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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAATCGCTAGTAATTTTGTCAAGTGCTTCAGATCTTCTTCTACGTGCCACAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcatcttaagaaaataaactttaatttcattcacataatagatagacaaaaacatttatagtaaaaaatacactcaaccaattcatttctcagttct...

Basic information

species Vitis vinifera
transcript Vv18s0157g00020.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0157g00020.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: LOC_Os01g08700.2 (Oryza sativa), 5'ss of exon 14
TGAATCGCTAGTAATTTTGTCAAGTGCTTCAGATCTTCTTCTACGTGCCACAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcatcttaagaaaataaa-ctttaatttca--ttcacataatagatagacaaaaaca-tttatagtaaaaaatacactca---accaattcatttc----tcagttct------
 ||| |  | || ||  |  | |||||||||||||||||||| || || || |||||||||||||| ||||| ||||| || || ||||| ||||| |||||| || ||| |   |  |   | |||  | ||  | |   | |   |||  ||     | ||| ||      |   | || |   |||  ||||| ||    ||| ||        
AGAAGCATTGGTGATCCTTGCTAGTGCTTCAGATCTTCTTCTTCGAGCAACTGATGGAATGCTTGTTGATGGTGAAGCTTGTACTTTACCACAATTAGAGgtaacaccttcattcatgaggtccttaggtgcaaatcccagtgaagaataatcagttctactttgtatggttcatctcgcttactgaccggttcatctcgggatcaattacgagcag

upper sequence: Vv18s0157g00020.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA09G07240.2 (Glycine max), 5'ss of exon 13
TGAATCGCTAGTAATTTTGTCAAGTGCTTCAGATCTTCTTCTACGTGCCACAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcatcttaagaaaataaactttaatttcattcacataatagatagacaaaaacatttatagtaaaaaatacactcaaccaat--tcatttctcagttct---
 |||||  |||||||| || ||||||| |||||| | || ||||| ||||||||||||||||| |||||||||||||| ||||| ||||| ||  || ||||| ||| || | | | ||    |||  |  || ||| |   | |    |||   | || |     |||  |    ||||   ||   ||  |  || |  |   
GGAATCATTAGTAATTGTGGCAAGTGCATCAGATTTACTACTACGAGCCACAGATGGAATGCTGGTGGATGGAGAAGCTTGCACTTTACCACAGCTGAAGgtaacatattcaaacattag--ctta--tctatgcacttt-caaaggttcaatgtctttcaaccagaaacctgtcttcaattcatgaccacatggcaataatgac

upper sequence: Vv18s0157g00020.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA20G30980.1 (Glycine max), 5'ss of exon 7
TGAATCGCTAGTAATTTTGTCAAGTGCTTCAGATCTTCTTCTACGTGCCACAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcat-cttaagaaaataaactttaatttcattcacataatagatagacaaaaacatttatagtaaa--aaatacactcaaccaattcatttctcagttct
 |||||  | |||||| || ||||| |||||||| | || || || ||||||||||| ||||| || ||||||||||| ||||| ||||| || |||||||||| ||  || |  || |  |   | || |  |        |  ||   ||  |   | | || | |    | ||          | | || |||   |   
AGAATCATTGGTAATTGTGGCAAGTTCTTCAGATTTACTACTGCGAGCCACAGATGGGATGCTGGTTGATGGAGAAGCTTGCACTTTACCACAGTTGGAGgtagtatgtttcaataagtgtatagttatattgtgtgtgatttctatgttcagtattgtatttaattagtttattaattgttgttcagtaatctctgcat---

upper sequence: Vv18s0157g00020.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA10G36600.2 (Glycine max), 5'ss of exon 13
TGAATCGCTAGTAATTTTGTCAAGTGCTTCAGATCTTCTTCTACGTGCCACAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcat-cttaagaaaataaactttaatttcattcacataatagatagacaaaaacatttatagtaaaaaatacactcaac--caattcatttctcagttct
 |||||  | |||||| || ||||| | |||||| | || || || ||||||||||| ||||| || ||||||||||| ||||| ||||| ||  ||||||||| ||  || |  || |  | | | || |  |        |  ||   |   |  || | || | |      || |        | | || |||  ||   
AGAATCATTGGTAATTGTGGCAAGTTCATCAGATTTACTACTGCGAGCCACAGATGGGATGCTGGTTGATGGAGAAGCTTGCACTTTACCACAGCTGGAGgtagtatatttcaacaagtgtattgttatattgtgtgtgatttctatgttccgtattatatttaattagtttatcaattggtgttcaataatctctgcgt---

upper sequence: Vv18s0157g00020.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: AT1G22770.1 (Arabidopsis thaliana), 5'ss of exon 12
TGAATCGCTAGTAATTTTGTCAAGTGCTTCAGATCTTCTTCTACGTGCCACAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgta--gcatcttaagaaaataaactttaatttcattca-cataatagatagacaaaaacatttatagtaaaaaatacactcaaccaattcatttctcagttct
||| || || || ||| |  ||||||| |||||||||||||| || || || |||||||||||||| ||||||||||| || || ||||||||| | ||||||  |||   | | | | |   ||| |||  | |||  |    ||||   | ||  |  ||   | |  |   ||   | |||   | ||            
TGAGTCACTGGTGATTCTCGCAAGTGCATCAGATCTTCTTCTGCGGGCAACTGATGGAATGCTTGTTGATGGAGAAGCTTGTACATTACCTCAACTTGAGgtactgcactgttatagattgctcttcaatgcccttcttcgggctagagtaataatcattttctgattccactgtattttaaacttttgcag-----------

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|110720009|gb|EE095626.1|EE095626
EST:     CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAG                         CTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
genomic: CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcatctt ... aaatgagcagCTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
EST: gi|329112329|gb|JG391797.1|JG391797
EST:     CACGTTACCTCAATTGGAG                         CTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
genomic: CACGTTACCTCAATTGGAGgtagcatctt ... aaatgagcagCTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
EST: gi|156738179|gb|EV242300.1|EV242300
EST:     CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAG                         CTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
genomic: CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcatctt ... aaatgagcagCTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
EST: gi|32269131|gb|CD718290.1|CD718290
EST:     CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAG                         CTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
genomic: CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcatctt ... aaatgagcagCTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
EST: gi|27586349|gb|CB009044.1|CB009044
EST:     CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAG                         CTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
genomic: CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcatctt ... aaatgagcagCTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
EST: gi|110381010|gb|EC946318.1|EC946318
EST:     CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAG                         CTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
genomic: CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcatctt ... aaatgagcagCTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
EST: gi|110396306|gb|EC961989.1|EC961989
EST:     CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAG                         CTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
genomic: CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcatctt ... aaatgagcagCTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
EST: gi|32269788|gb|CD718947.1|CD718947
EST:     CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAG                         CTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
genomic: CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcatctt ... aaatgagcagCTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
EST: gi|110393205|gb|EC958280.1|EC958280
EST:     CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAG                         CTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
genomic: CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcatctt ... aaatgagcagCTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
EST: gi|32460762|gb|CD801936.1|CD801936
EST:     CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAG                         CTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
genomic: CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcatctt ... aaatgagcagCTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
EST: gi|32249121|gb|CD714940.1|CD714940
EST:     CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAG                         CTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA
genomic: CAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcatctt ... aaatgagcagCTTCTGGAAGCAACAGCTAGAGCAGTTCAACTTGTACTGGAATGGGGAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAATCGCTAGTAATTTTGTCAAGTGCTTCAGATCTTCTTCTACGTGCCACAGATGGAATGCTTGTGGATGGAGAAGCATGCACGTTACCTCAATTGGAGgtagcatcttaagaaaataaactttaatttcattcacataatagatagacaaaaacatttatagtaaaaaatacactcaaccaattcatttctcagttct

- - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat