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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCAGAACTTACGGGCTTCTATTTGATTGGTTGTATCCTGCACATATGCCACTTCTCTTGAAAGGCATTTCGCACTGGACCGATACACCAGAGgtgaagtaaaatggttattttcttccttatttgatatattggacatggaagtggcccttttatcattaagtagtcaacttaaatcagaatggtcgtgtgc...

Basic information

species Vitis vinifera
transcript Vv13s0067g01920.t01
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g01920.t01 (Vitis vinifera), 5'ss of exon 23
lower sequence: GLYMA06G00520.1 (Glycine max), 5'ss of exon 15
CCGCAGAACTTACGGGCTTCTATTTGATTGGTTGTATCCTGCACATATGCCACTTCTCTTGAAAGGCATTTCGCACTGGACCGATACACCAGAGgtgaagtaaaatggttattttcttccttatttg---atatattggacatggaagtggcccttttatcattaagtagtcaacttaaatcagaatggtcgtgtgc
|||| |||| || || |||||||||||||||||||||||||||| ||||| || ||||| |||||||| || || ||||| || || |||||||| | | | || | || | || | | ||| ||| | | || | || ||| | ||| |||| | ||| | |||
CCGCCGAACATATGGATTTCTATTTGATTGGTTGTATCCTGCACACATGCCTCTACTCTTAAAAGGCATCTCACATTGGACAGACACCCCAGAGgtaatgaaccttgctgataattttttctgcctacatatacattcaaatggcgggttttggtcccattattcttcactca-tgtaaaactgaagatttgtga--

upper sequence: Vv13s0067g01920.t01 (Vitis vinifera), 5'ss of exon 23
lower sequence: GLYMA04G00430.1 (Glycine max), 5'ss of exon 21
CCGCAGAACTTACGGGCTTCTATTTGATTGGTTGTATCCTGCACATATGCCACTTCTCTTGAAAGGCATTTCGCACTGGACCGATACACCAGAGgtgaagtaaa--atggttattttcttccttatttg-atatattggacatggaagtggcccttttatcattaagtagtcaacttaaatcagaatggtcgtgtgc
||| |||| || || |||||||||||||||||||||||||||| ||||| || ||||| |||||||| || || ||||| || || || ||||| | | | ||| || ||| || || ||| | | | | || | || ||| | ||| | |||| ||| |||
CCGTCGAACGTATGGATTTCTATTTGATTGGTTGTATCCTGCACACATGCCTCTACTCTTAAAAGGCATCTCACATTGGACAGACACCCCTGAGgtaatgaaccttgtggataattttttatgcatacatatacactcaaatggtgggttttgatcccattattcttcactcatgtaaaatt-gaagatctgtga--
















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|351036060|gb|FQ463905.1|FQ463905
EST:     ATATGCCACTTCTCTTGAAAGGCATTTCGCACTGGACCGATACACCAGAG                         GTTACCACCCCATTATTAAAATTCATGGCAGAGTTCGTCTTAAACAAAGCC
genomic: ATATGCCACTTCTCTTGAAAGGCATTTCGCACTGGACCGATACACCAGAGgtgaagtaaa ... aatggtgcagGTTACCACCCCATTATTAAAATTCATGGCAGAGTTCGTCTTAAACAAAGCC
EST: gi|351026572|gb|FQ432470.1|FQ432470
EST:     ATATGCCACTTCTCTTGAAAGGCATTTCGCACTGGACCGATACACCAGAG                         GTTACCACCCCATTATTAAAATTCATGGCAGAGTTCGTCTTAAACAAAGCC
genomic: ATATGCCACTTCTCTTGAAAGGCATTTCGCACTGGACCGATACACCAGAGgtgaagtaaa ... aatggtgcagGTTACCACCCCATTATTAAAATTCATGGCAGAGTTCGTCTTAAACAAAGCC

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGCAGAACTTACGGGCTTCTATTTGATTGGTTGTATCCTGCACATATGCCACTTCTCTTGAAAGGCATTTCGCACTGGACCGATACACCAGAGgtgaagtaaaatggttattttcttccttatttgatatattggacatggaagtggcccttttatcattaagtagtcaacttaaatcagaatggtcgtgtgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatcaga