Special

MmuINT0040429 @ mm9

Intron Retention

Gene
ENSMUSG00000032572 | Col6a4
Description
collagen, type VI, alpha 4 [Source:MGI Symbol;Acc:MGI:1915803]
Coordinates
chr9:105962372-105962800:-
Coord C1 exon
chr9:105962655-105962800
Coord A exon
chr9:105962465-105962654
Coord C2 exon
chr9:105962372-105962464
Length
190 bp
Sequences
Splice sites
5' ss Seq
CTCGTGAGT
5' ss Score
8.41
3' ss Seq
ACACAGGTTCTGTGTTTCAGGAC
3' ss Score
8.1
Exon sequences
Seq C1 exon
GGCTCTCCGGACTGCTGCTCATCGGCCTGGGAGGTGCACATAAGTTAGAAGAGCTGCAGGAGCTGGAGTTTGGCAGAGGGTTTGCCTACAGGCAGCCTCTGAGCTCCAGTCTGCCATCCCTCCCAAGCGTCTTACTGAAGCAACTC
Seq A exon
GTGAGTCCTCTTCCAAAGCTTTGTTTTTCACTTGGTCCTGATGGTGGTAATGGTGGTGATGATGGTGACGACTTTGAAAACTTGTGGAGGGGTGGGATAGGGGGGTGAGGCAGGGGGAGAACTTTGCCTGTCTAGTGTGTAGTGTGACCCAGAAGAAAAAACCACATGTGACACAGGTTCTGTGTTTCAG
Seq C2 exon
GACACAATTGTGGAGAGGACATGCTGTAACATGTATGCCAAATGTTACGGAGACGATGGGATCAGAGGTGAACCTGGGAGTCGAGGGGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032572-Col6a4:NM_026763:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.387
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0139113=Collagen=PU(15.2=51.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000035186





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000112472
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr3:15195063-15195213 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr1:153880126-153880273 
Chicken
(galGal4)
chr2:42152904-42152997 
LOW PSI
GgaINT1001647
([1])
Chicken
(galGal3)
chr2:41572807-41572900 
Zebrafish
(danRer10)
chr9:24120373-24120667 
LOW PSI
DreINT0050200
(col6a3)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTCTCCGGACTGCTGCTCATC

				
R: 
CTCCCCTCGACTCCCAGGTT

				
Band lengths: 
234-424

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Pre-implantation embryo development
  • 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"