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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttgtatattatgctctcaattatagaagcataaattatattttatgattacttttcttctgttgaacttttcagCGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCTGGTGCTTTGGCAGAAGCGTGTAAAGTACTATTGCTAGATGAGCTCACAA

Basic information

species Vitis vinifera
transcript Vv04s0044g01320.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G15900.1 (Glycine max), 3'ss of exon 4
----gtaggttgt--atattatgctctcaattatagaagcataaattatattttatgattacttttcttctgttgaacttttcagCGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCTGGTGCTTTGGCAGAAGCGTGTAAAGTACTATTGCTAGATGAGCTCACAA
      ||| ||   |  ||  || |||||  | | | |  | |||||||   ||     ||||| ||||||||  | | ||||| || |||| || || || |||||||||||||| || ||||||||||||||||||||| | || ||||| |||||||| || ||| | |||||||||||||
gtattaaggatgacaaccttgagcactcaa--acaaatgtgtgaattatacaataaatgaactttccttctgttacaatattcagAGATCTGTCCAAACTCTGAGTGGTGGTCAGAAGCAGAGGGTTGCCATTGCTGGTGCTCTTGCTGAAGCTTGTAAAGTTCTGTTGTTGGATGAGCTCACAA

upper sequence: Vv04s0044g01320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G33460.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaggttgtatattatgctctcaattatagaagcataaattatattttatgattacttttc------------ttctgttgaacttttcagCGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCTGGTGCTTTGGCAGAAGCGTGTAAAGTACTATTGCTAGATGAGCTCACAA
    ||    |  | | |  | ||  | |  |   |   |||||| || |  || |||||             || || ||   ||| ||| ||||  |||| || || ||||||||||||||||||||  ||||||||||||||||||| || |||||||| ||||| |||||| | |||||||||||||
----gtcagtttatgtacattgaacaacaataa-gttgtttatatcttctagttccttttactaaagtatagattttggtgttgtttccagAGACCGATTCAAACTCTCAGTGGTGGTCAGAAACAAAGAATTGCCATTGCTGGTGCTTTAGCTGAAGCGTGCAAAGTGCTATTGTTGGATGAGCTCACAA
















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|71870320|gb|DT019375.1|DT019375
EST:     CAAGAGTGTCGAAAGCTCTGGATGCTGTGGGCATTTCTGACTACATGCAA                         CGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCT
genomic: CAAGAGTGTCGAAAGCTCTGGATGCTGTGGGCATTTCTGACTACATGCAAgtaggttgta ... aacttttcagCGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCT
EST: gi|30136356|gb|CB921694.1|CB921694
EST:     CAAGAGTGTCGAAAGCTCTGGATGCTGTGGGCATTTCTGACTACATGCAA                         CGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCT
genomic: CAAGAGTGTCGAAAGCTCTGGATGCTGTGGGCATTTCTGACTACATGCAAgtaggttgta ... aacttttcagCGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCT
EST: gi|77579760|gb|DV218758.1|DV218758
EST:     CAAGAGTGTCGAAAGCTCTGGATGCTGTGGGCATTTCTGACTACATGCAA                         CGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCT
genomic: CAAGAGTGTCGAAAGCTCTGGATGCTGTGGGCATTTCTGACTACATGCAAgtaggttgta ... aacttttcagCGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCT
EST: gi|71870537|gb|DT019592.1|DT019592
EST:     CAAGAGTGTCGAAAGCTCTGGATGCTGTGGGCATTTCTGACTACATGCAA                         CGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCT
genomic: CAAGAGTGTCGAAAGCTCTGGATGCTGTGGGCATTTCTGACTACATGCAAgtaggttgta ... aacttttcagCGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCT
EST: gi|71875168|gb|DT024223.1|DT024223
EST:     CAAGAGTGTCGAAAGCTCTGGATGCTGTGGGCATTTCTGACTACATGCAA                         CGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCT
genomic: CAAGAGTGTCGAAAGCTCTGGATGCTGTGGGCATTTCTGACTACATGCAAgtaggttgta ... aacttttcagCGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCT
EST: gi|71866041|gb|DT015096.1|DT015096
EST:     CAAGAGTGTCGAAAGCTCTGGATGCTGTGGGCATTTCTGACTACATGCAA                         CGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCT
genomic: CAAGAGTGTCGAAAGCTCTGGATGCTGTGGGCATTTCTGACTACATGCAAgtaggttgta ... aacttttcagCGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCT
EST: gi|77581718|gb|DV219803.1|DV219803
EST:     CAAGAGTGTCGAAAGCTCTGGATGCTGTGGGCATTTCTGACTACATGCAA                         CGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCT
genomic: CAAGAGTGTCGAAAGCTCTGGATGCTGTGGGCATTTCTGACTACATGCAAgtaggttgta ... aacttttcagCGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagaagcataaattatattttatgattacttttcttctgttgaacttttcagCGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCTGGTGCTTTGGCAGAAGCGTGTAAAGTACTATTGCTAGATGAGCTCACAA
                                               cttttc  CT-rich tract
          ataaattatattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggttgtatattatgctctcaattatagaagcataaattatattttatgattacttttcttctgttgaacttttcagCGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCTGGTGCTTTGGCAGAAGCGTGTAAAGTACTATTGCTAGATGAGCTCACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA