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

...tattttttctatggtgcattctaacagcattatatctttttgtttattttgatgtcgattgatagtgagccaactgtcttgccatttcttgattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG

Basic information

species Vitis vinifera
transcript Vv02s0236g00140.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0236g00140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G05580.1 (Glycine max), 3'ss of exon 2
tattttttctatggtgcattc-taacagcatta-tatctttttgtttattttgatgtc-gattgatagtgagccaactgtcttgccatttcttgattcttc-------agTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG
           || ||||||    | |  |||  | | | | | ||| |    ||||  | ||  ||||     ||||    |  ||||| ||  || | |       ||||| ||| ||||| ||||||||||| |||||||| || | |||||| |||||||||||  | ||||| ||  | |||| ||||
--------tagtgatgcatttgctataaaattgctctgtctctatttctccatatgttagctttgtagttta--aactcgtgtatcatttttttgttttccccttcccagTTACTGTCAGTGAGGTTGAAGCACTGTTTGAGCTTTTTAGGAGCATCAGCAGTTCTGTTGTCGATGACGGACTGATAAGCAAG

upper sequence: Vv02s0236g00140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G17615.2 (Arabidopsis thaliana), 3'ss of exon 2
tattttttctatggtgcattctaacagcattatatctttttgtttattt-tgatgtcgattgatagtgagccaactgtcttgcca---tttcttgattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG-----------------
     |   | ||    |||          | | | | ||||||| ||  || |     ||  |  ||| |     || ||||     ||| |   || | |||||||||||||||| ||||||||| |||||||||||||||||||||| |||||||| ||  ||||||||||  | || ||||||                 
----ctaaatgtgaattattagtctctttgtttgtttgtttgtttgttcctggtaattctttgttttgatctcgtagtgttgcttgtttttttctcttttccagTTAGTGTGAGTGAGGTTGAAGCATTATTTGAGCTATTCAAGAGCATAAGCAGTTCGGTTGTTGATGATGGTCTGATTAACAAGGTACAAAGTTTGTTTCT

upper sequence: Vv02s0236g00140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G17615.1 (Arabidopsis thaliana), 3'ss of exon 2
tattttttctatggtgcattctaacagcattatatctttttgtttattt-tgatgtcgattgatagtgagccaactgtcttgc---catttcttgattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG
     |   | ||    |||          | | | | ||||||| ||  || |     ||  |  ||| |     || ||||     ||| |   || | |||||||||||||||| ||||||||| |||||||||||||||||||||| |||||||| ||  ||||||||||  | || ||||||
----ctaaatgtgaattattagtctctttgtttgtttgtttgtttgttcctggtaattctttgttttgatctcgtagtgttgcttgtttttttctcttttccagTTAGTGTGAGTGAGGTTGAAGCATTATTTGAGCTATTCAAGAGCATAAGCAGTTCGGTTGTTGATGATGGTCTGATTAACAAG

upper sequence: Vv02s0236g00140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G47100.1 (Arabidopsis thaliana), 3'ss of exon 2
tattttttctatggtgcattctaacagcattatatctttttgtttattttgatgtcgattgatagtgagccaac-tgtcttgccattt-cttgattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG
 |  ||||| |     |||       |  || | | ||  || |     |||||| |||    | |    ||   || ||    ||||  ||| || |  ||||||||| ||||||||||||||| | | |||  | ||||||||||| ||||| || ||  |||| ||||| || |||||||||
-aagttttcaagaac-catcactttcgatttttgttttggtgatatacatgatgttgatgagaaatctcgcagtgtggctaattatttgtttgtttttctagTTAGTGTTAGTGAAGTTGAAGCATTGTATGAATTGTTCAAGAGCATAAGCAGCTCGGTTGTTGACGATGGCTTGATAAACAAG

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|352789785|gb|FQ478600.1|FQ478600
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGTA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|349822445|gb|FQ412709.1|FQ412709
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGTA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|71873772|gb|DT022827.1|DT022827
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|349820979|gb|FQ408687.1|FQ408687
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|349819279|gb|FQ412173.1|FQ412173
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAGGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|71872712|gb|DT021767.1|DT021767
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|349826413|gb|FQ417910.1|FQ417910
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGTA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|349832733|gb|FQ422257.1|FQ422257
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGTA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|161708395|gb|FC056127.1|FC056127
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|351019013|gb|FQ426512.1|FQ426512
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGTA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|71863154|gb|DT012209.1|DT012209
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|351055152|gb|FQ440491.1|FQ440491
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTGTTTGAGCTATTCAAGAGCATTAGTA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|71864022|gb|DT013077.1|DT013077
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|71877098|gb|DT026153.1|DT026153
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|351014198|gb|FQ434787.1|FQ434787
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGTA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|349815321|gb|FQ400476.1|FQ400476
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGTA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|351038650|gb|FQ464516.1|FQ464516
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCCT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGTA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|34549400|gb|CF517632.1|CF517632
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
EST: gi|110699550|gb|EE076647.1|EE076647
EST:     GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTT                         TTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA
genomic: GCAGTTTCCTGGACATGAGGACCCAGTAATTCTTGCTTCCCAAACAGCTTgtaagttgtt ... gattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgatgtcgattgatagtgagccaactgtcttgccatttcttgattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG
                                         tcttgat  putative branch site (score: 4)
                                       tttcttgattcttc  CT-rich tract
            attgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattttttctatggtgcattctaacagcattatatctttttgtttattttgatgtcgattgatagtgagccaactgtcttgccatttcttgattcttcagTTAGTGTGAGTGAAGTTGAAGCACTATTTGAGCTATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - -gcattct
- - - - - - - - - - - - cagcatt
- - - - - - - - - - - - - - - - - - - - - - - - -tgatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccaact