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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGAGGAGATGGCTCAGACATTCAGGCAGAGAATAGCTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAGgtattttaactgctattgtttacataattatttttttttcccaagtggaaaggtaaaaatgaagagacagaaggatgcatgagaggccataatttgacaa...

Basic information

species Vitis vinifera
transcript Vv05s0077g00450.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00450.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os03g20100.1 (Oryza sativa), 5'ss of exon 6
GCGGAGGAGATGGCTCAGACATTCAGGCAGAGAATAGCTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAGgtattttaactgctattgt-------ttacataattatttttttttcccaagtggaaaggtaaaaatgaagagacagaaggatgcatgagaggccataatttgacaa----------
|| || ||||||||||||| |||||||||||| |||||||||||||| || |||||||| || || ||| |||||||||| ||||||||| |   |     ||| |        | || ||| |  ||| | |  ||  |    |      | || ||  |||   || || || | |     |        |           
GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccatcatcattttattgaggctgcaaaatgaaatttatctgacat-tattcataagccactgcagtaacatttggctgaattaaattgtttctccctgtatctcttcacag

upper sequence: Vv05s0077g00450.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM5G862107_T01 (Zea mays), 5'ss of exon 6
GCGGAGGAGATGGCTCAGACATTCAGGCAGAGAATAGCTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAGgtattttaactgcta--ttgtttacataattatttt--------tttttcccaagtggaa----aggtaaaaatgaagagacagaaggatgcatgagaggccataatttgacaa--------
|| || ||||||||||||| ||||||||||||||||||||| ||||| ||||||||||| || |||||| | |||||||| || ||||||||  ||  | |   ||||| |    |   | |         |||   | || |  ||      ||  |||| | | | | ||   |  |     |  |      |  ||          
GCTGATGAGATGGCTCAGATATTCAGGCAGAGAATAGCTCAGGCAGAGGCTATGGCTCGTGCTGACATGTTGAGATTCCAGCCAGAGgtattgcaaacgttcccttgttaatgctaccgtgtcaaatcacatttcatctaacttcaactgtgtgtgtaaatcatgtggctgagctaatcgaatcatcctcctgctgtacctcttcacag

upper sequence: Vv05s0077g00450.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA17G04190.1 (Glycine max), 5'ss of exon 6
GCGGAGGAGATGGCTCAGACATTCAGGCAGAGAATAGCTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAGgtattttaactgctattgtttacataattatttttttttcccaagtggaaaggtaaaaatgaagagacagaaggatgc-atgagaggccataatttgacaa-
|||||||||||||||||||||||||| ||||||||||| |||||||||||||||||||| |||||||||||||| ||||| ||||||||||||       |||| |||    ||  | || |   ||| |            ||| || |  ||   |  ||  | ||  |||   | |     |||| 
GCGGAGGAGATGGCTCAGACATTCAGACAGAGAATAGCCCAAGCAGAAGCTATGGCTCGTGCAGACATGCTAAGGTTCCAGCCTGAGgtatttattggtttattatttgtccaa--aattctgaatccaataaaagtttaagaaactgcaaggattaagtgagactataggagataaaatgaacacaac

upper sequence: Vv05s0077g00450.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA15G14550.1 (Glycine max), 5'ss of exon 6
GCGGAGGAGATGGCTCAGACATTCAGGCAGAGAATAGCTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAGgtattttaactgctattgtttacataattatttttttttcccaagtggaaaggtaaaaatga-agagacagaaggatgcatgagaggcca-taatttgacaa---
|||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| || || ||||| |||||||| || |||||||||  | |  | ||| |||  |  | |   |||   | ||| |  ||| | | ||   | | ||    || | ||  | | |  | | |    | | ||   
GCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAGgtattt--att--tgttgattatttgttcaaaatttcaactcaa-taaaaatgaagaagcaacataggattaaaggtgactaaaatacaaatggcattaaaaaaa

upper sequence: Vv05s0077g00450.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA09G03660.1 (Glycine max), 5'ss of exon 6
GCGGAGGAGATGGCTCAGACATTCAGGCAGAGAATAGCTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAGgtattttaactgctattgtttacataat-tatttttttttcccaagtggaaaggta-aaaatgaagagacagaaggatgcatgagaggccataatttgacaa
|||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| || || ||||| |||||||| || |||||||||    |   ||| |||    ||  | |    |      || || |     |    || ||  |  |  |  || ||   |     | ||   | |  
GCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAGgtatttattttttgattatttgttcaaaatctcgactcaataaaaatgaagcaacacgggattaaaggtgactaaaatacaaatggcataaaaaaaagtc--

upper sequence: Vv05s0077g00450.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT5G30510.1 (Arabidopsis thaliana), 5'ss of exon 6
GCGGAGGAGATGGCTCAGACATTCAGGCAGAGAATAGCTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAGgtatt-ttaactgctattgtttacataattatttttttttcccaagtggaaaggtaaaaatgaagagacagaaggatgcatgagaggccataatttgacaa-
|| ||||||||||||||||||||||| |||||||| || ||||||||||| |||||||| |||||||||||  | ||||||||||||||||  ||  |  ||    |   |    ||||   |  ||    | |    |  |   ||| |||   || |||  | ||||    |  |  || | | |  
GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAGgtatcattctccacttgcctgatctcgtttatccatgcttattgatttctta--ttgcaatcaagttccaaaagtgtacatgtttagtaaccatctaagatt

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|83275688|gb|DV939696.1|DV939696
EST:     CTCAAGCAGAAGCTATGGCTCGGGCAGACATGCAAAGATTCCAACCTGAG                         AGTGGATTAACTCTCAATTCGGATGTAATCTTGGGCCCCGTTTCCG
genomic: CTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAGgtattttaac ... atttttgcagAGTGGATTAACTCTCAATTCGGATGGAATCTTGGGCCCCGTTTCCG
EST: gi|110375562|gb|EC940562.1|EC940562
EST:     CTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAG                         AGTGGATTAACTCTCAATTCGGATGGAATCTTGGGCCCCGTTTCCGCCGAC
genomic: CTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAGgtattttaac ... atttttgcagAGTGGATTAACTCTCAATTCGGATGGAATCTTGGGCCCCGTTTCCGCCGAC
EST: gi|33402614|gb|CF208241.1|CF208241
EST:     CTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAG                         AGTG-ATTTAACTCTCAA
genomic: CTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAGgtattttaac ... atttttgcagAGTGGATT-AACTCTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGAGGAGATGGCTCAGACATTCAGGCAGAGAATAGCTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAGgtattttaactgctattgtttacataattatttttttttcccaagtggaaaggtaaaaatgaagagacagaaggatgcatgagaggccataatttgacaa

- - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaagga