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

ATTGGAGATGAAACATTTATAATAGCAGCTCTTATGGCAATGAGACACCCTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatctattttcttgtttattttccatacaagagctgtacctttttgtgcttcggctttctccatttgttcttctgatgccccaatgcacgtgtg...

Basic information

species Vitis vinifera
transcript Vv04s0023g00380.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00380.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os11g28300.1 (Oryza sativa), 5'ss of exon 4
ATTGGAGATGAAACATTTATAATAGCAGCTCTTATGGCAATGAGACACCCTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatct---attttcttgttt-attttccatacaagagctgtacctttttgtgcttcggcttt-ctccatttgttcttctgatgccccaatgcacgtgtg
|||||||||||||| ||||| || || || || ||||||||| | ||||| || ||||| ||| | |||||||||||    ||  |    || |||||||| ||||       ||    |  |||  |||  | ||    |   |||    || ||     |  | | ||  | |||||    | | |    |||         
ATTGGAGATGAAACCTTTATTATTGCGGCGCTAATGGCAATGCGGCACCCCAAGTCAATCGTTCTGTCTGGTGCGCTATCGGCGCTCTACGTGATGACGgtgagctcctcgagatcaattcatttcgtttatcctatccaatgagtaaaacttagtatcatgcttatacttgacttgttaga-taaagttgtaatttgta----

upper sequence: Vv04s0023g00380.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA09G38640.1 (Glycine max), 5'ss of exon 4
ATTGGAGATGAAACATTTATAATAGCAGCTCTTATGGCAATGAGACACCCTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatctatt---ttcttgtttattttccatacaagagctgtacctttttgtgcttcggctttc-tccatttgttcttctgatgccccaatgcacgtgtg
||||| ||||| || ||||||||||||||||| ||||| ||| | |||||||| |||||||| || |||||||||||||||||| ||||| ||||||| |||||      ||    | | | |||  ||   ||| |   ||  |    |||        || || | |   |||||| || ||| |      |    |    
ATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCTAAGTCAATTGTCTTGTCTGGTGCGCTCAGTGCTCTGATTATAATGACAgtaagtgcaacatgggatgcatttttggttataatatatttgcattgttgtttctcatcatgggttgcatttttttgttgttgtgacggaatggtttgtg----

upper sequence: Vv04s0023g00380.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA18G47670.1 (Glycine max), 5'ss of exon 4
ATTGGAGATGAAACATTTATAATAGCAGCTCTTATGGCAATGAGACACCCTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagc----tatctattttcttgtttattttc-catacaagagctgtacctttttgtgcttcggctttctccatttgttcttctgatgccccaatgcacgtgtg------------------------------------------------------------------------------
||||| ||||| || ||||||||||||||||||||||| ||| | |||||||| |||||||| || |||||||| ||||||||| ||||| ||||||| |||||      ||    |   || ||  ||||   ||    |   |||   || |  |  || |   | ||   | |||| || |||||      |   ||                                                                                  
ATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACAgtaagtgcaacatgggatgcatttttggttttaatatttctgcattgttgtttctcattattggatgtactttttgtgttgttgtgatggaatggtttgcgcaactacagagcactatttctgggtgctctaacttttcatattaatgttatcaggattaaagttactgtacgtgtcaattag

upper sequence: Vv04s0023g00380.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G36290.1 (Arabidopsis thaliana), 5'ss of exon 5
ATTGGAGATGAAACATTTATAATAGCAGCTCTTATGGCAATGAGACACCCTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagct---atctattttcttgtttattttccatacaagagctgtacctttttgtgcttcggctttctccatttgttcttctgatgccccaatgcacgtgtg
||||| |||||||| ||||||||||| ||  | ||||| ||| |||| |||||| | | ||||||||||||||| |||   |||||| |||| ||||| ||||| |   |  || ||   ||| ||||     |   | |  |  | | |  |       ||  || || |  |||| |  |  | |   | ||    |   
ATTGGGGATGAAACTTTTATAATAGCGGCATTGATGGCTATGCGACATCCTAAAGCTACTGTTTTATCTGGTGCACTCTCAGCTTTGTTTGTTATGACTgtaagttgaaaattacttgtatgtatattcattgtgggaaaaat-catcgtactacagag-ggtattgtctaactgttgtgatttttctgaattgagtttag-

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|110375514|gb|EC940507.1|EC940507
EST:     CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|33405511|gb|CF211138.1|CF211138
EST:     GGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: GGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|30303671|gb|CB980465.1|CB980465
EST:     CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|71867156|gb|DT016211.1|DT016211
EST:     CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|110386306|gb|EC950891.1|EC950891
EST:     AATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: AATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|34320010|gb|CF372764.1|CF372764
EST:     CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTGGGCAGGATTGTGCCAAATNTGATATCAAGGAAG
genomic: CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|110403098|gb|EC964255.1|EC964255
EST:     CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|110398724|gb|EC965198.1|EC965198
EST:     GCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: GCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|110393823|gb|EC959339.1|EC959339
EST:     CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|30303609|gb|CB980403.1|CB980403
EST:     CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|161715778|gb|FC066182.1|FC066182
EST:     CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|110369298|gb|EC933452.1|EC933452
EST:     CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|294966027|gb|GW837394.1|GW837394
EST:     CTAAATCAATTGTTATATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCA
genomic: CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCA
EST: gi|77584187|gb|DV221146.1|DV221146
EST:     CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|110685575|gb|EE062425.1|EE062425
EST:     CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|110418308|gb|EC984450.1|EC984450
EST:     CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|71866927|gb|DT015982.1|DT015982
EST:     TGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: TGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
EST: gi|110418385|gb|EC984534.1|EC984534
EST:     CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG                         GTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG
genomic: CTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatc ... tgccaattagGTACTCTCCACTGGGCTTGGCAGGATTGTGCCAAATTTGATATCAAGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGGAGATGAAACATTTATAATAGCAGCTCTTATGGCAATGAGACACCCTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACGgtaagctatctattttcttgtttattttccatacaagagctgtacctttttgtgcttcggctttctccatttgttcttctgatgccccaatgcacgtgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atacaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttctcc