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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatgctgccttctgcttttgccaccatatagcgcattttccatcagatttttcatatctgggttgatttttaattttgtgtatgttttgcag

Basic information

species Vitis vinifera
transcript Vv14s0060g01290.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA10G28890.1 (Glycine max), 5'ss of exon 10
GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatgctgccttctg--cttttgccaccatatagcgcattttccatcagatttttcatatctgggttgatttttaattttgtgtatgttttgcag
|||||||| || || ||||| ||||||||||| |||  ||||||||| |||||||| |||||  |||| ||||||||||||| |||| ||||||||||| ||  | ||  |  |||  ||||||  |   ||| |     |    || |  |  || ||      ||    ||  |                    
GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAGTATGCTAAGCAGCTGGTTGAAGAAACATGGGGCAAGCACAAGGATgtaagtctttctatccactgatcttttggtatgctattgaaagat----atgatctccttaatgaaaatgtgttcttgcag-------------------

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 10
GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatgctgccttctgcttttgccaccatatagcgcattttccatcagatttttcatatctgggttgatttttaattttgtgtatgttttgcag
|||||||| || || ||||| ||||||||||| |||  ||||||||| || ||||| |||||| |||  ||||||||||||| |||| ||||||||||| ||  |      |  |   | |       | ||  | ||  |  ||   |      |  | ||   |  ||  | |  ||||||   | ||||||
GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAATATGCCAAGCAACTGGCTGAAGAAACATGGGGCAAGCACAAGGATgtaagttttttctattcattgatcttttttggtctaaggtatgct--attgaa------aggtatgatctccttaatgaaattgtgt---tcttgcag

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 9
GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatgctgccttctgcttttgccaccatatagcgcattttccatcagatttttcatatctgggttgatt-tttaattttgtgtatgttttgcag
|||||||||||  | |||||||||||||||||||| || ||||| || || ||||| ||| | |||| ||| ||||||||||  |||  |||||||||| ||| |        |   |||   ||  | | ||    ||||   |    ||| |  |  |||    || | |  ||| |  | |     ||||||
GTGAAATCAGGATCATTGTTCGACAATGTCTTGATCTGCGATGACCCAGACTATGCCAAGAAGTTGGCAGATGAAACATGGGGAAAGCTCAAGGATgtaggtgtttaaaatacccaattt---cataacacagtttttttttttttg--tttctggttactgatcagaatatccaatctaatat-cacattgcag

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|33401772|gb|CF207399.1|CF207399
EST:     CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
EST: gi|110381806|gb|EC935430.1|EC935430
EST:     CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
EST: gi|351056636|gb|FQ443263.1|FQ443263
EST:     CGGAGTATGCAAAGCAATTGGTAAAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
EST: gi|349816036|gb|FQ413550.1|FQ413550
EST:     CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTGATGAGGCAGAGATGAAGAGGGAAGAGGAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
EST: gi|351027478|gb|FQ444727.1|FQ444727
EST:     CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
EST: gi|349808465|gb|FQ405609.1|FQ405609
EST:     CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTTATGAGGCAGAGATGAAGAGGGAAGAGGAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
EST: gi|352794106|gb|FQ479348.1|FQ479348
EST:     CGGAGTATGCAAAGCAATTGGTAAAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
EST: gi|349826885|gb|FQ418976.1|FQ418976
EST:     CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
EST: gi|29781779|gb|CB346544.2|CB346544
EST:     CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTGATGAGATAGAGAAGAAGAGGGA-GATGGAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGA-GGAG
EST: gi|110687446|gb|EE064865.1|EE064865
EST:     CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
EST: gi|351043138|gb|FQ451311.1|FQ451311
EST:     CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTGATGAGGCAGAGATGAAGAGGGAAGAGGAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
EST: gi|351022735|gb|FQ428644.1|FQ428644
EST:     CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTGATGAGGCAGAGATGAAGAGGGAAGAGGAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
EST: gi|33402080|gb|CF207707.1|CF207707
EST:     CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTGATGAGGC
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGC
EST: gi|77578221|gb|DV217893.1|DV217893
EST:     CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAG
EST: gi|110708716|gb|EE086573.1|EE086573
EST:     CGGAGTATGCAAAACAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAAGGCA-CATTTGATGAAGCAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAA-GGCAGCATTTGATGAGGCAG
EST: gi|349810157|gb|FQ401603.1|FQ401603
EST:     CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT                         GCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAG
genomic: CGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatg ... tgttttgcagGCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGATgtatgtgatgctgccttctgcttttgccaccatatagcgcattttccatcagatttttcatatctgggttgatttttaattttgtgtatgttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA