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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGTGTTGCAAGTGGAGCAACTAGAGCTGCATTGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtgtgagtataagcattctgggctggatggaaactatacaaacttatgattaagtaactagtttcaaccatcaacttgttttatactttgacag

Basic information

species Vitis vinifera
transcript Vv01s0011g00500.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g00500.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os03g11500.1 (Oryza sativa), 5'ss of exon 9
CTGGTGTTGCAAGTGGAGCAACTAGAGCTGCATTGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtg--tgagtataagcattc--tgggctggatggaaactatacaaacttatgattaagtaactagtttcaaccatcaacttgttttatactttgacag
|||||||||| ||||||||||||||||| || || || || |||||||| |||   |||||||| || ||||||||||| |||||   |  | || | | |        ||  |||  || || |      ||   ||   |||   ||  |  | |  | | |  |  |   ||      
CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCGTTAACCCAGCATTTTGCACTTGCCAATAATGCAGCTGATATATCTGCAAAGgtaactttgcattatcttgtaacatcctaaatgccaattagatgg---taaatttctctaaactgtagctgc-agaagcatactcaacttttcag---

upper sequence: Vv01s0011g00500.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM5G846548_T01 (Zea mays), 5'ss of exon 9
CTGGTGTTGCAAGTGGAGCAACTAGAGCTGCATTGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtgtgagtataagcattct---gggctggatggaaactatacaaacttatgattaagtaactagtttcaaccatcaacttgttttatactttgacag
|||||||||| ||||||||||||||||| ||| | || || |||||||| |||  ||||||||| || ||||| ||||| |||||   ||     |||||||   |   |     ||  |  |      ||||  ||||  || |    |    ||  | | |  |  |   ||      
CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAGgta--agctagggcattcttcagaaatttgctgatcccttttggtattatttttaaaaaaatgaagttg--cacaagcatactcaacttttcag---

upper sequence: Vv01s0011g00500.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA02G13010.1 (Glycine max), 5'ss of exon 5
CTGGTGTTGCAAGTGGAGCAACTAGAGCTGCATTGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtgtgagt-ataagcattctgggctggatggaa-actatacaa-acttatgat--taagtaactagtttcaaccatcaacttgttt-tatactttgacag------------------------------
||||||||||||||||||| |||||||| || ||||| || ||||||||||||||  |||||||||||||||||||||| |||||   ||| | |   |||||   |||  | ||  | |||   | | |||   |  | | | | | ||        |  |  ||| | |||| ||||||                                
CTGGTGTTGCAAGTGGAGCCACTAGAGCAGCTTTGACTCAGCATTTTGCTCTTCAGGATAATGCTGCAGATATATCTGCAAAGgttcaagttacatttattctaa-ctgtttagatcattatctgagagttaaagtctttaatgagttgtgcattttttttatatgtatgtatattttgacttattaacatatatatatatatatatatatag

upper sequence: Vv01s0011g00500.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA01G07190.2 (Glycine max), 5'ss of exon 9
CTGGTGTTGCAAGTGGAGCAACTAGAGCTGCATTGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtgtgagt-ataagcattctgg--gctggatggaaactatacaaacttatgattaagt--aactagtttca-accatcaacttgttt-tatactttgacag
|||||||||||||||| || |||||||| || ||||| || ||||||||||||||  |||||||||||||||||||||| |||||   ||| | |   ||||     | | |||    | | |   |  | |||  ||  |  |  | |    | |   |  |||| ||  | ||  |  | ||
CTGGTGTTGCAAGTGGTGCCACTAGAGCAGCTTTGACTCAGCATTTTGCTCTTCAGGATAATGCTGCAGATATATCTGCAAAGgttctagttacagttattccaactgttagatcattatt-tgagagttaatgtctatattcagttgggcatatatatttgacttattaatgtatatctatag

upper sequence: Vv01s0011g00500.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT1G13770.2 (Arabidopsis thaliana), 5'ss of exon 8
CTGGTGTTGCAAGTGGAGCAACTAGAGCTGCATTGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtgtgagtataagcattctgggctggatggaaactatacaaacttatgattaagtaactagtttcaaccatcaact-tgttttatactttgacag
|||||||||||||||||||||| ||||| ||  | ||||| || |||||||||||| | ||||| || ||||||||||| |||||     | |   | |||| | |    || |   |||| ||||| || | |  | |  | |  | |  | |    | | ||||||   |||| ||
CTGGTGTTGCAAGTGGAGCAACCAGAGCAGCTCTAACACAGCACTTTGCTCTTCAAGACAATGCAGCGGATATATCTGCTAAGgtac---tctttac-ttcttgtcactgtgaatgatatagaaact-ataaatgtgaactttgagtaattctttgcttctattttatctattgaaag

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|161708215|gb|FC057847.1|FC057847
EST:     TGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAG                         GAAGGAAGTCAAGAGACAGTAGCAACAATGGTTGGCATGGCTTTTGGAATG
genomic: TGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtgtgagtat ... actttgacagGAAGGAAGTCAAGAGACAGTAGCAACAATGGTTGGCATGGCTTTTGGAATG
EST: gi|71879732|gb|DT028787.1|DT028787
EST:     TGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAG                         GAAGGAAGTCAAGAGACAGTAGCAACAATGGTTGGCATGGCTTTTGGAATG
genomic: TGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtgtgagtat ... actttgacagGAAGGAAGTCAAGAGACAGTAGCAACAATGGTTGGCATGGCTTTTGGAATG
EST: gi|71877796|gb|DT026851.1|DT026851
EST:     TGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAG                         GAAGGAAGTCAAGAGACAGTAGCAACAATGGTTGGCATGGCTTTTGGAATG
genomic: TGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtgtgagtat ... actttgacagGAAGGAAGTCAAGAGACAGTAGCAACAATGGTTGGCATGGCTTTTGGAATG
EST: gi|71878342|gb|DT027397.1|DT027397
EST:     TGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAG                         GAAGGAAGTCAAGAGACAGTAGCAACAATGGTTGGCATGGCTTTTGGAATG
genomic: TGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtgtgagtat ... actttgacagGAAGGAAGTCAAGAGACAGTAGCAACAATGGTTGGCATGGCTTTTGGAATG
EST: gi|71878071|gb|DT027126.1|DT027126
EST:     TGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAG                         GAAGGAAGTCAAGAGACAGTAGCAACAATGGTTGGCATGGCTTTTGGAATG
genomic: TGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtgtgagtat ... actttgacagGAAGGAAGTCAAGAGACAGTAGCAACAATGGTTGGCATGGCTTTTGGAATG
EST: gi|71879077|gb|DT028132.1|DT028132
EST:     TGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAG                         GAAGGAAGTCAAGAGACAGTAGCAACAATGGTTGGCATGGCTTTTGGAATG
genomic: TGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtgtgagtat ... actttgacagGAAGGAAGTCAAGAGACAGTAGCAACAATGGTTGGCATGGCTTTTGGAATG
EST: gi|71880088|gb|DT029143.1|DT029143
EST:     TGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAG                         GAAGGAAGTCAAGAGACAGTAGCAACAATGGTTGGCATGGCTTTTGGAATG
genomic: TGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtgtgagtat ... actttgacagGAAGGAAGTCAAGAGACAGTAGCAACAATGGTTGGCATGGCTTTTGGAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGTGTTGCAAGTGGAGCAACTAGAGCTGCATTGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtgtgagtataagcattctgggctggatggaaactatacaaacttatgattaagtaactagtttcaaccatcaacttgttttatactttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT