Special

MmuEX6025168 @ mm10

Exon Skipping

Gene
ENSMUSG00000026193 | Fn1
Description
fibronectin 1 [Source:MGI Symbol;Acc:MGI:95566]
Coordinates
chr1:71605885-71608020:-
Coord C1 exon
chr1:71607904-71608020
Coord A exon
chr1:71606703-71606792
Coord C2 exon
chr1:71605885-71606040
Length
90 bp
Sequences
Splice sites
3' ss Seq
CATCAACAACATTAAACCAGGAG
3' ss Score
1.55
5' ss Seq
CAGGTACAA
5' ss Score
7.09
Exon sequences
Seq C1 exon
TTTCTGATATTCCGAGAGATCTGGAGGTCATTGCCTCCACCCCCACCAGCCTGCTCATCAGTTGGGAACCCCCTGCCGTCTCTGTGCGCTATTACAGAATCACCTACGGAGAGACAG
Seq A exon
GAGCAGACTACACCATCACCCTGTATGCTGTCACTGGCCGTGGGGACAGTCCAGCAAGCAGCAAGCCAGTTTCCATCAATTATAAAACAG
Seq C2 exon
AAATTGACAAGCCGTCCCAGATGCAGGTGACAGATGTCCAGGACAACAGCATCAGTGTCAGGTGGCTGCCTTCAACTTCTCCTGTGACAGGCTACAGAGTGACCACCACTCCCAAAAATGGCCTAGGACCATCAAAAACTAAAACTGCCAGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026193-'54-60,'54-59,55-60
Average complexity
S*
Mappability confidence:
100%=100=100%
Protein Impact





	

	
Alternative protein isoforms (Ref)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.050 A=0.643 C2=0.722
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0004116=fn3=PU(45.1=92.5)

							
A:
PF0004116=fn3=PD(53.7=78.6)

							
C2:
PF0004116=fn3=PU(61.7=94.3)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000054499





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000139702, ENSMUSP00000140471, ENSMUSP00000140816, ENSMUSP00000140907, ENSMUSP00000140975, ENSMUSP00000141123
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr2:215384020-215384184 
HIGH PSI
HsaEX6018373
(FN1)
Human
(hg19)
chr2:216248743-216248907 
HIGH PSI
HsaEX6018373
(FN1)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr2:103901692-103901856 
HIGH PSI
BtaEX6011348
(FN1)
Chicken
(galGal4)
chr7:4348697-4348861 
HIGH PSI
GgaEX1066078
(fn1)
Chicken
(galGal3)
chr7:4377102-4377266 
HIGH PSI
GgaEX1066078
(FN1)
Zebrafish
(danRer10)
chr1:4815905-4816078 
HIGH PSI
DreEX0033170
(fn1b)
Zebrafish
(danRer10)
chr9:15406510-15406674 
HIGH PSI
DreEX6035645
(fn1a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTGCTCATCAGTTGGGAACCC

				
R: 
TGGTGGTCACTCTGTAGCCTG

				
Band lengths: 
175-265

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 4 annotated functions for this event 


PMID: 9533887
This event
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: structure based prediction. ELM ID: ELMI000105; ELM sequence: RGD; Overlap: FULL


PMID: 6325925
HsaEX6018373
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: cross linking study, overlapping binding peptide, x-ray crystallography. ELM ID: ELMI000104; ELM sequence: RGD; Overlap: FULL


PMID: 19738201
HsaEX6018373
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: cross linking study, overlapping binding peptide, x-ray crystallography. ELM ID: ELMI000104; ELM sequence: RGD; Overlap: FULL


PMID: 22451694
HsaEX6018373
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: cross linking study, overlapping binding peptide, x-ray crystallography. ELM ID: ELMI000104; ELM sequence: RGD; Overlap: FULL


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • 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"