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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattacttaaagccctgattaaagacaatggtttgtttatttttgtgttccagttcatccttgagctgacttggtttaccattacag

Basic information

species Vitis vinifera
transcript Vv13s0156g00180.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 16
TGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattacttaaagccctgattaaagacaatggtttgtt-tatttttgtgttccagttcatccttgagctgacttggtttaccattacag
||| || || ||||||||| | ||||| || |||||| ||||||  ||||| ||||||||||| |||||| |||||||||| |||||||| ||||| ||||||| | || |||   |||   ||   ||  | | | ||  | |       ||   ||     |      ||  |    || | |  |||
TGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagt-ctaaaatgtctgtccaactgcatggctctcttgcagtccaactatctcattgggattcttatcgatcta---tatcctgtcag

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 16
TGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattacttaaagccctgattaaagacaatggtttgttt-atttttgtgttccagttcatccttgagctgacttggtttaccattacag
||| ||||| ||||||||| | ||||| || |||||| | ||||  ||||| ||||||||||| |||||| |||||||||| |||||||| ||||| ||||||| |   ||||  |  | |  | | |  |  |  ||   | | |     |    || ||  | || ||  | |  || |         
TGGCTTTGGTCATGGAGTTCTACGTAAGACCGATCCACGGTATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagt--ctaaattctagctgcatggctctcttcagtcccactgtctcaataggatttata-tcgacctatcctctttcag--------

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 17
TGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattacttaaagccctgattaaagacaatggtttgtttatttttgtgttccagttcatccttgagctgacttggtttaccattacag
||| ||||| ||||||||| ||||||| ||||| ||| | |||   |||||||||||||||||  ||||||| ||||| || |||||||| ||||| |||||       |  | || |  |   |   ||| |  | |   || ||| |||| |   ||   || |    |  |  | | || || |||
TGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtc--cgtctggaacctttct---atctaattgcatttactttcttgagttcaa---caattttaa----aaataatattccgttgcag

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM2G063851_T05 (Zea mays), 5'ss of exon 2
TGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattacttaaagccctgattaaagacaatggtttgtttatttttgtgttccagttcatccttgagctga-cttggtttaccattacag
||||||||| ||||||||| ||||||| || || ||| | |||   |||||||||||||||||  ||||||| |||||  | |||||||| |||||  ||||   | ||  || |  | ||  ||        ||  |||| |||| ||          |  |  |  | | ||| | ||||        
TGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgt-ctggaaccttttatctaat-------ttcatttacttttttgagttgaacggttttaaatgtaatctttggttacag------

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA15G42300.2 (Glycine max), 5'ss of exon 16
TGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattacttaaagccctgattaaagacaatggtttgttt--atttttgtgttccagttcatccttgagctgacttg--gtttaccattacag
||| | ||| ||||| ||||| ||  | |||||||||||||| |  ||||| ||||||||||| |||||||| |||||| ||||||||   ||||||||||| || |||||    |||  || ||||   || ||| |||  | |  | | || |    || ||   |||| |||||    | ||| || |||
TGGATATGGACATGGGGTTTTACGCCAGACAGATCCAAGATACACATGTCAGAGGGAGTTTGCTTTGAAGCATTTGCCTAATGATCCATATTTCCAGCTGgtaatcacttatt-tcctatttcaagattgtgttttctttggagtgctttcttgcgacacagcca-aagctcacttgtaactgaccctttcag

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 16
TGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattacttaaagccctgattaaagacaatggtttgttt--atttttgtgttccagttcatccttgagctgacttggtttaccattacag----------------------------
||| | ||| ||||| ||||| ||  | |||||||||||||| |  ||||| ||||||||||| |||||||| |||||| ||||||||   |||||| |||| || |||||    ||| ||| ||||   || ||| |||  | |  | | || |    || ||   |||| |||||   |   ||| |                              
TGGATATGGACATGGGGTTTTACGCCAGACAGATCCAAGATACACATGTCAGAGGGAGTTTGCTTTGAAGCATTTGCCTAATGATCCATATTTCCAGTTGgtaatcacttatt-tcctaattcaagattgtgttttctttggagtgctttcttgcgacacagcca-aagctcacttgtaatttaatttcttcatgttctaatgcaactgaccctttcag

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 5'ss of exon 15
TGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattacttaaagccctgattaaagacaatggtttgtttatttttgtgttccagttcatccttgagctgacttggtttaccattacag
 || | ||| ||||| |||||||||||||| |||||||||||||| || ||||| |||||||| ||||||||  | ||||||||||| || || |||||||| | |  ||    |||| |        |||  || ||     |||    |     |    |   |  |      || ||         
AGGATATGGCCATGGTGTTTTGCGTAAAACGGATCCAAGATATATATGCCAAAGAGAGTTTGCCTTGAAGCATCTACCTGATGATCCTCTTTTTCAGCTGgtaactttttttccccctca--------aatctttggtcatgctttaaaattttactggctcacaaattatgcaagtctatag------

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|110391493|gb|EC956472.1|EC956472
EST:     AAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTG                         GTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
genomic: AAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattactt ... accattacagGTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
EST: gi|110418511|gb|EC984670.1|EC984670
EST:     GATGATCCACTGTTCCAGCTG                         GTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
genomic: GATGATCCACTGTTCCAGCTGgttattactt ... accattacagGTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
EST: gi|110361418|gb|EC924886.1|EC924886
EST:     AAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTG                         GTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
genomic: AAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattactt ... accattacagGTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
EST: gi|110429398|gb|EC995889.1|EC995889
EST:     AAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTG                         GTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
genomic: AAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattactt ... accattacagGTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
EST: gi|34320089|gb|CF372843.1|CF372843
EST:     AAGGGAGTTTGCATTGAAGCACTTGCCTGATGATTCC-CTGTTCCAGCTG                         GTTTCAAAGCTTTATGAAGTGGTGCCTCCTACTCTTACTGAGCTTGGCAAG
genomic: AAGGGAGTTTGCATTGAAGCACTTGCCTGATGA-TCCACTGTTCCAGCTGgttattactt ... accattacagGTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
EST: gi|29785895|gb|CB343236.2|CB343236
EST:     AAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTG                         GTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
genomic: AAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattactt ... accattacagGTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
EST: gi|110372355|gb|EC936513.1|EC936513
EST:     AAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTG                         GTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
genomic: AAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattactt ... accattacagGTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
EST: gi|110362967|gb|EC926531.1|EC926531
EST:     AAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTG                         GTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
genomic: AAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattactt ... accattacagGTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
EST: gi|77577886|gb|DV217693.1|DV217693
EST:     AAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTG                         GTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG
genomic: AAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattactt ... accattacagGTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattacttaaagccctgattaaagacaatggtttgtttatttttgtgttccagttcatccttgagctgacttggtttaccattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG