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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaactggaagacttgccatcttatatatgtttatttattacatatttaatgcagattttggtttgggaatagaaacctagtttttttattgctcctattcttcattattgtctttagtactattacttaaattattattatttcattatgtttttagGATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAACGAGGACCCGAGCTTGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTA

Basic information

species Vitis vinifera
transcript Vv12s0055g00360.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0055g00360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G05410.1 (Glycine max), 3'ss of exon 4
gtaaaactggaagacttgccatcttatatatgtttatttattacatatttaatgcagattttggtttgggaatagaaacctagtttttttattgctcctattcttcattattgtctttagtactattacttaaattattattatttcattatgtttttagGATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAACGAGGACCCGAGCTTGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTA
                                                                        |   || | |   || | ||| | | | ||  |   |   || |  |||  |||  || | | | |      ||    ||||    ||| || |||   |||    || || |||||||||||||| ||||||||||||||||| || || ||||||||||||||||||||||||||||| || ||| 
-----------------------------------------------------------------------gtgctaaacaaaaattgt-attac-cttgttgattgctg--gtttaaagttgtatatctaacagtttagcctgttgtccatgtc---agGCTTCTGACATTCCTACTACGGAACATGTTCCAAGGGTATTGCCAAAGAACGAGGATCCAAGTTTGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTT

upper sequence: Vv12s0055g00360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G19640.1 (Glycine max), 3'ss of exon 4
gtaaaactggaagacttgccatcttatatatgtttatttattacatatttaatgcagattttggtttgggaatagaaacctagtttttttattgctcctattc-ttcattattgtctttagtactattacttaaattat-tattatttcattatgt-ttttagGATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAACGAGGACCCGAGCTTGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTA
                                                                 |    ||  ||||  |  |    |||    || | ||| || ||| |||  || |       ||  ||| | |    |||     || |   ||| ||| || ||| | |||    ||||| |||||||||||||| ||||| ||||| ||||| || || ||||||||||||||||||||||||||||| || ||| 
----------------------------------------------------------------gtactaaactgaaattttatcaccttacc-ttcttgttcgttgattgttggtttcaacttgtatatctaactaacactttagcctgttgtccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCCTAAGAATGAGGATCCAAGTTTGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTT
















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|30255110|gb|CB971557.1|CB971557
EST:     GGCAAACTGGTTGGTCGAGGAAAGAAGGCAATCAAAGAGCAGCCAAGATG                         GATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAAC
genomic: GGCAAACTGGTTGGTCGAGGAAAGAAGGCAATCAAAGAGCAGCCAAGATGgtaaaactgg ... atgtttttagGATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAAC
EST: gi|110722678|gb|EE099124.1|EE099124
EST:     GGCAAACTGGTTGGTCGAGGAAAGAAGGCAATCAAAGAGCAGCCAAGATG                         GATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAAC
genomic: GGCAAACTGGTTGGTCGAGGAAAGAAGGCAATCAAAGAGCAGCCAAGATGgtaaaactgg ... atgtttttagGATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAAC
EST: gi|161717479|gb|FC067864.1|FC067864
EST:     GGCAAACTGGTTGGTCGAGGAAAGAAGGCAATCAAAGAGCAGCCAAGATG                         GATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAAC
genomic: GGCAAACTGGTTGGTCGAGGAAAGAAGGCAATCAAAGAGCAGCCAAGATGgtaaaactgg ... atgtttttagGATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAAC
EST: gi|110711839|gb|EE088776.1|EE088776
EST:     GGCAAACTGGTTGGTCGAGGAAAGAAGGCAATCAAAGAGCAGCCAAGATG                         GATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAAC
genomic: GGCAAACTGGTTGGTCGAGGAAAGAAGGCAATCAAAGAGCAGCCAAGATGgtaaaactgg ... atgtttttagGATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAAC
EST: gi|161714363|gb|FC063204.1|FC063204
EST:     GGCAAACTGGTTGGTCGAGGAAAGAAGGCAATCAAAGAGCAGCCAAGATG                         GATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAAC
genomic: GGCAAACTGGTTGGTCGAGGAAAGAAGGCAATCAAAGAGCAGCCAAGATGgtaaaactgg ... atgtttttagGATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAAC
EST: gi|110712516|gb|EE090229.1|EE090229
EST:     GGCAAACTGGTTGGTCGAGGAAAGAAGGCAATCAAAGAGCAGCCAAGATG                         GATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAAC
genomic: GGCAAACTGGTTGGTCGAGGAAAGAAGGCAATCAAAGAGCAGCCAAGATGgtaaaactgg ... atgtttttagGATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattattgtctttagtactattacttaaattattattatttcattatgtttttagGATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAACGAGGACCCGAGCTTGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTA
                                              tgttttt  CT-rich tract
               tactattacttaaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaactggaagacttgccatcttatatatgtttatttattacatatttaatgcagattttggtttgggaatagaaacctagtttttttattgctcctattcttcattattgtctttagtactattacttaaattattattatttcattatgtttttagGATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAACGAGGACCCGAGCTTGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA