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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGGAGTCTCGAATGGATCAGTACGAGATCATGGAGCAGATCGGACGCGGAGCGTTCGGGGCTGCCATTCTTGTGAATCACAAATCGGAGAAGAAGAAgtatttttatgatttttttttggcgcaatctatgaatttttggtgagttttgtaatgagatggtttggttttggagtgatcgagtggttcgattttcag

Basic information

species Vitis vinifera
transcript Vv06s0009g00690.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os05g36960.1 (Oryza sativa), 5'ss of exon 1
TCATGGAGTCTCGAATGGATCAGTACGAGATCATGGAGCAGATCGGACGCGGAGCGTTCGGGGCTGCCATTCTTGTGAATCACAAATCGGAGAAGAAGAAgt-atttttatgatttttttttggcgcaatctatgaatt--tttggtgagttttgt----------aatgagatg----gtttggttttggagtgatcg--agtggttcgattttcag------------------
 ||||||||| || ||||||||||||||||||||||||||| | || || || || || || ||||| || ||||||||||| ||    |||| |||||||| | |   ||  || | ||||      |||| |  |     ||| | |   || |          | | |||||    ||||| |||||  || |     |||      || || |                   
ACATGGAGTCGCGGATGGATCAGTACGAGATCATGGAGCAGGTTGGCCGGGGCGCCTTTGGTGCTGCAATCCTTGTGAATCATAAGATTGAGAGGAAGAAgtgagtggcatagttctattttattttcatctttttaacaacttgataacacttatgtttcctttcactaagatgaagagtttgattttgctgttaatattagtcaccatatatttatatatgttgtgttgcacag

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G137118_T02 (Zea mays), 5'ss of exon 2
TCATGGAGTCTCGAATGGATCAGTACGAGATCATGGAGCAGATCGGACGCGGAGCGTTCGGGGCTGCCATTCTTGTGAATCACAAATCGGAGAAGAAGAAgtatttttatgatttttttttggcgcaatctatgaatttttggtgagttttgtaatgagatggtttggttttggagtgatcgagtggttcgattttcag
|||||||||| || |||||||||||||| |||||||||||||| || || || || ||||| || ||||| || || ||||||||||| || |||||||||||   | ||     | ||    |  | | | |    | |   || | |||||       |    |    || | || |  |  || || |  || |||
TCATGGAGTCACGGATGGATCAGTACGAAATCATGGAGCAGATTGGCCGTGGGGCTTTCGGTGCCGCCATACTAGTCAATCACAAATCTGAAAAGAAGAAgtaagat-atagcgctcttccatc--agtatgtaggctatatatg-gctttgtccc----ttccctaccatttgggtaactgtatgatt-gtcttgcag

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G074262_T01 (Zea mays), 5'ss of exon 2
TCATGGAGTCTCGAATGGATCAGTACGAGATCATGGAGCAGATCGGACGCGGAGCGTTCGGGGCTGCCATTCTTGTGAATCACAAATCGGAGAAGAAGAAgtatttttatgatttttttttggcgcaatctatgaatttttggtgagttttgtaatgagatggtttggttttggagtgatcgagtggttcgattttcag
 ||||||||| || ||||||||||||||| |  |||||||||| || ||||| || || || |||||||| || || || |||||  | ||||| ||||||||   ||    ||  ||  ||    |  || |   ||    |||| |||    |   ||  || |  |  |    |  |  ||               
CCATGGAGTCACGGATGGATCAGTACGAGGTTTTGGAGCAGATTGGTCGCGGCGCCTTTGGTGCTGCCATCCTCGTCAACCACAAGACAGAGAAAAAGAAgtacggttcaatttagttactg----agcctgt---ttccccgtgaatttgcctagccgacagtcttttgctttgctactgcag---------------

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA12G31330.1 (Glycine max), 5'ss of exon 1
TCATGGAGTCTCGAATGGATCAGTACGAGATCATGGAGCAGATCGGACGCGGAGCGTTCGGGGCTGCCATTCTTGTGAATCACAAATCGGAGAAGAAGAAgtatttttatgatttttttttggcgcaatctatgaatttttggtgagttttgtaatgagatggtttggttttggagtgatcgagtggttcgattttcag-------
  |||||||| || |||||||| ||||||||||||||||||||||| || || ||||| || ||||| ||||| || || |||||| |||||||||||||||   |||  |  |   ||||   ||  |   |    | |   |  | ||||   | |      ||   ||  ||   | ||  | ||| | ||    |       
--ATGGAGTCGCGGATGGATCACTACGAGATCATGGAGCAGATCGGTCGTGGCGCGTTTGGCGCTGCGATTCTCGTAAACCACAAAGCGGAGAAGAAGAAgtgcgtttgcgtctccatttttttgcgtttggttgtgtctgtatttggtttgcgtttattcaaatt---ttgagaactaacggttcgtttggttcgtggattgcag

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA13G38980.1 (Glycine max), 5'ss of exon 1
TCATGGAGTCTCGAATGGATCAGTACGAGATCATGGAGCAGATCGGACGCGGAGCGTTCGGGGCTGCCATTCTTGTGAATCACAAATCGGAGAAGAAGAAgtatttttatgatttttttttggcgcaatctatgaatttttggtgagttttgtaatgagatggtttggttttg-gagtgatcgagtggttcgattttcag-------
  |||||||| || |||||||| ||||||||||||||||||||||| ||||| ||||| || ||||| ||||| || || |||||| | ||||||| |||||   |||  |  |   || |   ||  |      | |   ||| | ||   |  ||    | ||   ||||| ||   | ||  | ||| | ||    |       
--ATGGAGTCGCGGATGGATCACTACGAGATCATGGAGCAGATCGGCCGCGGCGCGTTTGGCGCTGCGATTCTCGTAAACCACAAAGCCGAGAAGATGAAgtgcgtttgcgtctcgattgtt-tgcgtttggctgagtc--ggtaa-ttggattgtgtttcgtttgaattttgagaactaacggttcgtttggttcgtggattgcag

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA12G09910.1 (Glycine max), 5'ss of exon 1
TCATGGAGTCTCGAATGGATCAGTACGAGATCATGGAGCAGATCGGACGCGGAGCGTTCGGGGCTGCCATTCTTGTGAATCACAAATCGGAGAAGAAGAAgta-----------tttttatgatttttttttggcgcaa--tctatgaatttttggtgagttttgtaatgagatggtttggttttggagtgatcgagtggttcgattttcag--------
  ||||||||||| ||||||||||| |||||||||||||||||||| || ||||| || || || || ||||||||  | |||||  | ||||||||||||||           ||||| |  ||  ||  ||| || |  | | |   ||  ||   | ||   | ||| |  ||||||    |    |||  ||  | || | |||   |        
--ATGGAGTCTCGGATGGATCAGTATGAGATCATGGAGCAGATCGGTCGAGGAGCATTTGGAGCGGCTATTCTTGTTCACCACAAGGCTGAGAAGAAGAAgtaatagtcaccactttttgtatttcattgatggggctacgtttttttgttcatgagaaattcgttgatgggtaggtttgtaagtttgatgactgaa-gctttgttttattgggttgcag

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA11G18340.1 (Glycine max), 5'ss of exon 1
TCATGGAGTCTCGAATGGATCAGTACGAGATCATGGAGCAGATCGGACGCGGAGCGTTCGGGGCTGCCATTCTTGTGAATCACAAATCGGAGAAGAAGAAgtatt---------tttatgatttttttt--tggcgcaatctatga--atttttggtgagttttgtaatgagatggtttg---gttttggagtgatcgagtggttcgattttcag--------
  ||||||||||| ||||||||||| ||||||||||||||||||||  | ||||| || || ||||| ||||||||  | |||||  | ||||| |||||||| |         ||| ||| |||  ||  ||| |  || | ||    ||  |    | ||   |  || |  ||||||   ||||     |||  ||  | || | ||| | |        
--ATGGAGTCTCGGATGGATCAGTATGAGATCATGGAGCAGATCGGTAGAGGAGCATTTGGAGCTGCTATTCTTGTTCACCACAAGGCTGAGAAAAAGAAgtaatagtcaccactttttgaatttcattgatggggttatgtttgtttgttcataagaaattcgttggtgggtaggtttgtaagtttgatgatgactgaa-gctttgttttactggattgcag

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT3G44200.1 (Arabidopsis thaliana), 5'ss of exon 1
TCATGGAGTCTCGAATGGATCAGTACGAGATCATGGAGCAGATCGGACGCGGAGCGTTCGGGGCTGCCATTCTTGTGAATCACAAATCGGAGAAGAAGAAgtatttttatgatttttttttggcgcaatctatgaatttttggtgagttttgtaatgagatggtttggttttggagtgatcgagtggttcgattttcag
  |||||||| |||||||||||||||||| | ||||| ||||||||  | |||||||| || ||||| ||| | ||  |||| ||| | ||||  ||||||||   ||  | || |   ||     | ||| |   | ||||  ||   ||    |       |||| |||| | ||  | | |||     ||||| ||
CGATGGAGTCACGAATGGATCAGTACGAGCTTATGGAACAGATCGGGAGAGGAGCGTTTGGTGCTGCTATTTTAGTTCATCATAAAGCTGAGAGAAAGAAgtaaaattg-gtttctccatttataaactcttt---tctttgaagatccttaggtt-------tttgatttttgtgtattggtgtgt----atttttag

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|71862067|gb|DT011122.1|DT011122
EST:     GGAGCGTTCGGGGCTGCCATTCTTGTGAATCACAAATCGGAGAAGAAGAA                         GTATGTATTGAAGAAGATCAGGTTGGCACGACAAACGGAGAGGTGCCGGAG
genomic: GGAGCGTTCGGGGCTGCCATTCTTGTGAATCACAAATCGGAGAAGAAGAAgtatttttat ... cgattttcagGTATGTATTGAAGAAGATCAGGTTGGCACGACAAACGGAGAGGTGCCGGAG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGGAGTCTCGAATGGATCAGTACGAGATCATGGAGCAGATCGGACGCGGAGCGTTCGGGGCTGCCATTCTTGTGAATCACAAATCGGAGAAGAAGAAgtatttttatgatttttttttggcgcaatctatgaatttttggtgagttttgtaatgagatggtttggttttggagtgatcgagtggttcgattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG