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

...ttcatgcattaaaggattattatgcttggtgcctgcctcacttacctcattattgaaggctcaataatgtctgtcaattgttttttattttccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTC

Basic information

species Vitis vinifera
transcript Vv08s0056g00200.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 2
----ttcatgcattaaaggattattatgcttggtgcctgcctcacttacctcattattgaaggctcaataatgtctgtcaattgttttttattttccttcac-agGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTC
     ||| | |  |||| ||| || || |   || | || | | ||   |      |  |   ||  | |||    |||    ||| | |  | | |  |  ||||||| ||||||||||||||| | || ||||||||||| |  || || || || ||| |||| |||||||||||||||||||||||||| || ||||| |
ctttctcacggacgaaag-attgttctgttc--tgtcagcataatttgatttgcaggtatactgtct-tcatgcac-tcacccttttgtgaaatacatgtattagGGTGCTCCTGAGAAATGGAGACTAGTGAAGGCTCATGGAACAGCTGTGGGTCTCCCATCTGATGATGACATGGGCAACAGTGAAGTTGGTCACAATGCAC

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 2
-ttcatgcattaaaggattattatgcttggtgcctgcctcacttacctcattattgaaggctcaata-atgtctgtcaattgtttttt--attttccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTC
  |    | |  ||| |  ||| | ||    | | || | | ||   |      |  |   || |||    | |    |   ||   |  | | |   |   |||| || ||||||||||||||| | || ||||||||||| |  || || || || ||| |||| |||||||||||||||||||||||||| || ||||| |
tctttctcttgtaagaaagattgttct----gtcagcataatttgttttgcaggtatactgtctatatgcttttacttacccttcagtgaaatatgtatattagGGCGCTCCTGAGAAATGGAGACTAGTGAAGGCTCATGGAACAGCTGTGGGCCTCCCATCTGATGATGACATGGGCAACAGTGAAGTTGGTCACAATGCAC

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 1
---ttcatgcattaaaggattattatgcttggtgcctgcctcacttacctcattattgaaggctcaataatgtctgtcaattgttttttattttccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTC
   | |||   |||   |   |   || ||    |  |  |  ||  ||  |     | || ||   ||       | |||     ||| | ||   | |||||||||||||||    ||||||||||||| ||||||||| |  || ||||| |||||||| || ||||||||||| || ||||||||||| || |||||||
gtgtccattt-ttagtagccgacggtgtttcaaacagggttgcct--ccgaaccgaagtagactggttagatgaaattaatcaggatttttattgtcttacagGGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTC

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 2
ttcatgcattaaaggattat-tatgcttggtgcctgcctcacttacct--cattattgaaggctcaataatgtctgtcaattgttttttattttccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTC
       |   |||||  ||   ||   ||   |  |  ||   | ||     || |    | |  || |  |   |||   |  |||| ||||     ||||||||| |||||    ||||||||||| | ||||||||| | ||| ||||| |||||||| || |||||||||||||| ||||||||||| || ||||| |
cctccaaaccgaaggaggatacctgtgaggaaacaacaacaaaaatctattgctagtttgagttagatgaaattaatca---ggatttttttttgtactacagGGTGCTCCTGAACGGTGGAGATTGGTCAGGGCTCATGGTACTGCTGTAGGACTTCCAACAGAAGATGACATGGGCAATAGTGAAGTTGGTCACAATGCCC

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 1
ttcatgcattaaaggattattatgcttggtgcctgcctcacttacctcattattgaaggctcaataatgtctgtcaattgttttttattttccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTC
   |||  |       |  ||||      | | | ||||  | |  ||  |          | || |||    ||||  |||   | || | ||||||||||    || || | |||||| ||| | || |||||||| |  || || || || || |  || || |||||||| ||||||||||||||||| |||||||
-gtatgtttccttttttgtttatatccacttctttcctcgatgatttcgctg----gattccgattatggacttcaacggttcgattttattcttcacagGGGAAGCCCGACACATGGAGGTTGATCAAAGCTCATGGTACCGCCGTTGGTCTCCCCAGCGAAGACGACATGGGAAACAGTGAAGTTGGCCACAATGCTC

upper sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S145_164V6.2 (Physcomitrella patens), 3'ss of exon 2
-ttcatgcattaaaggattattatgcttggtgcctgcctcacttacctcattattgaaggctcaataatgtctgtca-attgttttttattttccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTC
    ||     |    |||  |||  |||| |||||    |   |  |     |   |   |||    ||      | |||| | |||  |    |    ||  ||| || ||||| ||| ||||| |||| || |||||   ||| |||||||| || || ||||| |||||||| |||||||| ||||||||||||||| 
ccagatttgacatcaaattggtatttttggagcctgat--aaccattttggagtcatattgtcacggctgataccgagattgctctttcataatttgtgtagACTGCTCCGGAGAAGTGGCGATTGCTTAAAGCCCATGGAGCTGCGGTAGGGCTACCTACGGAGGAGGACATGGGTAACAGTGAGGTTGGCCATAATGCTT

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|110418028|gb|EC984140.1|EC984140
EST:     ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAG                         GGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
genomic: ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAGgtctcttcct ... tccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
EST: gi|71858573|gb|DT007628.1|DT007628
EST:     ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAG                         GGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
genomic: ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAGgtctcttcct ... tccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
EST: gi|110732942|gb|EE108671.1|EE108671
EST:     ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAG                         GGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
genomic: ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAGgtctcttcct ... tccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
EST: gi|294965964|gb|GW839303.1|GW839303
EST:     ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAG                         GGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
genomic: ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAGgtctcttcct ... tccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
EST: gi|110731939|gb|EE106787.1|EE106787
EST:     ACAACTGCATCCACGTCGCCGACACCCCCACCATGGATTCCCTCAAGAAG                         GGTGCCCCCGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
genomic: ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAGgtctcttcct ... tccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
EST: gi|71856163|gb|DT005218.1|DT005218
EST:     ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAG                         GGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
genomic: ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAGgtctcttcct ... tccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
EST: gi|110720962|gb|EE097416.1|EE097416
EST:     ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAG                         GGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
genomic: ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAGgtctcttcct ... tccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
EST: gi|161715825|gb|FC067428.1|FC067428
EST:     ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAG                         GGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
genomic: ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAGgtctcttcct ... tccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
EST: gi|110718255|gb|EE094880.1|EE094880
EST:     ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAG                         GGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
genomic: ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAGgtctcttcct ... tccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
EST: gi|110721142|gb|EE097804.1|EE097804
EST:     ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAG                         GGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
genomic: ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAGgtctcttcct ... tccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
EST: gi|71855635|gb|DT004690.1|DT004690
EST:     ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAG                         GGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
genomic: ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAGgtctcttcct ... tccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
EST: gi|110723612|gb|EE101122.1|EE101122
EST:     ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAG                         GGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG
genomic: ACAACTGCATCCACGTCGCCGACACTCCCACCATGGATTCCCTCAAGAAGgtctcttcct ... tccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcattattgaaggctcaataatgtctgtcaattgttttttattttccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTC
                                ttgttttttattttcc  CT-rich tract
                            tcaattgttttttatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatgcattaaaggattattatgcttggtgcctgcctcacttacctcattattgaaggctcaataatgtctgtcaattgttttttattttccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
-tcatgca
- - - - -taaagga
- - - - - - - - - - - tgcttgg
- - - - - - - - - - - - - - - gcctgcc
- - - - - - - - - - - - - - - - - - - - - -acctcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtcaa