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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCTGGATTTCCGGAAAAGAGAATAGGATATCTTGGCCTCATGTTGCTTCTTGATGAAAGGCAAGAAGTTCTTATGTTGGTTACAAACTCATTAAAACAgtatccaattctaagtaggttttatttttcatttgcttgactaatttcagaccaggcagctggtccttgtctttaccaagataaactttatcactagtac...

Basic information

species Vitis vinifera
transcript Vv01s0026g00310.t01
intron # 2
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA01G03890.1 (Glycine max), 5'ss of exon 2
CGGCTGGATTTCCGGAAAAGAGAATAGGATATCTTGGCCTCATGTTGCTTCTTGATGAAAGGCAAGAAGTTCTTATGTTGGTTACAAACTCATTAAAACAgtatccaattctaagt--aggttttatttttcatttgcttgactaatttcagaccaggcagctggtccttgtctttac-caagataaactttatcactagtac---------------------------------------------------------
|  |||||||||| || ||||||||||| |||||||||||||||||||||||||||||||| ||||||||||| |||||||| || || || || |||||||||||| || | |||  | ||| | ||| |  |||   |   || |  | ||         ||    ||     |     |  |  |  |  | |||   |                                                          
CTCCTGGATTTCCAGAGAAGAGAATAGGTTATCTTGGCCTCATGTTGCTTCTTGATGAAAGACAAGAAGTTCTAATGTTGGTCACCAATTCTTTGAAACAgtatccagtttttagtcaaagttctgtttattttttttatttatattccctgatttttacattgcattttacaaatgtgttattttgatctacttactgaaataaaatgagggaacaaatattaataatgggttatagcagagccttaactgaatcacag

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA02G03800.1 (Glycine max), 5'ss of exon 1
CGGCTGGATTTCCGGAAAAGAGAATAGGATATCTTGGCCTCATGTTGCTTCTTGATGAAAGGCAAGAAGTTCTTATGTTGGTTACAAACTCATTAAAACAgtatccaattctaagt--aggttttatttttcatttgc--ttgactaattt---------------cagaccaggcagctggtccttgtctttaccaagataaactttatcactagtac---------------------------------------
|  ||| |||||| || ||||||||||| |||||||||||||||||||||||||||||||| ||||||||||| |||||||| || || || || |||||||||||| || | |||  | ||| | ||| || |||    ||| || ||||               || |   |  |  | |  ||| |  ||||  | | ||| |  |  |  |  |                                        
CTCCTGAATTTCCAGAGAAGAGAATAGGTTATCTTGGCCTCATGTTGCTTCTTGATGAAAGACAAGAAGTTCTAATGTTGGTCACCAATTCTTTGAAACAgtatccagtttttagtcaaagttctgtttatctttttatattgcctgatttttacatttcactttacaaatgtgttattttgatcttctacttactgaaacaaaatgaagaaaaaaaaatattaataatgggttagtagagccttaactgaatcacag

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA08G39930.1 (Glycine max), 5'ss of exon 2
CGGCTGGATTTCCGGAAAAGAGAATAGGATATCTTGGCCTCATGTTGCTTCTTGATGAAAGGCAAGAAGTTCTTATGTTGGTTACAAACTCATTAAAACAgtatccaattctaagt--aggttttatttttcatttgcttgactaatttc-------------------agaccaggcagctggtccttgtctttac---caagataaactttatcactagtac--
|  | ||||||||||| |||||||| || || |||||||| ||||||||||| |||||||| ||||| ||||| |||||||| || || || || ||||||||||||| |  | ||  | |||| |||| |  ||   ||   ||||||                    |  | ||| |||| |   |  |  | |      | | |||| ||| |      ||  
CTCCAGGATTTCCGGAGAAGAGAATGGGTTACCTTGGCCTTATGTTGCTTCTCGATGAAAGACAAGAGGTTCTAATGTTGGTCACCAATTCTTTGAAACAgtatccaaattcatgtcaatgtttcatttgtttttgtgttccttaatttttagattccattttacaaatatgctagggagctagcaataatggtgatgggttataaaaaccttagctaagtcacag

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT1G60070.1 (Arabidopsis thaliana), 5'ss of exon 2
CGGCTGGATTTCCGGAAAAGAGAATAGGATATCTTGGCCTCATGTTGCTTCTTGATGAAAGGCAAGAAGTTCTTATGTTGGTTACAAACTCATTAAAACAgtatccaattctaagtaggttttatttttcatttgcttgactaatttcagaccaggcagctggtccttgtctttaccaagataaactt-tatcactagtac----------------
|  |||||||||| || ||||| || || ||||||||  | |||||||||||||||||||||||||||||  | ||| | || || |||||  | || ||||||||  |     ||   ||||   |||   || | |   || | |   | |     |||||    |      |      |||  |  | |    || ||                
CTCCTGGATTTCCTGAGAAGAGGATTGGTTATCTTGGATTAATGTTGCTTCTTGATGAAAGGCAAGAAGTATTAATGCTTGTCACCAACTCGCTGAAGCAgtatcctttatggtgttaatttttgattttgattccctag-tagtgttttaactttttgctggcatcttcgcacaaatttttaagttcatcttgtgagaaccttgacttacgtctag

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|161718068|gb|FC068577.1|FC068577
EST:     CTTGATGAAAGGCAAGAAGTTCTTATGTTGGTTACAAACTCATTAAAACA                         AGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCT
genomic: CTTGATGAAAGGCAAGAAGTTCTTATGTTGGTTACAAACTCATTAAAACAgtatccaatt ... ttatatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCT
EST: gi|110720727|gb|EE096900.1|EE096900
EST:     CTTGATGAAAGGCAAGAAGTTCTTATGTTGGTTACAAACTCATTAAAACA                         AGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCT
genomic: CTTGATGAAAGGCAAGAAGTTCTTATGTTGGTTACAAACTCATTAAAACAgtatccaatt ... ttatatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCTGGATTTCCGGAAAAGAGAATAGGATATCTTGGCCTCATGTTGCTTCTTGATGAAAGGCAAGAAGTTCTTATGTTGGTTACAAACTCATTAAAACAgtatccaattctaagtaggttttatttttcatttgcttgactaatttcagaccaggcagctggtccttgtctttaccaagataaactttatcactagtac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagataa