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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATAGCGCCTGCTTCTGGCTTGAGAGAACCCAATGGGAATACTGTTGGTGTTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAGgtggatcatgtggttcctttgcttcattttttcttcttcttctctttttgatttattgttgggccatcttaaatctgtcttgatatcttgtag

Basic information

species Vitis vinifera
transcript Vv07s0005g02100.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA02G01220.3 (Glycine max), 5'ss of exon 2
CATAGCGCCTGCTTCTGGCTTGAGAGAACCCAATGGGAATACTGTTGGTGTTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAGgtggatcatgtggttcctttgcttcattttttcttcttcttctctttttgatttattgttgggccatcttaaatctgtcttgatatct-tgtag------------------------------------
  |||| |||||||||||  | |||||    ||||  | | |||||| |||||| |||||||||||||||||||||| |||||||||||||||||| | |||  |         ||  ||   || |  | | ||   |||    |||  ||      ||   |||| | |      || |||||  | |||||                                    
TGTAGCACCTGCTTCTGGGGTAAGAGATGTGAATGCAAGTTCTGTTGCTGTTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGGgtaaagttaaaatgtctattttatcttggtctgtttgcctttcactttgcatcacgccttcacccatttgagcaacttcctgataaatatgtagtatacttatgtagtaacctgttaaaacaaaatgcag

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G01280.2 (Glycine max), 5'ss of exon 2
---------------------------------------------------------------------------------CATAGCGCCTGCTTCTGGCTTGAGAGAACCCAATGGGAATACTGTTGGTGTTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAGgtggatcatgtggttcctttgcttcattttttcttcttcttctctttttgatttattgttgggccatcttaaatctgtcttgatatcttgtag
                                                                                   |||| |||||||||||  | |||||    ||||  ||| | |||| |||||| |||||||||||||||||||||| |||||||||||||||||| | |||  |  ||    |  || |                                                                         
CTGTGTGACCTGTTATTTTAGTTGAATCGAAGCCGCGACCAAATCTTCCTGATCTTTGCCTGAGGTGATGGCATCGGCGGGTGTAGCACCTGCTTCTGGAgtaagagatgtgaatgcaaattcggttgctgttgaaaggttgcctgatgagatgaatggcatgaaaattagggatgaaagggtaaag-ataaaatgtctat-------------------------------------------------------------------------

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G01280.1 (Glycine max), 5'ss of exon 2
CATAGCGCCTGCTTCTGGCTTGAGAGAACCCAATGGGAATACTGTTGGTGTTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAGgt--ggatcatgtggttcctttgcttcatt----ttttcttcttcttctctttttg--atttattgttgggccatctt------aaatctgtcttga---tatcttgtag-------------------
  |||| |||||||||||  | |||||    ||||  ||| | |||| |||||| |||||||||||||||||||||| |||||||||||||||||| | |||   ||| |  ||  |  |||   |   |    ||  |||   |||| | |   |  ||  ||  || |  || |||      |||| |||  ||    ||| |||||                    
TGTAGCACCTGCTTCTGGAGTAAGAGATGTGAATGCAAATTCGGTTGCTGTTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGGgtaaagataaaatgtctattttatcttggtctgtttgcctttcacttcgcatcacgccatcaatcatttgagcaacttcctggtaaatatgttgtgtacttatgttgtaacttgttaaactaaatgcag

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|161705537|gb|FC055340.1|FC055340
EST:     TTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAG                         GAAATGGAAGATACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATA
genomic: TTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAGgtggatcatg ... tatcttgtagGAAATGGAAGATACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATA
EST: gi|161717738|gb|FC065945.1|FC065945
EST:     TTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAG                         GAAATGGAAGATACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATA
genomic: TTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAGgtggatcatg ... tatcttgtagGAAATGGAAGATACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATA
EST: gi|71862885|gb|DT011940.1|DT011940
EST:     TTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAG                         GAAATGGAAGCTACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATA
genomic: TTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAGgtggatcatg ... tatcttgtagGAAATGGAAGATACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATA
EST: gi|110703118|gb|EE079682.1|EE079682
EST:     TTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAG                         GAAATGGAAGATACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATA
genomic: TTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAGgtggatcatg ... tatcttgtagGAAATGGAAGATACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATA
EST: gi|110685785|gb|EE062810.1|EE062810
EST:     TTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAG                         GAAATGGAAGCTACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATA
genomic: TTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAGgtggatcatg ... tatcttgtagGAAATGGAAGATACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATA
EST: gi|71875370|gb|DT024425.1|DT024425
EST:     GAAAATTAGGGATGACAAG                         GAAATGGAAGCTACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATA
genomic: GAAAATTAGGGATGACAAGgtggatcatg ... tatcttgtagGAAATGGAAGATACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATA
EST: gi|71875374|gb|DT024429.1|DT024429
EST:     GAAAATTAGGGATGACAAG                         GAAATGGAAGCTACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATA
genomic: GAAAATTAGGGATGACAAGgtggatcatg ... tatcttgtagGAAATGGAAGATACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATAGCGCCTGCTTCTGGCTTGAGAGAACCCAATGGGAATACTGTTGGTGTTGATAGGTTGCCTGATGAGATGAATGACATGAAAATTAGGGATGACAAGgtggatcatgtggttcctttgcttcattttttcttcttcttctctttttgatttattgttgggccatcttaaatctgtcttgatatcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG