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

GTCATGGTGGTTCTCGTGCTGCGGAGTTTTTGAAGGAGCATCTCTTTGAGAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAAgtgagtttaagttttctaactctcaattgttatgcatgattttttctgtgcattatcaggattgtgtttttgtagcgtatccttttggtgtcacagtttt...

Basic information

species Vitis vinifera
transcript Vv16s0050g02570.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g02570.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os05g50970.1 (Oryza sativa), 5'ss of exon 4
GTCATGGTGGTTCTCGTGCTGCGGAGTTTTTGAAGGAGCATCTCTTTGAGAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAAgtgagtttaagttttctaactct--caattg-ttatgcatgattttttctgtgcattatcaggattgtgtttttgtagcgtatccttttggtgtcacagtttt
||||||||||||| |||||||| |||| ||||||||||||  | ||||||||  | ||||| ||||||||||||||||||||||| ||||| || ||||||  | |   |||  ||| || |  || | | || | || |||  | |   |   || |   ||| | ||      | |  |||  |       |||||    
GTCATGGTGGTTCACGTGCTGCTGAGTATTTGAAGGAGCACTTGTTTGAGAACCTCATGAAACATCCAGAGTTCATGACAAATACAAAATTAGCAATAAgtatgatattgttc-ctagctgtaccactagcttcttcaagatcctgttgatat-ttcttgtgatggagta-----aactgatcaatggtaatccacag----

upper sequence: Vv16s0050g02570.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G158818_T02 (Zea mays), 5'ss of exon 2
-GTCATGGTGGTTCTCGTGCTGCGGAGTTTTTGAAGGAGCATCTCTTTGAGAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAAgt--gagtttaagttttctaactc---tcaattgttatgcatgattttttctgtgcattatcaggattgtgtt--tttgtagcgtatccttttggtgtcacagtttt
 ||||||| ||||| |||||||| |||| ||||||||||||| | ||||||||  | ||||| |||||||||||||||||||| || ||||| || ||||||  ||  ||     |   |  ||   | |    |    ||| |  |   |    ||| | | |  |  ||      || ||                         
GGTCATGGCGGTTCACGTGCTGCTGAGTATTTGAAGGAGCATTTGTTTGAGAACCTCATGAAACATCCAGAGTTCATGACAAACACAAAATTAGCAATAAgtatgaaattgcacatagcatttccagttatccatcgaccatcaagtcacccagtcatcacctgattaatggcaacctgcag-------------------------

upper sequence: Vv16s0050g02570.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G412937_T01 (Zea mays), 5'ss of exon 4
GTCATGGTGGTTCTCGTGCTGCGGAGTTTTTGAAGGAGCATCTCTTTGAGAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAAgt--gagtttaagttttctaactctcaattgttatgcatgattttttctgtgcattatcaggattgtgtttttgtagcgtatccttttggtgtcacagtttt
||||||||||||| |||||||| |||| ||||||||||||  | ||||||||  | ||||| ||||| ||||||||||||||||| ||||| ||  |||||  ||  ||     | | |  ||| | ||   ||  || |||   |||   | | || |         |   |                            
GTCATGGTGGTTCACGTGCTGCTGAGTATTTGAAGGAGCACTTGTTTGAGAACCTCATGAAACATCCGGAGTTCATGACAAATACAAAATTAGCATTAAgtatgatattgcacatgccatttct-agttaccattgatcattaagtcttcacctgattaacgacaacctgcag----------------------------

upper sequence: Vv16s0050g02570.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA13G08090.2 (Glycine max), 5'ss of exon 4
GTCATGGTGGTTCTCGTGCTGCGGAGTTTTTGAAGGAGCATCTCTTTGAGAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAAgtgagtttaagttttctaactctcaattgttatgcatgattttttctgtgcattatcaggattgtgtttttgtagcgtatccttttggtgtcacagtttt-----
|||||||||||||||||||||| |||| ||| ||||||||||| ||||| ||| |  ||||||||||| | ||  ||||| || |||||||||||||||||| ||||   || ||| | |    ||| | ||| |||  |  |  | |   || |    |||   || || |    |||  | ||  ||      | |      
GTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAATTTTTTGACAGATGCCAAATTGGCTATAAgtgtgtttgctttctctcattt---attttcatgaatgtctcgtaatatcttttgttt--atttgtttattatttgttattttgttaatgctttcatgtgtgttc

upper sequence: Vv16s0050g02570.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA14G31890.1 (Glycine max), 5'ss of exon 5
GTCATGGTGGTTCTCGTGCTGCGGAGTTTTTGAAGGAGCATCTCTTTGAGAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAAgtgagtttaagttttctaactc-------tcaattgttatgcatgattttttctgtgcattatcaggattgtgtttttgtagcgtatccttttggtgtcacagtttt
|||| ||||||||||||||||| |||| ||| ||||||||||| ||||| ||| |  ||||||||||| | ||  ||||| || |||||||||||||||||| ||||   |||||| | |        |||||   |     | || | || |||  |||||  |  || | || ||   || |  |  | || |   |||     
GTCACGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAAATTTTTGACAGATGCCAAATTGGCTATAAgtgtgtttgctttttctcatttattttcgtcaatgtctcattgtaatatcttttgtttattatttg--ttattttgttaatgctttactgtgtgttccaaca-----

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|351049251|gb|FQ428994.1|FQ428994
EST:     AATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTTGGCTATAA                         GTGAAACATATCAACAAACTGACATGAATTTTCTGGATGCTGAAAGAAATA
genomic: AATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATT-GGCTATAAgtgagtttaa ... aaacttgcagGTGAAACATATCAACAAACTGACATGAATTTTCTGGATGCTGAAAGAGATA
EST: gi|351026149|gb|FQ428161.1|FQ428161
EST:     GATTTTGATGAAGCATCCAGAGTTCATGACCAATACCAAATTGGCTATAA                         GTGAAACATATCATCAAACTGACATGAATTTTCTGGATGCTGAAAGAGATA
genomic: GAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAAgtgagtttaa ... aaacttgcagGTGAAACATATCAACAAACTGACATGAATTTTCTGGATGCTGAAAGAGATA
EST: gi|351015894|gb|FQ431849.1|FQ431849
EST:     GAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAA                         GTGAAACATATCAACAAACCTGACATGAATTTTCTGGATGCTGAAAGAGAT
genomic: GAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAAgtgagtttaa ... aaacttgcagGTGAAACATATCAACAAAC-TGACATGAATTTTCTGGATGCTGAAAGAGAT
EST: gi|351026397|gb|FQ428409.1|FQ428409
EST:     GAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAA                         GTGAAACATATCAACAAACTGACATGAATTTTCTGGATGCTGAAAGAGATA
genomic: GAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAAgtgagtttaa ... aaacttgcagGTGAAACATATCAACAAACTGACATGAATTTTCTGGATGCTGAAAGAGATA
EST: gi|110392544|gb|EC958041.1|EC958041
EST:     GAATTTGATGAAGCATCCAGAGTTCATGACAAATGCCCAATTGGCTATAA                         GTGAAACTTATCAACAAACTGACATGAATTTTCTGGATGCTGAAAGAGATA
genomic: GAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAAgtgagtttaa ... aaacttgcagGTGAAACATATCAACAAACTGACATGAATTTTCTGGATGCTGAAAGAGATA
EST: gi|110690250|gb|EE067195.1|EE067195
EST:     GAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAA                         GTGAAACATATCAACAAACTGACATGAATTTTCTGGATGCTGAAAGAGATA
genomic: GAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAAgtgagtttaa ... aaacttgcagGTGAAACATATCAACAAACTGACATGAATTTTCTGGATGCTGAAAGAGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATGGTGGTTCTCGTGCTGCGGAGTTTTTGAAGGAGCATCTCTTTGAGAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAAgtgagtttaagttttctaactctcaattgttatgcatgattttttctgtgcattatcaggattgtgtttttgtagcgtatccttttggtgtcacagtttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC