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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGAGTATGTCCCTGAGACTGTTCATCGGGTGATCAAACACTACAATAAGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtttgtattatatatatatatagtctgattttattaactttgctgttttttatttttattccacaatcctgttgaatttatatctttatatggcactatt...

Basic information

species Vitis vinifera
transcript Vv07s0005g02100.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os05g04340.2 (Oryza sativa), 5'ss of exon 5
GCTTGAGTATGTCCCTGAGACTGTTCATCGGGTGATCAAACACTACAATAAGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtttgtattatatatatatatagtctgattt-tattaactttgctgt-tttttatttttattccacaatcctgttg-aatttatatctttatatggcactatt
|||||||||||| || ||||||| ||| || || || ||||| ||||| |||||||||||  | |||||| |||||||||  ||||| ||||  || |||||     ||| | |  || ||  ||| || | |  || |     | |   || | | | |      || ||| ||  |||| | |                  
GCTTGAGTATGTGCCAGAGACTGCTCACCGTGTAATTAAACATTACAACAAGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAGgta-acgttacacacctagatcttctaatctatcctagcacaattatgcattgagtataacatggaaaacctattataattgacag-----------------

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os01g19150.4 (Oryza sativa), 5'ss of exon 4
GCTTGAGTATGTCCCTGAGACTGTTCATCGGGTGATCAAACACTACAATAAGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtttgtattatatatatat-atagtctgattttattaa--ctttgctgttttttatttttattcca---caatcctgttgaatttatatctttatatggcactatt
 ||||| ||||| || || ||||||||||| || || | ||| ||||||||||||| |||  | |||||| |||| ||||| |||||||| |  ||||||||  |  ||  |      | | |     | | ||   |  |  |  |  |||| ||  | |||  |    ||  ||||| | | |   |  |  | |  ||     
TCTTGAATATGTGCCAGAAACTGTTCATCGTGTTATTAGACATTACAATAAGATGAGCCAACGCATGCCATTGATTTATGTTAAACTTTATATGTACCAGgtaag-gttgcaggcgccttacaacacaactatagctatgcactattagttttgataatgattttaactgaaaactgttcattgtcatttctgttctttcag----

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G075992_T01 (Zea mays), 5'ss of exon 1
GCTTGAGTATGTCCCTGAGACTGTTCATCGGGTGATCAAACACTACAATAAGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtt-tgtattatat---atatatatagtctgatttta--ttaactttgctgttttttatttttattccacaatcctgttgaatttata-tctttatatggcactatt-----
|||||| ||||| || || |||||||| || || || ||||| |||||||||||||||||  |||||||| |||| ||||| |||||||| |  || |||||  ||| ||  ||    ||  ||   ||  ||      || | | ||   |||||| |    ||     | |  |  ||||  | |  | |||||  | |   |||     
GCTTGAATATGTGCCAGAAACTGTTCACCGTGTTATTAAACATTACAATAAGATGAACCAACGGATGCCATTGATTTATGTTAAACTTTATATGTATCAGgtaatgtctttcattttgtaagtaccttccaatacagctttgattgtgtccttttttgtaccaataat-tatttttactgaacctttggtttttattggactaaatttacag

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G155836_T01 (Zea mays), 5'ss of exon 5
GCTTGAGTATGTCCCTGAGACTGTTCATCGGGTGATCAAACACTACAATAAGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtttgtattatatatatatatagtctgattttattaactttgctgttttttatttttattccacaatcctgttgaatttatatctttatatggcactatt
|||||||||||| || ||||||| |||||| || |||||||| ||||| |||||||||||| | |||||  |||| ||||  ||||| || |  || |||||         |    ||    |   |   || || ||       |  | |||   |     |||||  |      |  | | ||||      |||    
GCTTGAGTATGTACCGGAGACTGCTCATCGTGTCATCAAACATTACAACAAGATGAACCAGCGCATGCCTTTGATTTATGCAAAACTGTATATGTATCAGgta--------aagcttactctgctgggagttgttgacag----atcctgtataactgcatgacaatagtaacatgtcaa-acctttgcgattcacag--

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G01280.1 (Glycine max), 5'ss of exon 5
GCTTGAGTATGTCCCTGAGACTGTTCATCGGGTGATCAAACACTACAATAAGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgt-ttgtattatatatatatatagtctgattttattaactttgctgttttttatttttattccacaatcctgttgaattt-atatctt-tatatggcactatt---
 ||||||||||| ||||||||||| || || || |||| ||| ||||| || ||||| || || |||||  |||||||||||||||| ||   |||||||||  | ||||| | || ||| |  |    | || | |  ||| || ||       ||   |  |  |   |||||  | | || |||| ||| |   | | ||   
ACTTGAGTATGTTCCTGAGACTGTCCACCGAGTTATCAGACATTACAACAAAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAGgtactatattaaa-atttattttcttctttcttgtaagttttactattaaggcaattgtctatatcactttgttggttctcatttcttctatttcttattttttag

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|33405137|gb|CF210764.1|CF210764
EST:     AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAG                         ATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGCCACAGG
genomic: AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtttgtatta ... ttttctacagATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGCCACAGG
EST: gi|30125127|gb|CB910466.1|CB910466
EST:     AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAG                         ATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGCCACAGG
genomic: AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtttgtatta ... ttttctacagATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGCCACAGG
EST: gi|161712353|gb|FC061927.1|FC061927
EST:     AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAG                         ATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGCCACAGG
genomic: AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtttgtatta ... ttttctacagATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGCCACAGG
EST: gi|110685785|gb|EE062810.1|EE062810
EST:     AGATGAACCAGAAGATGCCAATGATATATGTGAAACTTTACACTTACCAG                         ATTTGTAGAGCGCTGGGCT-ACATTCATGGTGGTATTGGAGTATGC-ACAG
genomic: AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtttgtatta ... ttttctacagATTTGTAGAGCGCTGG-CTTACATTCATGGTGGTATTGGAGTATGCCACAG
EST: gi|30133168|gb|CB918507.1|CB918507
EST:     AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAG                         ATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGCCACAGG
genomic: AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtttgtatta ... ttttctacagATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGCCACAGG
EST: gi|110710881|gb|EE087442.1|EE087442
EST:     AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAG                         ATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGCCACAGG
genomic: AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtttgtatta ... ttttctacagATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGCCACAGG
EST: gi|71875370|gb|DT024425.1|DT024425
EST:     AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAG                         ATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGCCACAGG
genomic: AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtttgtatta ... ttttctacagATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGCCACAGG
EST: gi|30252766|gb|CB970317.1|CB970317
EST:     AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAG                         ATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGCCTCAGG
genomic: AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtttgtatta ... ttttctacagATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGCCACAGG
EST: gi|71875374|gb|DT024429.1|DT024429
EST:     AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAG                         ATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGC
genomic: AGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtttgtatta ... ttttctacagATTTGTAGAGCGCTGGCTTACATTCATGGTGGTATTGGAGTATGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTGAGTATGTCCCTGAGACTGTTCATCGGGTGATCAAACACTACAATAAGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgtttgtattatatatatatatagtctgattttattaactttgctgttttttatttttattccacaatcctgttgaatttatatctttatatggcactatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG