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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatttaactgatttccatttttaatgtattttttctctttttaaccaaaaagtcatgctttttatcagtttcttagtatcatgaattggtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTTGCAGCTGGTTCCAATGTGACTCTTCTTGCTGATCAG

Basic information

species Vitis vinifera
transcript Vv17s0000g08390.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 2
-------ttcatttaactgatttccat-ttttaatgtattttttctctttt-taaccaaaaagtcatgctttttatcagtttcttagtatcatgaattggtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTTGCAGCTGGTTCCAATGTGACTCTTCTTGCTGATCAG
       |||||| || | | ||  |  |   ||||     ||| | || | |      ||     |  | | | |   |||||| | || |  ||           ||||| ||||||||||||| |||||||| ||||||||| |  |||| || ||||| ||||| ||||||||||||||||| |||||||||
tgagctattcattgaaattagttggacatgaaaatgcgacgtttatattctgtggtactaatagtgttttatcttttcttttctttgcataactaa---------aaagACATTGGACATAGTTGCGGAGAATCCAGATAAATTCCGGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG

upper sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 2
ttcatttaactgatttccatttttaatgtattttttctctttttaaccaaaaagtcatgctttttatcagtttcttagtatcatgaattggtctttgc--agACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTTGCAGCTGGTTCCAATGTGACTCTTCTTGCTGATCAG
    ||| |      || |  | |  |   || |      | |||| | | |     || | ||   |||        |  |||   ||      |||  ||||| ||||||| ||||| |||||||||||||| |||||| |||| || ||||| ||||| |||||||| || ||||| |||||||||
--tgtttgatgttaatcaacatctcttaccttatgataagtattaaactagagacactgatattctgcagcactaatattccatcttttacataatgcaaagACATTGGACATTGTTGCGGAGAATCCTGATAAGTTCAGAGTTGTTGCTCTTGCTGCTGGATCCAATGTCACGCTTCTAGCTGATCAG

upper sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G036290_T01 (Zea mays), 3'ss of exon 2
----ttcatttaactgatttccatttttaatgtattttttctctttttaaccaaaaagtcatgctttttatcagt--ttcttagtatcatgaattggtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTTGCAGCTGGTTCCAATGTGACTCTTCTTGCTGATCAG
        |  || ||| ||    | |  ||| | || ||   ||   ||| |     | ||  | |  | || |  |  | | | |  |  ||    |   | ||||| ||||||| ||||| |||||||||||||| |||||| |||| || ||| | ||||| |||||||| || ||||| |||||||||
ttttcctgtgaaattgaatt--gatatctatgaaattcttgggttccaaac-aggctattatattctgcagcactaatattcaatcttttacataacgc---gaagACATTGGACATTGTTGCGGAGAATCCTGATAAGTTCAGAGTTGTTGCTCTTTCTGCTGGATCCAATGTCACGCTTCTAGCTGATCAG

upper sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G036290_T02 (Zea mays), 3'ss of exon 3
------------------------------------ttcatttaactgatttccatttttaatgtattttttctctttttaaccaaaaagt--catgctttttatcagtttct-tagtatcatgaattggtcttt----------gcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTTGCAGCTGGTTCCAATGTGACTCTTCTTGCTGATCAG
                                        ||    |  ||| | | |  |||  | ||  | ||| |  ||       ||  ||  |    ||| |  ||||  || |  |  | |   |||||          | ||||| ||||||| ||||| |||||||||||||| |||||| |||| || |||                                    
atgaaactagagacacttggaacatgggaaattttccctgttcctgtatttttcctgtgaaattgaattgatatctatgaaattcttgggttccaaacagGCTATTATATTCTGCAGCACTAATATTCAATCTTTTACATAACGCGAAGACATTGGACATTGTTGCGGAGAATCCTGATAAGTTCAGAGTTGTTGCTCTT------------------------------------

upper sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G09740.1 (Glycine max), 3'ss of exon 2
-----ttcatttaactgatt-tccatttttaatgtattttttctctttttaaccaaaaagtcatgctttttatcagt-ttcttagtatcatgaattggtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTTGCAGCTGGTTCCAATGTGACTCTTCTTGCTGATCAG
          || | || || ||| || |  |||||  ||  ||    ||  |       | || ||||     |||   | |  |  | || ||  |  |||| ||||||| || || || ||||||||||| ||||| || | | |||||||||||||||||||||| ||||| ||||||||||| || |||
ctagaaattgttgattgtttatcccttgtagatgtagcttgacttgccttgtctc-----ttatcctttgatgtagtgcaccttttcccctgtat--gcttttgtagACACTAGATATTGTGGCAGAGAATCCAGATAAGTTTAAAGTTGTGGCACTTGCAGCTGGTTCAAATGTTACTCTTCTTGCAGACCAG

upper sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 2
------ttcatttaactgatttccatttttaatgtattttttctctttttaaccaaaaagtcatgctttttatcagtttcttagtatcatgaattggtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTTGCAGCTGGTTCCAATGTGACTCTTCTTGCTGATCAG
           || | || || ||  || ||      ||    |   |||  |       | || | ||| ||    | | |  | ||     |  |  |||| ||||||| || || || ||||||||||| ||||| || | | |||||||||||||||||||||| ||||| ||||||||||| || |||
actagaaattgttgattgtttaccccttgtagatggcttggcttgcctttgtctc-----ttat-cctttgatgtagtgcatcttttcccctgtatgcttttgtagACACTAGATATTGTGGCAGAGAATCCAGATAAGTTTAAAGTTGTGGCACTTGCAGCTGGTTCAAATGTTACTCTTCTTGCAGACCAG

upper sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------ttcatttaactgatttccatttttaatgtattttttctctttttaaccaaaaagtcatgctttttatcagtttcttagtatcatgaattggtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTTGCAGCTGGTTCCAATGTGACTCTTCTTGCTGATCAG
                                                        ||  | | |   ||  | |   | |  | |   |     |||||    |   ||| ||   ||  |||| |||  | | |  |  | ||    |||||||||| |||| || || || ||||||||||| ||||||||| ||||||| || || |||||||| ||||| ||||| ||||||||||||
gttttatttcgattaaggcattattgtgcagttcttgagtatgaccagactttaagtttgtcttatgaatgactagactcatagaagaatgatatttttttcttactgagttat-tgttgcatcatttttatcg-acaagaacttccattttgcagACATTGGATATTGTGGCTGAGAATCCTGACAAATTCAGAGTTGTGGCTCTAGCTGCTGGTTCGAATGTTACTCTACTTGCTGATCAG

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|71860243|gb|DT009298.1|DT009298
EST:     GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAG                         ACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
genomic: GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAGgtaaaattct ... gtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
EST: gi|71862330|gb|DT011385.1|DT011385
EST:     GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAG                         ACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
genomic: GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAGgtaaaattct ... gtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
EST: gi|71862394|gb|DT011449.1|DT011449
EST:     GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAG                         ACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
genomic: GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAGgtaaaattct ... gtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
EST: gi|71864647|gb|DT013702.1|DT013702
EST:     GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAG                         ACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
genomic: GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAGgtaaaattct ... gtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
EST: gi|71864397|gb|DT013452.1|DT013452
EST:     GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAG                         ACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
genomic: GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAGgtaaaattct ... gtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
EST: gi|71864012|gb|DT013067.1|DT013067
EST:     GTCCAAAGCCTCTCTCAGTTGCTGGATCTACTGGCTCCATTGGAACTCAG                         ACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
genomic: GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAGgtaaaattct ... gtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
EST: gi|161712672|gb|FC062244.1|FC062244
EST:     GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAG                         ACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
genomic: GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAGgtaaaattct ... gtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
EST: gi|71863910|gb|DT012965.1|DT012965
EST:     GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAG                         ACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
genomic: GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAGgtaaaattct ... gtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
EST: gi|71858714|gb|DT007769.1|DT007769
EST:     GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAG                         ACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
genomic: GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAGgtaaaattct ... gtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
EST: gi|71864042|gb|DT013097.1|DT013097
EST:     GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAG                         ACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
genomic: GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAGgtaaaattct ... gtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
EST: gi|161706321|gb|FC056288.1|FC056288
EST:     GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAG                         ACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT
genomic: GTCCAAAGCCTCTCTCAGTTGTTGGATCTACTGGCTCCATTGGAACTCAGgtaaaattct ... gtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accaaaaagtcatgctttttatcagtttcttagtatcatgaattggtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTTGCAGCTGGTTCCAATGTGACTCTTCTTGCTGATCAG
 ttttaac  putative branch site (score: 2)
                                              tctttgc  putative PPT
               tttttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatttaactgatttccatttttaatgtattttttctctttttaaccaaaaagtcatgctttttatcagtttcttagtatcatgaattggtctttgcagACACTGGACATAGTTGCAGAGAATCCTGATAAATTCAGAATTGTGGCACTTGCAGCTGGTTCCAATGTGACTCTTCTTGCTGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - ccatttt
- - - - - - - - - - - - - - - - - - - - - -taaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - agtcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaat