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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacaccatttcaacataagcttatgtagttacatttaatgtgtttgtggtagattatatttgtgtcttaacttcattaccattttctatttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTATGATGTCGATCCAATCAATTCAGTACAGTTCTCAAATCACACAG

Basic information

species Vitis vinifera
transcript Vv14s0006g01660.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os12g40830.1 (Oryza sativa), 3'ss of exon 2
aaacaccatttcaacataagcttatgt----agttacatttaatgtgtttgtggta-gattatatttgtgtcttaacttcattaccattttctatttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTATGATGTCGATCCAATCAATTCAGTACAGTTCTCAAATCACACAG------
       | |  |  ||    || | |    |||      | |||| || ||  |  | ||  || ||| |  |   ||         ||| | |||    ||||||||| |||||||| ||||| || ||||||||||| || || ||||||| |||||| ||||| || || || |||||||| || ||||| ||||      
-----ttagtgtatgatggatttgttttacaagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAG

upper sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 2
aaacaccatttcaacataagcttatgt----agttacatttaatgtgtttgtggta-gattatatttgtgtcttaacttcattaccattttctatttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTATGATGTCGATCCAATCAATTCAGTACAGTTCTCAAATCACACAG
       | |  |  ||    || | |    |||      | |||| || ||  |  | ||  || ||| |  |   ||         ||| | |||    ||||||||| |||||||| ||||| || ||||||||||| || || ||||||| |||||| ||||| || || || |||||||| || ||||| ||||
-----ttagtgtatgatggatttgttttacaagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG

upper sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 3
aaacaccatttcaacataagcttat-gtagttacatttaatgtgtttgtggtagattatatttgtgtcttaacttcattaccattttctatttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTATGATGTCGATCCAATCAATTCAGTACAGTTCTCAAATCACACAG
| |  |   ||| |  |    | |  | |   |   || | |  |||    |   |||| |    | ||   ||||     |  |   |  | |   | |||| ||||||||||| |||||||| ||||||||||| ||||| || |||| |||||| |||||||| || || |||||||| || ||||| ||||
atagtctgcttcgattttgtttcagagcaagaatcattga-gcattttcactttcttatttgatagcctgctcttctcattctctgattgctccaattcagGGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTTGATGTGGATCCAATAAACTCTGTACAGTTTTCTAATCATACAG

upper sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G04360.1 (Glycine max), 3'ss of exon 2
--aaacaccatttcaacataagcttatgtagttacatttaatgtgtttgtggtagattatatttgtgtcttaacttcattaccattttctatttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTATGATGTCGATCCAATCAATTCAGTACAGTTCTCAAATCACACAG-
        || ||     ||| ||| ||  ||||   | ||| ||  ||  |     ||| |   |  ||| ||||  |  |  ||| |||||   | | |||| |||||||| |||||||| |||||||| || || || |||||||| ||||||||||||||||| ||||| || ||||| || ||||| |||| 
tttcttggcaatttgcagtaatctt-tgatgttattatcaat-tgcatgcagcttgctatgtaattaccttgactttgtggctgtttgctattattc-tcaggGGTATGTTGGTAATAAATCCGCTGTCTTCCCTCTGCAACTACTGGGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGG

upper sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G37850.3 (Arabidopsis thaliana), 3'ss of exon 2
aaacaccatttcaacataagcttatgtagttacatttaatgtgtttgtg-gtagattatatttgtgtcttaacttcattaccattttctatttccc-cttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTATGATGTCGATCCAATCAATTCAGTACAGTTCTCAAATCACACAG
      |  |  |   |    || || |  |   |||  | ||| |||| ||   |  ||   |     | |   ||||     | |||||| |   |||||||||||||||| || ||||| ||||||||||| || ||  |  |||| |||||||| ||||||||||| || ||||| ||||| ||||| ||||
--ctgtctctctatgcttgagttctgcaacttttttttttttgtgtgtgtgtgtgtgttaccagaaatgtgatgccattttatatgtctattactttcttagGGATATGTTGGTAACAAATCAGCTGTCTTTCCTCTTCAATTGTTGGGGTATGATGTGGATCCAATCAACTCTGTACAATTCTCGAATCATACAG

upper sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ27991 (Selaginella moellendorffii), 3'ss of exon 1
aaacaccatttcaacataagcttatgtagttacatttaatgtgtttgtggtagattatatttgtgtcttaacttcattaccattttctatttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTATGATGTCGATCCAATCAATTCAGTACAGTTCTCAAATCACACAG
                         |||    |  | ||| | |      | ||||  |  ||   |  | |||  ||||  |  || |         ||||||| ||||| ||||||||||| ||||||||| | ||||| ||||| |  ||||| ||||| ||||| ||                       
-------------------------gtaa--gcgctcaatatctc---actggattgcaagtgatcccgagctt--ttactctactcgaga------cagGGATACGTTGGAAATAAATCGGCGGTCTTTCCCTTGCAGCTCCTGGGATTCGATGTTGATCCGATCAACTCC----------------------

upper sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ29421 (Selaginella moellendorffii), 3'ss of exon 1
aaacaccatttcaacataagcttatgtagttacatttaatgtgtttgtggtagattatatttgtgtcttaacttcattaccattttctatttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTATGATGTCGATCCAATCAATTCAGTACAGTTCTCAAATCACACAG
                         |||    |  | ||  | |      | ||||  |  ||   |  | |||  ||||  |  || |         ||||||| ||||| ||||||||||| ||||||||| | ||||| ||||| |  ||||| ||||| ||||| ||                       
-------------------------gtaa--gcgctcaaaatctc---actggattgcaagtgatcccgagctt--ttactctactcgaga------cagGGATACGTTGGAAATAAATCGGCGGTCTTTCCCTTGCAGCTCCTGGGATTCGATGTTGATCCGATCAACTCC----------------------

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|110715098|gb|EE092763.1|EE092763
EST:     TGCCCTCGGAGACTGGACGAGTTCTCAGCATTCAGTCTCATACTGTGCAG                         GGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTAT
genomic: TGCCCTCGGAGACTGGACGAGTTCTCAGCATTCAGTCTCATACTGTGCAGgtatgggatt ... ttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTAT
EST: gi|71859315|gb|DT008370.1|DT008370
EST:     TGCCCTCGGAGACTGGACGAGTTCTCAGCATTCAGTCTCATACTGTGCAG                         GGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTAT
genomic: TGCCCTCGGAGACTGGACGAGTTCTCAGCATTCAGTCTCATACTGTGCAGgtatgggatt ... ttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTAT
EST: gi|294966903|gb|GW839778.1|GW839778
EST:     TGCCCTCGGAGACTGGACGAGTTCTCAGCATTCAGTCTCATACTGTGCAG                         GGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTAT
genomic: TGCCCTCGGAGACTGGACGAGTTCTCAGCATTCAGTCTCATACTGTGCAGgtatgggatt ... ttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTAT
EST: gi|37186505|gb|CF605858.1|CF605858
EST:     TGCCCTCGGAGACTGGACGAGTTCTCAGCATTCAGTCTCATACTGTGCAG                         GGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTAT
genomic: TGCCCTCGGAGACTGGACGAGTTCTCAGCATTCAGTCTCATACTGTGCAGgtatgggatt ... ttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTAT
EST: gi|71863971|gb|DT013026.1|DT013026
EST:     TGCCCTCGGAGACTGGACGAGTTCTCAGCATTCAGTCTCATACTGTGCAG                         GGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTAT
genomic: TGCCCTCGGAGACTGGACGAGTTCTCAGCATTCAGTCTCATACTGTGCAGgtatgggatt ... ttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTAT
EST: gi|71859789|gb|DT008844.1|DT008844
EST:     TGCCCTCGGAGACTGGACGAGTTCTCAGCATTCAGTCTCATACTGTGCAG                         GGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTAT
genomic: TGCCCTCGGAGACTGGACGAGTTCTCAGCATTCAGTCTCATACTGTGCAGgtatgggatt ... ttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTAT
EST: gi|161712131|gb|FC061503.1|FC061503
EST:     TGCCCTCGGAGACTGGACGAGTTCTCAGCATTCAGTCTCATACTGTGCAG                         GGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTAT
genomic: TGCCCTCGGAGACTGGACGAGTTCTCAGCATTCAGTCTCATACTGTGCAGgtatgggatt ... ttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggtagattatatttgtgtcttaacttcattaccattttctatttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTATGATGTCGATCCAATCAATTCAGTACAGTTCTCAAATCACACAG
                    tcttaac  putative branch site (score: 2)
                          cttcattaccattttc  CT-rich tract
     tagattatatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacaccatttcaacataagcttatgtagttacatttaatgtgtttgtggtagattatatttgtgtcttaacttcattaccattttctatttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTATGATGTCGATCCAATCAATTCAGTACAGTTCTCAAATCACACAG

aaacacc
- - - - - - aacataa
- - - - - - - - - -gcttatg
- - - - - - - - - - - - - - - - - - - - - - ttgtggt