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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAATCAGTTGGTGCAGGTTGCACAGAAATGCCAAAGCACAATTGCTGAAAGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACATgtgagttaaatggagcaatgtctgaactccttttctttggcaaatagatgttctgttatcagcctaaccttcccttctctcctgtgcctgcgcacagtgt...

Basic information

species Vitis vinifera
transcript Vv16s0100g00500.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA16G32250.1 (Glycine max), 5'ss of exon 6
TGAATCAGTTGGTGCAGGTTGCACAGAAATGCCAAAGCACAATTGCTGAAAGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACATgtgagttaaatggagcaatgtctgaactccttttctttggcaaatagatgttctgttatcagcctaaccttcccttctctcctgtgcctgcgcacagtgt---
| || || || || ||||| || || |||||||| || |||||||||||||||||  |||||||| |||||||||| |||||||||||||| |||||||||| |||||| |  |    |||          ||  | |    | || ||  ||  |        ||   ||| |||  || |    | |       |  |   
TCAACCAATTAGTTCAGGTAGCTCAAAAATGCCAGAGTACAATTGCTGAAAGTGGGGCTGATGGGGTTTCTCAGCAAGACTTACAAACAAACAGCAACATgtaagttaa-tacattgttgttctttaatgattggtgtatttagtaaatcctccttagctgagata--tttctctttactgcacaccttatatgatgcctgct

upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA16G32260.1 (Glycine max), 5'ss of exon 8
TGAATCAGTTGGTGCAGGTTGCACAGAAATGCCAAAGCACAATTGCTGAAAGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACATgtgagttaaatggagcaatgtctgaactcct-tttctttggcaaatagatgttctgttatcagcctaaccttcccttctctcctgtgcctgcgcacagtgt---------
| || ||||| || ||||| ||  | ||||| ||||| ||||||||||||||||| ||||||||| ||||||| || ||| | |||||||| |||||||||| || |   |      ||  || |||  || | | |||   ||||     |||| | || |   ||   ||| |||   | |  |||||  | |   |||         
TCAACCAGTTAGTTCAGGTAGCTAAAAAATGTCAAAGTACAATTGCTGAAAGTGGTTCTGATGGGGTTTCTCAACAAGACATCCAAACAAACAGCAACATgtaagattgtt------attcctcaacaactgtgtgtttactaaatctgccttctctgatga---tatatttctcttgattgc-atgccttgggatgatgtaatcttgga

upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA09G26970.1 (Glycine max), 5'ss of exon 6
TGAATCAGTTGGTGCAGGTTGCACAGAAATGCCAAAGCACAATTGCTGAAAGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACATgtgagttaaatggagcaatgtctgaactccttttctttggcaaatagatgttctgttatcagccta-accttcccttctctcctgtgcctgcgcacagtgt---------
| || ||||| || ||||| ||  | ||||| ||||| ||||||||||||||||| ||||||||| ||||||| || ||| | ||||||||  ||||||||| || ||  |      ||  ||||||  || ||  ||  |   || ||  ||  || ||||   | |  || |  |   |    ||| |    |   |||         
TCAACCAGTTAGTTCAGGTAGCTAAAAAATGTCAAAGTACAATTGCTGAAAGTGGGTCTGATGGGGTTTCTCAACAAGACATTCAAACAAACGGCAACATgtaagatagtt------attcctgaacaactgtttgtttac---taaatcctcc-ttctcagatgatatatttctcttgattggatgctttgtgatgttgtaatcttgga

upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA09G26960.1 (Glycine max), 5'ss of exon 8
TGAATCAGTTGGTGCAGGTTGCACAGAAATGCCAAAGCACAATTGCTGAAAGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACATgtgagttaaatggagcaatgtctgaactccttttctttggcaaatagatgttctgttatcagcctaaccttcccttctctcctgtgcctgcgcacagtgt--
| || || ||  | ||||| || || ||||| || || |||||||||||||||||  | ||| || |||||||||| || || |||||||| |||||||||| |||||| || |    |||          ||  | |    | || ||  ||  |        ||    | | | ||   |         | |   |||  
TCAACCAATTAATTCAGGTAGCTCAAAAATGTCAGAGTACAATTGCTGAAAGTGGGGCGGATTGGGTTTCTCAGCAAGATTTGCAAACAAACAGCAACATgtaagttaa-tgcattgttgttccttaatgattggtgtatttagtaaatcctccttagctgatatatttattcttactgcacaccttacatg-atgctgtta

upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT5G62090.2 (Arabidopsis thaliana), 5'ss of exon 7
TGAATCAGTTGGTGCAGGTTGCACAGAAATGCCAAAGCACAATTGCTGAAAGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACATgtgagt-taaatggagcaatgtctgaactccttttctttggcaaatagatgttctgtta--tcagcctaaccttcccttctctcctgtgc-----ctgcgcacagtgt----------------------------------------------------------------------------------
|||| || ||| | ||||||||| ||||||| || |||||||||| | |||||||||| |||||||||  ||| || || || ||| | ||||||||||||||||| |  |||   | |      |  ||  | |||||     |||  |  ||  | |  |||   | |   |  |||   || ||| |      |  | |   | |                                                                                  
TGAACCAATTGCTTCAGGTTGCAGAGAAATGTCAGAGCACAATTGATCAAAGTGGATCAGATGGGATTCATCAACAAGATTTGCAAGCTAATAGCAACATgtgagtcttgatgattctagacaatatttcactctctttcttccatattt-ctcaatcaattcaatttcattgtttcttgcatcttgtacggtaattaggtaagatttttcactgatgcaaagaagatcaaagcgattttagcttaatatatacaaatatgatgtactgatgccaagtcttttgctccag

upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT4G25520.1 (Arabidopsis thaliana), 5'ss of exon 7
TGAATCAGTTGGTGCAGGTTGCACAGAAATGCCAAAGCACAATTGCTGAAAGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACATgtgagttaa-atggagcaatgtctgaactccttttctttggcaaatagatgttctg-ttatcagcctaaccttcccttctctcctgtgcctgcgcacagtgt
|||| || ||| | |||||||||||||||||||| ||||| ||  | || ||||| || || ||| ||||||||||||| |||||  ||||||| ||||||| ||||||     |  | | | | |    |  | || |||||  |   | |  || || | | | |  |         | |  |||  | |          
TGAACCAATTGCTTCAGGTTGCACAGAAATGCCAGAGCACGATCTCAGAGAGTGGGTCAGAGGGGGTTTCTCAGCAGGATTTACAGTCAAATAGTAACATgtaagttaatgcacattattcttttattgtcgatactctggcatttgtttctagtgctttttatcattgctgggtgccattttgtgtatcag----------

upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT4G25515.1 (Arabidopsis thaliana), 5'ss of exon 6
TGAATCAGTTGGTGCAGGTTGCACAGAAATGCCAAAGCACAATTGCTGAAAGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACATgtgagtta---------aatggagcaatgtctgaac-tccttttctttggcaaatagatgttctgttatcagcctaacctt---cccttctctcctgtgcctgcgcacagtgt----------------------
|||| |||||| | |||||||| ||||||||||| ||||| ||| |||| ||||| ||  | ||  |||||||||||||  ||||  |||| || ||||||| |||||         | |  |   |  | || || |||  ||   |||     |  | |||| ||||  |  ||   |    |  || ||||  ||||      |   | |                      
TGAACCAGTTGCTTCAGGTTGCTCAGAAATGCCAGAGCACGATTTCTGAGAGTGGTTCACAGGGAGTTTCTCAGCAGGATATACAGTCAAACAGTAACATgtaagttaatccctaacactaaatttacctttgtacatccaatttggtggatgccaactattcttttatttgtatatgttctggcttttgtctctagtgctc-tatatcatttccggtgctaatttatgtgtcag

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|37187404|gb|CF606757.1|CF606757
EST:     AGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACAT                         GGTTTTGACAGCTGGGCGTCAGCTTGCAAGAAGTTTAGAGTCTCAGTCGCT
genomic: AGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACATgtgagttaaa ... tcacccttagGGTTTTGACAGCTGGGCGTCAGCTTGCAAGAAGTTTAGAGTCTCAGTCACT
EST: gi|161705769|gb|FC056640.1|FC056640
EST:     AGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACAT                         GGTTTTGACAGCTGGGCGTCAGCTTGCAAGAAGTTTAGAGTCTCAGTCGCT
genomic: AGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACATgtgagttaaa ... tcacccttagGGTTTTGACAGCTGGGCGTCAGCTTGCAAGAAGTTTAGAGTCTCAGTCACT
EST: gi|161720327|gb|FC071180.1|FC071180
EST:     AGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACAT                         GGTTTTGACAGCTGGGCGTCAGCTTGCAAGAAGTTTAGAGTCTCAGTCGCT
genomic: AGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACATgtgagttaaa ... tcacccttagGGTTTTGACAGCTGGGCGTCAGCTTGCAAGAAGTTTAGAGTCTCAGTCACT
EST: gi|161708994|gb|FC058786.1|FC058786
EST:     AGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACTT                         GGTTTTGACAGCTGGGCGTTC-GCTTGCAAGAAGTTTAGAGTCTCAGTCGC
genomic: AGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACATgtgagttaaa ... tcacccttagGGTTTTGACAGCTGGGCGT-CAGCTTGCAAGAAGTTTAGAGTCTCAGTCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAATCAGTTGGTGCAGGTTGCACAGAAATGCCAAAGCACAATTGCTGAAAGTGGATCTGATGGGATTTCTCAGCAGGACTTACAAACAAATAGCAACATgtgagttaaatggagcaatgtctgaactccttttctttggcaaatagatgttctgttatcagcctaaccttcccttctctcctgtgcctgcgcacagtgt

- - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctcct