   | |  | ||| | | | |      |   | |   |||||         
TGGAACCCAAATGAACGATGAAAGTTCAAGATCTCATCTCATTCTATCGATTGTAATTGAAAGTACCAACCTTCAAAGTCAGTCAGTTGCAAGGGGAAAGgtatattttacatttcttt-------tcctttcaacaacaataatatatcatcttttagaaataggactagaaa-agtagaagacagatagaaagaaatgaactttat

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|30252243|gb|CB969794.1|CB969794
EST:     TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAG                         CTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
genomic: TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctt ... ctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
EST: gi|71877730|gb|DT026785.1|DT026785
EST:     TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAG                         CTAATTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCACGCTCT
genomic: TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctt ... ctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
EST: gi|71880280|gb|DT029335.1|DT029335
EST:     TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAG                         CTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
genomic: TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctt ... ctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
EST: gi|110361383|gb|EC924851.1|EC924851
EST:     TGCCAGAGGAAAG                         CTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
genomic: TGCCAGAGGAAAGgtattatctt ... ctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
EST: gi|30252330|gb|CB969881.1|CB969881
EST:     TCAGTTGCCAGAGGAAAG                         CTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
genomic: TCAGTTGCCAGAGGAAAGgtattatctt ... ctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
EST: gi|30252250|gb|CB969801.1|CB969801
EST:     TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAG                         CTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
genomic: TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctt ... ctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCACTCAAATGAATGAAGAAAGTTCAAGATCTCATTTGATTCTTTCAATTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctttatcacttggagcatattctcttgggttaatttctttgacctcccctgagattttgcctaaatacacttagtttccattggtttgaaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataca