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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGATACTAGAATATTGGGCTGATGCACCAGAAATACAACGCTCAGCAGACCTATATGAAGATCTTATCAAGTGTTGTGTTGCAGATGCAATGAGTGAGgtatttgtgtcagatagctttcctttttataatgttcatggacagttcatggacagtgacaagtgccgatttggctttggcacacattttattataatta...

Basic information

species Vitis vinifera
transcript Vv07s0005g05030.t01
intron # 8
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 8
lower sequence: LOC_Os04g42840.1 (Oryza sativa), 5'ss of exon 11
CTTGATACTAGAATATTGGGCTGATGCACCAGAAATACAACGCTCAGCAGACCTATATGAAGATCTTATCAAGTGTTGTGTTGCAGATGCAATGAGTGAGgtatttgtgtcagatagctttcctttttataatgttcatggacagttcatggacagtgacaagtgccgatttggctttggcacacattttattataatta--
 || ||||| || |||||||||||||| || || |||||||| ||||| ||  |||| |||||||| || ||||| ||||| |||||||| ||||||||||||      |  | |   |    |   |         ||      ||  |    | ||| ||||    |||    |||      || |  |  ||||  |  
TTTAATACTGGAGTATTGGGCTGATGCCCCGGAGATACAACGTTCAGCTGATTTATACGAAGATCTAATAAAGTGCTGTGTAGCAGATGCGATGAGTGAGgtaggatcttttgctgaatgcattccatggctcacctattttatctttgtttgtattga-aagtaattattcaatttttaataccactgcac-ataaaaaac

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os02g40430.1 (Oryza sativa), 5'ss of exon 12
CTTGATACTAGAATATTGGGCTGATGCACCAGAAATACAACGCTCAGCAGACCTATATGAAGATCTTATCAAGTGTTGTGTTGCAGATGCAATGAGTGAGgta---tttgtgtcagatagctttccttttt---------ataatgttcatggacagttcatggacagtgacaagtgccgatttggctttgg-cacacattttattataatta---
| | ||| | ||||||||||| ||||| || |||||||| ||  || | ||  |||| |||||||| || || || ||||| || ||||||||||||||||||    |     ||   |  ||||||   |         ||||||||||     | ||  |  |       || |   | ||||   ||   |        | ||  || |    
CCTAATATTGGAATATTGGGCAGATGCTCCTGAAATACAGCGTGCATCTGATATATACGAAGATCTAATAAAATGCTGTGTGGCTGATGCAATGAGTGAGgtagggctaacaccatccatttttcctgacttaagtcaccataatgttcagtattaattattaaatgcctgaaaat-ttgttttgatgttattcttgtgccgtgttgcaaatgcag

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G052078_T02 (Zea mays), 5'ss of exon 11
CTTGATACTAGAATATTGGGCTGATGCACCAGAAATACAACGCTCAGCAGACCTATATGAAGATCTTATCAAGTGTTGTGTTGCAGATGCAATGAGTGAGgtatttgtgtcagatagctttcctttttataatgttcatggacagttcatgg--acagtgacaagtgccgatttggct----ttggcacacattttattataatta
  ||||||| || ||||||||||||||  ||||||||||||| ||||| ||  ||||||| ||| | || || || ||||| |||||||| ||||| |||||||     |||  |  || | |||| |   || | |||||   ||||||     || ||| | |   | ||||| |     |||    ||  |||| |   ||  
TCTGATACTGGAGTATTGGGCTGATGCCTCAGAAATACAACGTTCAGCTGATTTATATGAGGATATGATAAAATGCTGTGTCGCAGATGCGATGAGCGAGgtatg---atcaattttctatactttgtcgcatat-catggcatgttcatttttgcactgaaatggagccatttgtccaaaattgaattactctttactcccat--

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G081907_T01 (Zea mays), 5'ss of exon 8
CTTGATACTAGAATATTGGGCTGATGCACCAGAAATACAACGCTCAGCAGACCTATATGAAGATCTTATCAAGTGTTGTGTTGCAGATGCAATGAGTGAGgtatttgtgtcagatagctttcctttttataatgttcatggacagttcatggacag--tgacaagtgccgatttggctttggcacacattttattataatta-
  | ||  |||| || |||| |||| | |||||||||||  | ||||| ||||| || ||||| ||||| || |||||| | ||||||||||  ||||||||||||   |    |  | ||| ||  |     |||  | |  | ||| ||    |  || |   |     |||| ||  |  || ||     | ||   |  
ACTAATGTTAGAGTACTGGGTTGATACTCCAGAAATACAGAGATCAGCTGACCTGTACGAAGACCTTATAAAATGTTGTATAGCAGATGCAACTAGTGAGgtatttacattgtgt--cattcattcattctccgtttcttgttatttcttgagaggattgcctgttagaagtttgactcggatac-cacaaggtcatctcttc

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA19G35460.1 (Glycine max), 5'ss of exon 11
CTTGATACTAGAATATTGGGCTGATGCACCAGAAATACAACGCTCAGCAGACCTATATGAAGATCTTATCAAGTGTTGTGTTGCAGATGCAATGAGTGAGgtatttgtgtcagatagctttcctttttataatgttcatggacagttcatggacagtgacaagtgccgatttggctttggcacacattttattataatta--
 ||| | |||||| ||||| ||||||||||||||||||| || ||||| ||  ||||||| ||||| || |||||||||||| |||| |||||||||||||||  | | |    |    ||  |   |||   ||  ||  | ||| ||| || | |   ||   | || |  |||||  ||     |||  | |  ||   
TTTGGTCCTAGAACATTGGCCTGATGCACCAGAAATACATCGATCAGCTGATTTATATGAGGATCTGATAAAGTGTTGTGTTTCAGACGCAATGAGTGAGgtagctttatagttttaggttattggatatttggtaaatatatagtgcattga-atttgtaaactctgact-agcttttccattgggttttctcttcttcct

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA03G32710.1 (Glycine max), 5'ss of exon 11
CTTGATACTAGAATATTGGGCTGATGCACCAGAAATACAACGCTCAGCAGACCTATATGAAGATCTTATCAAGTGTTGTGTTGCAGATGCAATGAGTGAGgtatttgtgtcagatagctttcctttttataatgttcatggacagttcatggacagtgacaagtgccgatttggctttggcacacattttattataatta--
 ||| | |||||| ||||| |||||||||| |||||||| || ||||| ||  ||||||| ||||| || |||||||||||| |||| |||||||||||||||  | | |    |    ||  ||   ||   ||  ||  | ||| |||  | | |   ||   | || |  |||||  ||     |||  | |  ||   
TTTGGTCCTAGAACATTGGCCTGATGCACCTGAAATACATCGATCAGCTGATTTATATGAGGATCTGATAAAGTGTTGTGTTTCAGACGCAATGAGTGAGgtagctttatagttttaggttatttgacatttggtaaatatatagtgcattaa-atttgtaaactctgact-agcttttccattgggttttctcttcttcct

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA13G19230.1 (Glycine max), 5'ss of exon 11
CTTGATACTAGAATATTGGGCTGATGCACCAGAAATACAACGCTCAGCAGACCTATATGAAGATCTTATCAAGTGTTGTGTTGCAGATGCAATGAGTGAGgtatttgtgtcagatagctttcctttttataatgttcatggacagttcatggacagtgacaagtgccgatttggctttggcacacattttattataatta-----
 |||||||||||| ||||| |||||||| ||||| ||||||| || || || |||||||| ||| | || | |||||||||| |||| |||||||||||||||  | |     |||| |||   || | |||||||  ||  || |  |      |   ||  |  | | ||||  |  ||   |||| | ||    ||      
TTTGATACTAGAACATTGGCCTGATGCAGCAGAAGTACAACGATCGGCTGATCTATATGAGGATATGATAAGGTGTTGTGTTTCAGACGCAATGAGTGAGgtaactttc----atagttttaggttatttaatgtttttgatcaatatagaccgtgcatcatatttctacttggact-agctttcattgttttgctctttttcct

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA10G04850.1 (Glycine max), 5'ss of exon 11
CTTGATACTAGAATATTGGGCTGATGCACCAGAAATACAACGCTCAGCAGACCTATATGAAGATCTTATCAAGTGTTGTGTTGCAGATGCAATGAGTGAGgtatttgtgtcagatagctttcctttttataatgttcatggacagttcatggacagtgacaagtgccgatttggctttggcacacattttattataatta----
 |||||| ||||| ||||| |||||||| ||||| ||||||| || || || |||||||| ||| | || | ||| |||||| ||||||||||||||||||||  | |     |||| |||   || ||| ||| |  ||  || |  |          ||  |  | | ||||  | |     |||| | ||    ||     
TTTGATATTAGAACATTGGCCTGATGCAGCAGAAGTACAACGATCGGCTGATCTATATGAGGATATGATAAGGTGCTGTGTTTCAGATGCAATGAGTGAGgtaactttt----atagttttaggttatatgatgattttgatcaatatagactgtacatcatatttctacttggactagcttttcattgttttgctctttttcc

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT2G20190.1 (Arabidopsis thaliana), 5'ss of exon 11
CTTGATACTAGAATATTGGGCTGATGCACCAGAAATACAACGCTCAGCAGACCTATATGAAGATCTTATCAAGTGTTGTGTTGCAGATGCAATGAGTGAGgtatttgtgtcagatagctttcctttttataa--tgttcatggacagttcatggacagtgacaagtgccgatttggctttggcacacattttattataatta-
 || | ||| ||| ||||| ||||||| |||||||| ||||| ||||  ||  ||||||||||||| || |  || |||||||||||||| ||||||||||||  | | |   |    ||||| |  ||  |  |||| | | |  ||| ||||    |      |    || |||   || ||   |||    |   ||   
GTTAACACTTGAACATTGGCCTGATGCTCCAGAAATTCAACGATCAGTTGATTTATATGAAGATCTGATTAGATGCTGTGTTGCAGATGCTATGAGTGAGgtaggtttctggtaccattttccataatacgagatgttgaagtagggtttatggttgcttgtttatat--atgtggtaatg-cagttattcggattcgatgca

upper sequence: Vv07s0005g05030.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: EFJ14058 (Selaginella moellendorffii), 5'ss of exon 5
CTTGATACTAGAATATTGGGCTGATGCACCAGAAATACAACGCTCAGCAGACCTATATGAAGATCTTATCAAGTGTTGTGTTGCAGATGCAATGAGTGAGgtatttgtgtcagatagctttcctttttataatgttcatggacagttcatggacagtgacaagtgccgatttggctttggcacacattttattataatta
 |||||||||||| | ||| | ||| | |||||||| ||||| ||||| || || ||||||||||||||||| || ||||||| |||||| ||||| ||||||  | |  |  |||  |         | |    |||   ||   |  |   |||                                            
TTTGATACTAGAACAGTGGCCGGATACTCCAGAAATCCAACGTTCAGCCGAACTTTATGAAGATCTTATCAAATGCTGTGTTGTAGATGCTATGAGCGAGgtaactttcgctaatatgtgaaagaaacaaatgaatca--aactcgttgtatccag--------------------------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGATACTAGAATATTGGGCTGATGCACCAGAAATACAACGCTCAGCAGACCTATATGAAGATCTTATCAAGTGTTGTGTTGCAGATGCAATGAGTGAGgtatttgtgtcagatagctttcctttttataatgttcatggacagttcatggacagtgacaagtgccgatttggctttggcacacattttattataatta

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG