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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAATGGTCCAGCAAGCTATGCAGTATATTGACCAGACACCGGATATTGAATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAGgtcaatacatatatctataagtttcagcttatattatgttggacaatgtttttttttgttttgagctttttagttaattatatctgcattattatgtag

Basic information

species Vitis vinifera
transcript Vv07s0031g01970.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA04G39520.1 (Glycine max), 5'ss of exon 3
TGCAATGGTCCAGCAAGCTATGCAGTATATTGACCAGACACCGGATATTGAATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAGgtcaatacat-atatctataagtttcagcttatattat-gttggacaatgtttttttttgttttgagctttttagttaattatatctgcattattatgtag
 |||||||||||||| |||||||| ||||||||  ||||||| ||| ||||| ||   || || ||||| ||||   | |||||||| |||||||||||||| |  | || || | |  |   ||||     | ||||  |    ||||||  | | | | |    | ||  ||      ||| | || || |||   |||
AGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCAGATCTTGAAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAGgtgagcatatgatgttttcactcttcattcctttttattatcctccaatgtagtctatcgatgcatgtttaata------tatgt-tgtatcatttgctag

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA08G15340.1 (Glycine max), 5'ss of exon 3
TGCAATGGTCCAGCAAGCTATGCAGTATATTGACCAGACACCGGATATTGAATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAGgtcaatacatatatctataagtttcagcttatattatgttggacaatgtttttttttgttttgagctttttagttaattatatctgcattattatgtag
 || ||||| || || |||||||| ||||||||| ||||||| ||||| ||| ||   || || ||||| |||||  | ||||||||||||||||| ||||||  |     ||| | | |  ||  | || | || |           |||||  || ||      | | |  || || || | |  || |||   |||
AGCTATGGTGCAACAGGCTATGCAATATATTGACGAGACACCAGATATCGAAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtcggtgtgc-tatgtttgaacttttgtttgtttttta---------atttttcattattggattatgtatgatttat-atgtttttatcatttattag

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA05G32030.2 (Glycine max), 5'ss of exon 3
TGCAATGGTCCAGCAAGCTATGCAGTATATTGACCAGACACCGGATATTGAATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAGgtcaatacatatatctataagtttcagcttatattatgttggacaatgtttttttttgttttgagctttttagttaattatatctgcattattatgtag
 || ||||| || ||||||||||| ||||||||  ||||||| ||||| ||| ||   || || ||||| |||||  | ||||||||||||||||| |||||   |           || |||| | ||| |  | ||||  | |   |||  || |||  | |  | | |  || || || | |  || |||   |||
AGCTATGGTGCAACAAGCTATGCAATATATTGATGAGACACCAGATATCGAAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc-------tatgtttgaactttttgtttgttttatagcttttcattatgtgatta--tgtatgatttat-atgtttttatcatttattag

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA06G15330.1 (Glycine max), 5'ss of exon 3
TGCAATGGTCCAGCAAGCTATGCAGTATATTGACCAGACACCGGATATTGAATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAGgtcaatacatatatctataagtttcagcttatattatgttggacaatgtttttttttgttttgagctttttagttaattatat-ctgcattattatgtag
 || |||||||| || |||||||| |||| |||  ||||||||||| ||||| ||   || || ||||| |||||  | |||||||| ||||||||||||||  || |||||    ||   ||    |||   |  | ||  |  ||  |    |||  | |     | |  ||| | |||||  || || |||   |||
AGCGATGGTCCAACAGGCTATGCAATATACTGATGAGACACCGGATCTTGAAACTCGTATAGAACTCATCAAAACCTTGAACAGTGTATCTGCAGGAAAGgttgat-catatg---atgttttcactcttcattccttttttattattctccaatttagtctatcgatgtatgtttaatatatgttgtatcatttgttag

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 5'ss of exon 3
TGCAATGGTCCAGCAAGCTATGCAGTATATTGACCAGACACCGGATATTGAATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAGgtcaatacatatatctataagtttcagcttatattatgttggacaatgtttttttttgttttga--gctttttagttaattatatctgcattattatgtag
  | ||||| |||||||| ||||||||||| || |||||||| || |||||| ||  ||| ||||| || || || || |||| ||| ||||| ||||||||          | |||| |   | |   | |||| | |   | ||  |  |  ||   | | |  | ||   | |  ||| ||  || ||          
ATCCATGGTGCAGCAAGCAATGCAGTATATCGATCAGACACCAGACATTGAAACTCGGATAGAGCTTATCAAGACGCTGAACAATGTATCTGCTGGAAAGgt------gcgaaactatgaaactgatggtgtattctttataataacttcatcattctgtgtaattgtttaccattgcattttacatgtatag--------

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S58_256V6.1 (Physcomitrella patens), 5'ss of exon 3
TGCAATGGTCCAGCAAGCTATGCAGTATATTGACCAGACACCGGATATTGAATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAGgt-------caatacata--tatctataagtttcagcttatattatgttggacaatgtttttttttgttttgagctttttagttaattatatctgcattattatgtag
||| ||||| |||||||||||||||||||||||  | || || ||  | ||| ||   |||||| | ||| | || || |||| ||| |||||||| |||||       |  |   |   |    | |   |   | | |||| ||||||  || ||| ||||       |   | | ||  || ||  |    |  |||||  ||||
TGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttcgttgtctgattgctcacatactcttgatgatatcatgttgagcagtgtcttttga-acagtatccatattgattcatcgt--tggttttattg-gtag

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|351035869|gb|FQ463714.1|FQ463714
EST:     AATCTAAGATTGAGCTCATTAAAACACTTAACAATGTGTCTGCAGGAAAG                         ACATATGTTGAAATAGAGAGGGCTCGGCTGATCAAGAAACTAGCAAAAATA
genomic: AATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAGgtcaatacat ... tattatgtagATATATGTTGAAATAGAGAGGGCTCGGCTGATCAAGAAACTAGCAAAAATA
EST: gi|110391070|gb|EC956024.1|EC956024
EST:     AACAGTGTGTCTGCAGGAAAG                         ATATATGTTGAAATAGAGAGGGCTCGGCTGATCAAGAAACTAGCAAAAATA
genomic: AACAGTGTGTCTGCAGGAAAGgtcaatacat ... tattatgtagATATATGTTGAAATAGAGAGGGCTCGGCTGATCAAGAAACTAGCAAAAATA
EST: gi|27583566|gb|CB006261.1|CB006261
EST:     AATCTAAGATTGAGCTCATTAAAACACTTAACAATGTGTCTGCAGGAAAG                         ATATATGTTGAAATAGAGAGGGCTCGGCTGATCAAGAAACTAGCAAAAATA
genomic: AATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAGgtcaatacat ... tattatgtagATATATGTTGAAATAGAGAGGGCTCGGCTGATCAAGAAACTAGCAAAAATA
EST: gi|349825795|gb|FQ423090.1|FQ423090
EST:     AATCTAAGATTGAGCTCATTAAAACACTTAACAATGTGTCTGCAGGAAAG                         ATATATGTTGAAATAGAGAGGGCTCGGCTGATCAAGAAACTAGCAAAAATA
genomic: AATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAGgtcaatacat ... tattatgtagATATATGTTGAAATAGAGAGGGCTCGGCTGATCAAGAAACTAGCAAAAATA
EST: gi|161712574|gb|FC062176.1|FC062176
EST:     AATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAG                         ATATATGTTGAAATAGAGAGGGCTCGGCTGATCAAGAAACTAGCAAAAATA
genomic: AATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAGgtcaatacat ... tattatgtagATATATGTTGAAATAGAGAGGGCTCGGCTGATCAAGAAACTAGCAAAAATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAATGGTCCAGCAAGCTATGCAGTATATTGACCAGACACCGGATATTGAATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAGgtcaatacatatatctataagtttcagcttatattatgttggacaatgtttttttttgttttgagctttttagttaattatatctgcattattatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG