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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGATGACTCTTTGGATTATGGTGCAAATTTTTCACACATGTTGGGATTTGATAGTCCAAAAATGCAAGAGCTAATGAGGCTTTATGTCACCATCCATAGgtgggtgtatatttctcatcttatggcaatgataatatgtaggattttcttattggatcatataacaatcatatgcttattaatttttaaaatgtgttccag

Basic information

species Vitis vinifera
transcript Vv13s0156g00180.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 5'ss of exon 11
AGGATGACTCTTTGGATTATGGTGCAAATTTTTCACACATGTTGGGATTTGATAGTCCAAAAATGCAAGAGCTAATGAGGCTTTATGTCACCATCCATAGgt-------gggtgtatatttctcatcttatggcaatgat---aatatgtaggattttcttattggatcatataacaatcatatgcttattaatttttaaaatgtgttccag-------------------------------------------------------
  ||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||  | ||| ||||||| ||||||||||||||||| ||||| ||||       || | | |   | ||| | | |  || | ||   ||||  || | |    || |    | ||||||  || || | | | ||| |||   || | |   | |                                                        
TAGATGATTCTTTGGATTATGGTGCAAATTTTTCACACATGCTGGGATTTGATAGTCCTCAGATGAAAGAGCTCATGAGGCTTTATGTCACTATCCACAGgttagtcctggttctcttcgtttcaacatgtctcattaattagaatacataagctaaagttttcttgt-atataatgatgatcttcct-ttattttaccaactcttaccaaatttctatagcatgatcaaggtttttttttcccttgtctactggtttctgttttag

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 12
AGGATGACTCTTTGGATTATGGTGCAAATTTTTCACACATGTTGGGATTTGATAGTCCAAAAATGCAAGAGCTAATGAGGCTTTATGTCACCATCCATAGgtgggtgtatatttc--tcatct---tatggcaatgataatatgtaggattttcttattggatcatataacaatcatatgcttattaat------ttttaaaatgtgttccag---------------------
  ||| | |||||||||||||||||||||||||| ||||||||||||||||||  |  |||  || ||||||| |||||||||||  |||||||||| ||||  || |  ||||   ||| |     ||| |      |||| |    ||| |||| |    |  | |     |  || |  | | |||      || || ||  | || |                       
CAGATAAATCTTTGGATTATGGTGCAAATTTTTCCCACATGTTGGGATTTGATGATGAAAAGGTGAAAGAGCTCATGAGGCTTTACATCACCATCCACAGgtctgtattaattttcgtcacccatgcatgtctccttaaataagcttaattatcttgtaaatttgtttgttctttttaagactttaaatagacctttgtataacattttgcttttctactattttttgctctag
















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|29785895|gb|CB343236.2|CB343236
EST:     ATAGTCCAAAAATGC-CGATCNTAATGAGGCTTTATGTCACCATCCATAG                         TGATCATGAAGGCGGGAATGTCAGTCGCTCACACTGGTCATCTA
genomic: ATAGTCCAAAAATGCAAGAGC-TAATGAGGCTTTATGTCACCATCCATAGgtgggtgtat ... tgtgttccagTGATCATGAAGGCGGGAATGTCAGT-GCTCACACTGGTCATCTA
EST: gi|110372355|gb|EC936513.1|EC936513
EST:     GATAGTCCAAAAATGCAAGAGCTAATGAGGCTTTATGTCACCATCCATAG                         TGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
genomic: GATAGTCCAAAAATGCAAGAGCTAATGAGGCTTTATGTCACCATCCATAGgtgggtgtat ... tgtgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
EST: gi|77577886|gb|DV217693.1|DV217693
EST:     GATAGTCCAAAAATGCAAGAGCTAATGAGGCTTTATGTCACCATCCATAG                         TGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
genomic: GATAGTCCAAAAATGCAAGAGCTAATGAGGCTTTATGTCACCATCCATAGgtgggtgtat ... tgtgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGATGACTCTTTGGATTATGGTGCAAATTTTTCACACATGTTGGGATTTGATAGTCCAAAAATGCAAGAGCTAATGAGGCTTTATGTCACCATCCATAGgtgggtgtatatttctcatcttatggcaatgataatatgtaggattttcttattggatcatataacaatcatatgcttattaatttttaaaatgtgttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT