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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACGgtaatatttatttttttaaaattttatttgcctcctgttttcttttgaatgtgctgctttaattgtgtccttgggtttctag

Basic information

species Vitis vinifera
transcript Vv07s0005g05030.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os02g40430.1 (Oryza sativa), 5'ss of exon 10
GTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACGgtaatatttatttttttaaaattttatttgcctcctgttttcttttgaatgtgctgctttaattgtgtccttgggtttctag
|| |||||||||||||||||||| || || ||||| ||||| || || || || |||||||||||||| || | ||   | | ||      | ||  ||   |      |||    | |    |   ||  |        | |  ||  ||
GTACTTTTCAAGCTTGTTGTGATAACTGTGCTTGTTATTGCTGAATCCGCCGACAACTGCATAAAAACTgtgagatacctatattcttgtatgtaactgtggcacaacctctcagtactcatttttctttttgacaattattgtctttcag

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G081907_T01 (Zea mays), 5'ss of exon 6
GTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACGgta---atatttatttttttaaaatt-ttatttgcctcctgttttcttttgaatgtgctgctttaattgtgtcc-ttgggtt-tctag------------
|||||| | |||  ||| ||||| ||| | ||||||||||| ||||||||||||||||| ||||||  ||||   ||  | |     |     |    ||||   |    | || |||||     |   || ||  || ||   || |||  |||              
GTCCTTCTTAAGAATGTCGTGATCACCATCCTTGTAATTGCTGAGTCTGCTGATAACTGTATAAAAGAGgtacacatgctcaagcgctagctctggccattttgttttcatcttgttttgcgaaagggcctctagctgagttggttaggtggtctgagtagcactcctc

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA03G32710.1 (Glycine max), 5'ss of exon 9
GTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACGgtaatatt-tatttttttaaaattttatttgcctcctgttttcttttga-atgtgctgctttaattgtgtccttgggtttctag
|||||||||||||| ||||||||||| || |||||||||||||||||||| ||||||||||| ||||||||| | |  ||| ||  |  ||||   ||    | |   |  || |||  |||||    ||| |   |  |||    |||  ||
GTCCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAGTCTGCAGATAACTGCATTAAAACGgtactgtaatatgttcatttaattaccttcattttcgtatccctcttgctatgtgtcattttcacctttgcctctactttgcag

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA19G35460.1 (Glycine max), 5'ss of exon 9
GTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACGgtaatatt-tatttttttaaaattttatttgcctcctgttttcttttga-atgtgctgctttaattgtgtccttgggtttctag
|||||||||||||| ||||||||||| || |||||||||||||||||||| ||||||||||| ||||||||| | |  ||| ||  |  ||||   |     | ||  |  || |||  |||||    ||| |   |  |||    |||  ||
GTCCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAGTCTGCAGATAACTGCATTAAAACGgtactgtaatatgttcatttaattacctgcattttcttatccctcttgctatgtgtcattttcacctttgcctctactttgcag

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA13G19230.1 (Glycine max), 5'ss of exon 9
GTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACGgtaatat--ttatttttttaaaattttatttgcctcctgttttcttttga------atgtgctgctttaattgtgtccttgggtttctag
|||||| | ||||| ||||||||||| || ||||||||||| || ||||| ||||||||||||||||||||||| |  | ||  || | || |||        |  | |   |||||||       | | ||| | | || |  ||||    |||| ||
GTCCTTCTGAAGCTGGTTGTGATTACTGTGCTTGTAATTGCGGAATCTGCAGATAACTGCATAAAAACGgtaatttgataatacttattaattttctgcattgtattatggccttttgactttctgtatcctgttgtgat-gcatcctctactttccag

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA10G04850.1 (Glycine max), 5'ss of exon 9
GTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACGgtaatatt-tatttttttaaaattttatttgcctcctgttttcttttgaatgtgctgctttaattgtgtccttgggtttctag--------------------
|||||||| ||||| ||||||||||| || |||||||||||||| ||||| || ||||||||||||| |||||| |  |||  ||||    |||| |||     | |    |||   ||| |      ||||||| || |  | | | |||                     
GTCCTTTTGAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAATCTGCGGACAACTGCATAAAAATGgtaatttgatatacttttttttttttttttttgatcagcaaacttaataatatata---ttaattgagtaccagaggtactaacagtacaagtatcaatccag

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT2G20190.1 (Arabidopsis thaliana), 5'ss of exon 9
GTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACGgtaa--tatttatttttttaaaatt-ttatttgcctcctgttttctt--ttgaatgtgctgctt---taattgtgtccttgggtttctag
|| ||||||||||| ||||||||||| || |||||||||||||| ||||||||||||||||||||||||||||  ||||   |   |||   |  ||  | |   | ||  | ||    | | | |  |||||    |  ||  | ||||   ||| ||
GTGCTTTTCAAGCTGGTTGTGATTACTGTGCTTGTAATTGCAGAATCTGCTGATAACTGCATAAAAACGgtaaattattagctcgcttattttggtttctagaaccatgcctgctcggctaagttttgtgcttacacagatggtttcttgctattccag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCTTTTCAAGCTTGTTGTGATTACCGTACTTGTAATTGCAGAGTCTGCTGATAACTGCATAAAAACGgtaatatttatttttttaaaattttatttgcctcctgttttcttttgaatgtgctgctttaattgtgtccttgggtttctag

- - - - - - - - - - - - - - - - - - - - - - - - GCTGAT