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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGATGGGAGGATGATGAGACCGTTGAAGAAGCAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtcccttttcctgcttgataattgccattgtagctattgtggatgtgcatatgtattccattacttgaactgcaagaagagagaacttcactttgc...

Basic information

species Vitis vinifera
transcript Vv14s0068g00870.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g00870.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G26440.1 (Glycine max), 5'ss of exon 2
GGTGGATGGGAGGATGATGAGACCGTTGAAGAAGCAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccc--ttttcctgcttgataattgccattgtagctattgtggatgtg--catatgtattccattacttgaactgcaagaagagagaacttcactttgc
||||||||||||||||||||||| |||  |||||| || |||||||||||  |||||||||||||||| ||||| ||| | |  ||| |      | ||| |  ||||   ||   |   |   | |    |||     || |   ||   | ||  |||  |  | ||  |   |  ||   |||  
GGTGGATGGGAGGATGATGAGACTGTTACAGAAGCTGCTTGCCGTGAAGCGCTAGAGGAAGCAGGAGTCAAAGGGATTGTAAGGgtaggctatgatattcatcattgaatgtt-taagcatcattttgaaagatagaaccaaagaaatattagtatatgagtttaatgatcatgaa--ttggtttta-

upper sequence: Vv14s0068g00870.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G05080.1 (Glycine max), 5'ss of exon 3
GGTGGATGGGAGGATGATGAGACCGTTGAAGAAGCAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtcccttttcctgcttgataattgccattgtagctattgtggatgtgcatatgtattccattacttgaac-tgcaagaagagagaacttcactttgc--
||||||||||||||||||||||| |||  |||||| || ||||| || || ||||||||||||||||| |||||||| || |  ||| || |  |||||  || | |  ||    |  | | ||| ||  ||   |     |  |  | |  || ||| | | |      |  ||   ||   |   
GGTGGATGGGAGGATGATGAGACTGTTACAGAAGCTGCTTGCCGCGAGGCTTTAGAGGAAGCAGGAGTTAAAGGAATACTAAGAgtaggttcaatttccctctaggttgtttaagtattggttatagtccattctc---catcatggaatgtttaaacataccaattagaatgacacaacaaaggga

upper sequence: Vv14s0068g00870.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G07450.1 (Glycine max), 5'ss of exon 5
GGTGGATGGGAGGATGATGAGACCGTTGAAGAAGCAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccc--ttttcctgcttgataatt--gccattgtagctattgtggatgtgcatatgtattccattacttgaactgcaagaagagagaacttcactttgc
||||||||||||||||||||||| ||   |||||| || |||||||||||  |||||||||| ||||| ||||| ||| | |  ||| |      | ||| |  ||||   ||   ||| |      | | |  ||   |||     |  || |  |   | ||  |    |  | |  |||   |  
GGTGGATGGGAGGATGATGAGACTGTCACAGAAGCTGCTTGCCGTGAAGCTCTAGAGGAAGCTGGAGTCAAAGGGATTATAAGGgtaggctatgatgttcatcattgaatgttcaaccaattcgatgagttta-ataatcatgaac-tgacaatgttcacattgtcaaccaattgtaaatcatcat--

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|33402883|gb|CF208510.1|CF208510
EST:     CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAAT                         GAAAAATCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
genomic: CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccct ... ctttgttcagGAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
EST: gi|83274830|gb|DV938926.1|DV938926
EST:     AGGAAGCAGGAGTGAAAGGAATTCTTAAT                         GAAAAATCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
genomic: AGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccct ... ctttgttcagGAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
EST: gi|254915183|gb|GR904614.1|GR904614
EST:     GCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAAT                         GAAAAATCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
genomic: GCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccct ... ctttgttcagGAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
EST: gi|32265358|gb|CD716211.1|CD716211
EST:     CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAAT                         GAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
genomic: CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccct ... ctttgttcagGAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
EST: gi|30296756|gb|CB973550.1|CB973550
EST:     CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAAT                         GAAAAATCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
genomic: CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccct ... ctttgttcagGAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
EST: gi|30296688|gb|CB973482.1|CB973482
EST:     CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTTTTAAT                         GAAAAATCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
genomic: CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccct ... ctttgttcagGAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
EST: gi|110412202|gb|EC977942.1|EC977942
EST:     CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAAT                         GAAAAATCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
genomic: CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccct ... ctttgttcagGAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
EST: gi|32272355|gb|CD721514.1|CD721514
EST:     CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAAT                         GAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
genomic: CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccct ... ctttgttcagGAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
EST: gi|30324328|gb|CD007590.1|CD007590
EST:     CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAAT                         GAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
genomic: CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccct ... ctttgttcagGAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
EST: gi|110389979|gb|EC954859.1|EC954859
EST:     CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAAT                         GAAAAATCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
genomic: CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccct ... ctttgttcagGAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
EST: gi|110417324|gb|EC983371.1|EC983371
EST:     CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAAT                         GAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
genomic: CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccct ... ctttgttcagGAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
EST: gi|33402870|gb|CF208497.1|CF208497
EST:     CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAAT                         GAAAAATCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
genomic: CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccct ... ctttgttcagGAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
EST: gi|77587339|gb|DV222811.1|DV222811
EST:     CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAAT                         GAAAAATCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC
genomic: CAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtccct ... ctttgttcagGAAAAACCCCTGGGTGTTTGGGAGTTCAGAAGCAAGAGCAGACAAGAAAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGATGGGAGGATGATGAGACCGTTGAAGAAGCAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAATgtatgtcccttttcctgcttgataattgccattgtagctattgtggatgtgcatatgtattccattacttgaactgcaagaagagagaacttcactttgc

- - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaga