Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atccattctgttgcttttctgcatgtactcagttgcactaccttctgttgggaattttaatgaaaatttacttatagaaaatccattattttgttgtcagGCACAACTATTTGAATGATTTGCCTTCATTGGACCCAGAATTATACCGCCACCTTATTTTCTTAAAG

Basic information

species Vitis vinifera
transcript Vv05s0077g00470.t01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 18
-atccattctgttgcttttctgcatgtactcagttgcactaccttctgttgggaattt-taatgaaaatttacttatagaaaatccattattttgttgtcagGCACAACTATTTGAATGATTTGCCTTCATTGGACCCAGAATTATACCGCCACCTTATTTTCTTAAAG
 |           | |  | ||  |  | |  |       |   | |  | ||| | | || |      || ||||   |   |   ||  | |  |  ||||||||||||||||||||| |||||||| ||||||||||||||||| || || || |||||  | |||
aaaaaggaacaaaggtagtatgtgttaagtagggactggaatgctataataggattctgtatttcttgctttctta--aacctttagtttctcttataccagGCACAACTATTTGAATGACTTGCCTTCCTTGGACCCAGAATTATATCGTCATCTCATTTTTCTTAAG

upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA07G36390.1 (Glycine max), 3'ss of exon 18
atccattctgttgcttttct-gcatgtactcagttgc-act---accttctgttgggaattt-taatgaaaatttacttatagaaaatccattattttgttgtcagGCACAACTATTTGAATGATTTGCCTTCATTGGACCCAGAATTATACCGCCACCTTATTTTCTTAAAG
    |    |   |   | | | ||||| | ||| |  |||   |   | |  | ||| | | || |      || ||||   |   |   ||  | |  |  ||||||||||||||||||||| |||||||| || |||||||||||||| || || || |||||  | |||
----aaggaggaacaaatgtagtatgtattaagtagggactggaatgctataataggattctgtatttctcgctttctta--aacctttagtttctcttataccagGCACAACTATTTGAATGACTTGCCTTCCTTAGACCCAGAATTATATCGTCATCTCATTTTTCTTAAG

upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA09G03680.1 (Glycine max), 3'ss of exon 6
atccattctgttgcttttctgcatgtactcagttgcactac-cttctgttgggaattttaatgaaaatttacttatagaaaatccattattttgt---tgtcagGCACAACTATTTGAATGATTTGCCTTCATTGGACCCAGAATTATACCGCCACCTTATTTTCTTAAAG
    ||| ||     |||  | ||| | |       | |   ||  || |   |     |   | | ||      |    | ||  ||  ||      | |||||||||||||||||||||| ||| ||||  |||||||||||||||| || || ||||| ||  |||||
---aattatgactaatttgag-atgcattagagattagtgtgctaatgctataagaggaagctatacttcctcctttcttattctttttcttcccatgtatcagGCACAACTATTTGAATGACTTGTCTTCCCTGGACCCAGAATTATATCGTCATCTTATCTTTCTAAAG

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|71889221|gb|DT038276.1|DT038276
EST:     CTTGTGGATATACCATTTGCAACATTCTTTTTGAGCAAATTAAAACAAAA                         GCACAACTATTTGAATGAT
genomic: CTTGTGGATATACCATTTGCAACATTCTTTTTGAGCAAATTAAAACAAAAgtaaggcttc ... ttgttgtcagGCACAACTATTTGAATGAT
EST: gi|71884176|gb|DT033231.1|DT033231
EST:     CTTGTGGATATACCATTTGCAACATTCTTTTTGAGCAAATTAAAACAAAA                         GCACAACTATTTGAATGATTTG
genomic: CTTGTGGATATACCATTTGCAACATTCTTTTTGAGCAAATTAAAACAAAAgtaaggcttc ... ttgttgtcagGCACAACTATTTGAATGATTTG
EST: gi|71881320|gb|DT030375.1|DT030375
EST:     CTTGTGGATATACCATTTGCAACATTCTTTTTGAGCAAATTAAAACAAAA                         GCACAACTATTTGAATGATTTGCCTTCATTGGACCCAG
genomic: CTTGTGGATATACCATTTGCAACATTCTTTTTGAGCAAATTAAAACAAAAgtaaggcttc ... ttgttgtcagGCACAACTATTTGAATGATTTGCCTTCATTGGACCCAG
EST: gi|110370035|gb|EC934210.1|EC934210
EST:     CTTGTGGATATACCATTTGCAACATTCTTTTTGAGCAAATTAAAACAAAA                         GCACAACTATTTGAATGATTTGCCTTCATTGGACCCAGAATTATACCGCCA
genomic: CTTGTGGATATACCATTTGCAACATTCTTTTTGAGCAAATTAAAACAAAAgtaaggcttc ... ttgttgtcagGCACAACTATTTGAATGATTTGCCTTCATTGGACCCAGAATTATACCGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgggaattttaatgaaaatttacttatagaaaatccattattttgttgtcagGCACAACTATTTGAATGATTTGCCTTCATTGGACCCAGAATTATACCGCCACCTTATTTTCTTAAAG
         ttttaat  putative branch site (score: 3)
                                        ttatttt  putative PPT
       aattttaatgaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atccattctgttgcttttctgcatgtactcagttgcactaccttctgttgggaattttaatgaaaatttacttatagaaaatccattattttgttgtcagGCACAACTATTTGAATGATTTGCCTTCATTGGACCCAGAATTATACCGCCACCTTATTTTCTTAAAG

- ccattct
- - - - - - - - - - gcatgta
- - - - - - - - - - - - - - -cagttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaat