Special

MmuINT0040470 @ mm9

Intron Retention

Gene
ENSMUSG00000043719 | Col6a6
Description
collagen, type VI, alpha 6 [Source:MGI Symbol;Acc:MGI:2444259]
Coordinates
chr9:105657981-105660519:-
Coord C1 exon
chr9:105660493-105660519
Coord A exon
chr9:105658026-105660492
Coord C2 exon
chr9:105657981-105658025
Length
2467 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATG
5' ss Score
8.73
3' ss Seq
AATCACATCTGTCTCTGCAGGGT
3' ss Score
8.96
Exon sequences
Seq C1 exon
GGAACCAGAGGACTCAGTGGAGAAGAG
Seq A exon
GTAATGGCACCAGGCCCTGCATTTTATTTACCCTTCAGTTATCCAGAAATTCACATCTATCTATCTATCTATTTATTTATTTATTTATTTATTTATTTATTTATTTTTGGTATCAGCTATTTTATTTAAGGTTTTGTTTTGTTTTGTTTTTTGAGATTATTACAGTATTTCTCTCTTCCCTTTCTTCCATCCAAACCCTCTCATATAATGCTCCTCTTTCTCTTTCAAATCCATGGCCTCTTTTTTGTTGTTGTTGTTCATTGTTGTTGCAAGCCTATATGTACATGCATATAAAGACAGCCTGCTCAGTCTGTATAATATTCTTTGTCTATGTGTTTTCAGAGTTGACTGTTTAATGTTGGATGACCAGTTACTATACTCTTCTCTGGGGAACGCTATTTCTCCTGCTTGTATTCTTAGTTGACTATAGTTCTTTGTGTAGGATTGCGGGCTCTTTCCATTCATCCTGACATTTCTATTACTGTTATCCTTGTGTAACTCATGTTTATGGAGTCATGTTGGTGAGATTTTATGAGTGTAGCTTCTGGTGTTACTAGGAGACACAATCTCACAGCAAATCCTCTGATCTCCTGGCTTTCGCAATCCTCCTTTCCCACAATGTTCCTAAGGCCTTAAGTGTTTTGCAGGTGTATCCATTATGTCTGTGCTTCAAAACTCTGTGTTTTGATTGGTTGTGACTTTCTGTAATAGCCTCTGTCTGCTGCCTCTGTCTGTTGCCGCAAGGAAGTTTCTTTGATATGTGGGAGGTGTGAGGAGTACACTTACCTGGGGCACGAGGACAAATGTTTAGAGTATTGTTTGGGAGTTGCTAGATTAGTAAAATTGTGGGTTCTCCACCAAGATCCATGACTTCACTAGCACTGAGAGGCTGCCTAGGTCTCAAGTACCATGTTTTCATTCTTGTTGAGCAGATCTTAAGTACAGTTAGAGAGCTGTTGGTTACCACCAAGGTGTACATGCCACTACTGCGCCCTTAGAATTCTTGTGCCATGCTGGTCATGGTGGCTCATGGGTATCATAGCTGGCAAGGACGTTGGTTGTCTCCCGTCTTTGGAAGCTTACACGGTATGTTCTGGAACCATGAAGGCTAGTCCTCAGGGAGGAGGCATTCAGATCATTCCAGTTCTGCATCTCTGGGCTCTGGGTCTGAGATGGATGGAGTCCTCAGCAATAGGGACTTACCTTCCACCTCTGTGGGGCAGGCAAGGACAATAGCAATAGGCTGTATGTTTCAAGGATCTCCTGGCCAACAATTCAAAAAAGGGCTTCTTATGTCTGGTATTGGACTTATATTTAGGTGGGTTTTGGCTCTCACAGAGACCAGTGTCAGCCCAGATGAGAAAAGTTCACCAAACTATATATTTATATTTATACACTGAGTTACATATATTATAGGATCATTTTGGCAAATAGTTAATAATATTCCTTACAGCCTTAGCAGACATCCTTATTTGTATTTTGCCCACTTTCCTCCTCTTCCTGGATTTCCTTCCCTACCCCTCCCTAAAAAGCCCCCCTTTACCCATTTCCGATATCAGGTACCTTGTGCCCAGCTCTCTTCCTTGCCCTCCTCCTACCTTCTGTATTTGCCTCCTCTCCCCCAAGGATCCCCCTTTCCCATTTCCCTAATCAGATCGCTGAGAGCCTGCTATTGCCCTCCTGTTCCCCAACCTCCCTATCCTGGCAATGTCCCATTTATTCCCCTGGGTTCTGTAGTCACTCCAGGCTATTCACTCACATCTGAAGATTCAGGGTGAGGACCTCCAATGAGAGAGGGCACACAGCATTTGCCTTTCTGGGTCCAGGTTCCCTCCCTCACTAGTCTTTTCTAGCCCTGTCATTTTCCTGTGCAGTTCATGATGACATTTGTCTTTCTAGCTGACTAGTATCCTATAGTGTGTATGTGCCACAGTTTCATTATTTGTCAGCTCTCGGACATTTAGGTTGTTTCCATTTCCTAGCTATTGTGAATAGAGCAGCCCTGAGCATGGCCGAGCTAGTAACTATAGAGTATGATGTCCAGGCCTACCAAGGGGGTGTGGCTGGGTCATATGGTAGATTTTAGTTTTTAGCCTTTTGATAGTTCTCCACGTGGGTTTCCATAGTGACCACAGCAGTTTGCAATCTCAGCAGCAGTGAGTGAGGCTCCCCTTGCCCATCATTCCTTCTGGCGTTTGCTGTCCGTCATTTTGTTGGTATTTGGCATGCTGACTGGGGTACTATGAACTCAAAGTTGTCTTGATTTACATCTTACCTCTGCCTCTCGTTGCCAGACAGGCCTTGTTTATTATGACAGCTTCTATTACTGAAATTAATCTTCAACATTACCCAGGCATCGCCTAACAGAGGCTGTTGCCTGCCGCATAACCCCTGAGACTGTTTTGGGTTTTGGTTGTGGTGTTTCTGACAGATGCGCTCTGTGTTCTAATCACATCTGTCTCTGCAG
Seq C2 exon
GGTGAAGTCGGGGAAGATGGGCTTGATGGATTAGATGGAGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043719-Col6a6:NM_001102607:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0139113=Collagen=PD(3.2=22.2),PF0139113=Collagen=FE(7.8=100)

							
A:
NA

							
C2:
PF0139113=Collagen=FE(13.7=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000096040





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr3:130592723-130593060 
LOW PSI
HsaINT0039588
(COL6A6)
Human
(hg19)
chr3:130311567-130311904 
HsaINT0039588
(COL6A6)
Rat
(rn6)
chr8:114417310-114419796 
ALTERNATIVE
RnoINT0040268
(Col6a6)
Cow
(bosTau6)
chr1:153402111-153402433 
ALTERNATIVE
BtaINT0042234
(COL6A6)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
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"