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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgaattctctttgtgtatgcaatgattgatcaaatgaagttctttattataactgtcctaggaaatatatcatgtctcctttctgtttgtctggacagCGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTAGAGGATCAGAATGTAAAGCGTAGGAGGGAGCGCTACCAGAAGCAGTCCTCCCTCCTTTCAAAA

Basic information

species Vitis vinifera
transcript Vv18s0089g00350.t01
intron # 20
splice site 3'
intron type U2

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|33402994|gb|CF208621.1|CF208621
EST:     GTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG                         CGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTAGAGGATCAGAATGT
genomic: GTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAGgtaaagagat ... gtctggacagCGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTAGAGGATCAGAATGT
EST: gi|34364107|gb|CF405692.1|CF405692
EST:     GTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG                         CGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTAGAGGATCAGAATGT
genomic: GTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAGgtaaagagat ... gtctggacagCGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTAGAGGATCAGAATGT
EST: gi|30251129|gb|CB968862.1|CB968862
EST:     GTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG                         CGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTAGAGGATCAGAATGT
genomic: GTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAGgtaaagagat ... gtctggacagCGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTAGAGGATCAGAATGT
EST: gi|161714373|gb|FC063214.1|FC063214
EST:     GTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG                         CGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTA
genomic: GTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAGgtaaagagat ... gtctggacagCGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTA
EST: gi|37185438|gb|CF604791.1|CF604791
EST:     GTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG                         CGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTAGAGGATCAGAATGT
genomic: GTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAGgtaaagagat ... gtctggacagCGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTAGAGGATCAGAATGT
EST: gi|34364376|gb|CF405961.1|CF405961
EST:     GTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG                         CGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTAGAGGATCAGAATGT
genomic: GTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAGgtaaagagat ... gtctggacagCGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTAGAGGATCAGAATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattataactgtcctaggaaatatatcatgtctcctttctgtttgtctggacagCGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTAGAGGATCAGAATGTAAAGCGTAGGAGGGAGCGCTACCAGAAGCAGTCCTCCCTCCTTTCAAAA
   ttataac  putative branch site (score: 2)
                               tctcctttctgtttgt  putative PPT
                   aaatatatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgaattctctttgtgtatgcaatgattgatcaaatgaagttctttattataactgtcctaggaaatatatcatgtctcctttctgtttgtctggacagCGCACAAAGCACAGCAAGGATCGAAGAGCTCCTTCTAGAGGATCAGAATGTAAAGCGTAGGAGGGAGCGCTACCAGAAGCAGTCCTCCCTCCTTTCAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
catgaat
- - - - - - - - gtatgca
- - - - - - - - - - - - - - - - -aaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaata