Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtctttctttttgttttgtttttttttctaatatgatctaacactttcctggtgatgatattccaattgggtgtatttgaactagtgtgattttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTTTCCAGCTTCTCAAGTGGGACTGAGAGAGCTGTAAAAACTTGGCAG

Basic information

species Vitis vinifera
transcript Vv05s0051g00860.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0051g00860.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G33590.1 (Glycine max), 3'ss of exon 1
-----tgtctttctttttgttttgtttttttttctaatatgatctaacactttcctggtgatg-atattccaattgggtgtatttgaactagtgtgattttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTTTCCAGCTTCTCAAGTGGGACTGAGAGAGCTGTAAAAACTTGGCAG
     | |||     |  |     |  ||| ||  ||| ||  |    |   |    |  |||   | ||  | | | ||| ||  || |    | |      ||||||||| |    || ||||| ||||| ||||| ||||||||  |||| | |||||||||||||||||| |||||| | ||||| || |||||||| 
ttaattatctactagtacgaggattggtttgttgcaatctgcacgtggataattggtgcaatgtggaatcttacttgatgtgttgaaaatgaaataa------cagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACTGAGCGTGCTGTGAAGACTTGGCAA

upper sequence: Vv05s0051g00860.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G34000.1 (Glycine max), 3'ss of exon 2
tgtctttctttttgttttgtttttttttctaatatgatctaacactttcctggtgatgatattccaattgggtgt-atttgaactagtgtgattttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTTTCCAGCTTCTCAAGTGGGACTGAGAGAGCTGTAAAAACTTGGCAG
 | | ||  || | |  |  |        |  | || |  ||      | |||  |     | |||  |   | | | |||    | |||     |  ||||||||| |    || ||||| ||||| ||||| ||||||||  |||| | |||||||||||||||||| || ||| | ||||| || |||||||| 
-gaccttaattatctactagtacgaagatttgtttgttgcaatctgcacgtggataattggtgccatgtaaatcttacttggtgcattgttgaaatatcagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACCGAGCGTGCTGTGAAGACTTGGCAA
















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|351043546|gb|FQ431020.1|FQ431020
EST:     GGAAGACATTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAT                         GAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|349808650|gb|FQ405794.1|FQ405794
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|349818868|gb|FQ409402.1|FQ409402
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|349824834|gb|FQ414692.1|FQ414692
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|28964467|gb|CB343500.1|CB343500
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|351049107|gb|FQ431651.1|FQ431651
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|349816194|gb|FQ403690.1|FQ403690
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|351012243|gb|FQ426965.1|FQ426965
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCACCTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|349826206|gb|FQ416011.1|FQ416011
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCACTTCANAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|349814900|gb|FQ410123.1|FQ410123
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|349807273|gb|FQ401265.1|FQ401265
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCATTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|349819286|gb|FQ412180.1|FQ412180
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|349818094|gb|FQ408869.1|FQ408869
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|349808040|gb|FQ402431.1|FQ402431
EST:     GAAGACGTTGAGGGTAGGTTCTAAAGGAGAAGAGGTTCGGGCAATGCCAG                         GAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATT
genomic: GAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGC-AGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATT
EST: gi|351043539|gb|FQ431013.1|FQ431013
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|351029340|gb|FQ436734.1|FQ436734
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
EST: gi|349822599|gb|FQ412863.1|FQ412863
EST:     GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAG                         GAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT
genomic: GGAAGACGTTGAGGGTAGGTTCTGAAGGAGAAGAGGTTCGGGCAATGCAGgtctgctcgc ... attttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctggtgatgatattccaattgggtgtatttgaactagtgtgattttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTTTCCAGCTTCTCAAGTGGGACTGAGAGAGCTGTAAAAACTTGGCAG
          atgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtctttctttttgttttgtttttttttctaatatgatctaacactttcctggtgatgatattccaattgggtgtatttgaactagtgtgattttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTTTCCAGCTTCTCAAGTGGGACTGAGAGAGCTGTAAAAACTTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - -ggtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgggtg