Special

MmuEX0020088 @ mm10

Exon Skipping

Gene
ENSMUSG00000038860 | Garnl3
Description
GTPase activating RANGAP domain-like 3 [Source:MGI Symbol;Acc:MGI:2139309]
Coordinates
chr2:33064004-33105023:-
Coord C1 exon
chr2:33104853-33105023
Coord A exon
chr2:33085875-33085944
Coord C2 exon
chr2:33064004-33064078
Length
70 bp
Sequences
Splice sites
3' ss Seq
ATGAAGCATTTTTGTTCCAGCTC
3' ss Score
4.98
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
Exon sequences
Seq C1 exon
CACAGCACCTCAGCCTCCAGGCCCACTGATGGATCCACTGACCAAGGGGTCCTGTGGGAGTCAGCTGGCACAAACCCTCCTCTGGAAAGCGAAGTCATCTCTCTCTTTCGGCATCCAGCCCCTTCAGACTTGGCCAACAAAAGATCCTGAACTAGAGTCCCAGGTCAACCT
Seq A exon
CTCTGTCTCAGAAGACCTAGGCTGTAGACGTGGGGATTTCAGTAGGAAGCATTATGGATCTGTGGAGCTG
Seq C2 exon
CTCATCTCTAGTGATGCCGATGGAGCCATCCAAAGGGCAGGAAGATTCCGAGTGGAGAATGGCTCTACAGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038860_MULTIEX3-1/5=C1-2
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact





	

	
ORF disruption upon sequence exclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.242 A=0.017 C2=0.330
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NO

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000119973





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000057582, ENSMUSP00000099874, ENSMUSP00000122576, ENSMUSP00000123601
          









    
Other Skipping Isoforms:
NA
  



Associated events







Other assemblies


mm9




Conservation


Human
(hg38)
chr9:127264952-127265021 
ALTERNATIVE
HsaEX0027034
(GARNL3)
Human
(hg19)
chr9:130027231-130027300 
ALTERNATIVE
HsaEX0027034
(GARNL3)
Rat
(rn6)
chr3:12136894-12136964 
ALTERNATIVE
RnoEX0037765
(Garnl3)
Cow
(bosTau6)
chr11:98028447-98028516 
ALTERNATIVE
BtaEX0015382
(GARNL3)
Chicken
(galGal4)
chr17:10414670-10414739 
HIGH PSI
GgaEX6015689
(GARNL3)
Chicken
(galGal3)
chr17:11145213-11145282 
HIGH PSI
GgaEX6015689
(GARNL3)
Zebrafish
(danRer10)
chr5:32825856-32825925 
HIGH PSI
DreEX0034303
(garnl3)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CAAACCCTCCTCTGGAAAGCG

				
R: 
AGAGCCATTCTCCACTCGGAA

				
Band lengths: 
167-237

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 1 annotated functions for this event 


PMID: 31911676
HsaEX0027034
[CRISPR screen]. Conserved poison exon with negative fitness/survivability impact when depleted: HeLa Depleted at 14 days (FC=0.774, FDR=0.001), PC9 No Change at 14 days (FC=1.238, FDR=0.436), Late Xenograft No change (FC=0.852, FDR=0.023).


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Pre-implantation embryo development
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types





Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"