Special

MmuINT0179334 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr13:67884727-67885426:+
Coord C1 exon
chr13:67884727-67884853
Coord A exon
chr13:67884854-67885330
Coord C2 exon
chr13:67885331-67885426
Length
477 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGG
5' ss Score
9.08
3' ss Seq
TTATTCCCCTTTCCAAACAGGTC
3' ss Score
12.02
Exon sequences
Seq C1 exon
AAACTGCTGTCATTCAGAGATGTGGCCATTGATTTCTCTGCAGAGGAGCGTGAATGTCTGGACTCTGCTCAGTGGAATTTGTATAAGGAAGTGATGTTGGAGAATTACAGCCACCTTGTGTTCCTGG
Seq A exon
GTAAGGATCACTTCCATTGTGAACTCTTATTTCACTGTCAAAAGGAACTGCCTCCATTTGTAGGGTAACTCATGTTGGAGAGTTTGTGCCTTCCAACAATGTAGCTCATGTGCCTGCCTTTAAAGAGAAAAAGATGGAATGTGATGGGGCTAAGAAATATTTTAGAGTATGCTTAGCCTGTTTGTGGAGGTATGCACCCTCCATTGTAGTGGCCTTGTTAGTAGCTCGGTAGCAGGAGGCTGGAACACATGTTAGAGAAAATGCCTCATCCTTCTGCGTTAATACTTTTCCTTGTAATGAGGCTCAAGGAATCGCAGGTTGTAAATGACTCCTAAGAATATCATCTTTCAGGAAGTGTGTTAATCATAGAATTTTCTGCAGTTGTTCATAATCTCTTCCCATATATGCATAGAACTAAGTCCAAATGTTAATTTCCAGGAGAAAAGAGCCAAGCATCTTATTCCCCTTTCCAAACAG
Seq C2 exon
GTCTTGCTTTCTCCAAGCCACACCTGATCACATTTCTGGAACGACGACCAGAGCCTTGGAATGTGAAGACACAGGCAAGTGTAGGCACATACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
-Zfp493:NM_028402:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=NA A=NA C2=NA
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
NA

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000132282





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr7:64441861-64442367 
HsaINT0186172
(ZNF117)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr18:60423699-60423988 
Chicken
(galGal4)
chr16:206560-206998 
HIGH PSI
GgaINT1004613
([1])
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGCTGTCATTCAGAGATGTGGC

				
R: 
GGTATGTGCCTACACTTGCCT

				
Band lengths: 
216-693

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • 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"