Special

MmuINT0040459 @ mm9

Intron Retention

Gene
ENSMUSG00000032572 | Col6a4
Description
collagen, type VI, alpha 4 [Source:MGI Symbol;Acc:MGI:1915803]
Coordinates
chr9:105974245-105977761:-
Coord C1 exon
chr9:105977153-105977761
Coord A exon
chr9:105974890-105977152
Coord C2 exon
chr9:105974245-105974889
Length
2263 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
CTGTGTCTTTTGGTTTTCAGAAT
3' ss Score
10.64
Exon sequences
Seq C1 exon
AGTCTACCAAGACCTACGCAGACGTGGTCTTTCTTATTGACACCTCCCAGGGGACATCACAGGCTAGTTTCCAGTGGATGCAGAATTTCATCTCTAGAATTATTGGCATCCTGGAGGTCGGCCAGGACAAATACCAGATTGGGCTGGCTCAGTATAGCGATCAAGGTCACACTGAGTTTTTGTTCAATACCCACAAGACCCGGAATGAGATGGTCGCACACATCCATGAACTCTTGGTGTTCCAAGGTGGCTCCAGGAAGACTGGCCAAGGCCTTCGGTTTCTTCATCGGACTTTCTTCCAGGAGGCAGCAGGAAGCCGGCTCTTACAGGGTGTCCCTCAGTATGTGGTAGTCATTACTTCAGGGAAATCTGAGGACGAGGTCGGAGAGGTCGCACAGATCCTGAGGAAGAGAGGCGTGGACATCGTGTCTGTGGGCTTGCAGGACTTTGACAGGGCAGAACTGGAGGGGATAGGGCCTGTAGTGCTTGTGTCTGACCTGCAGGGAGAAGATAGAATCAGACAGCTAATGCTGGATGTGAATATGTTCATCCAGGGGAGTCCAAAGCCTCCACGGGTCATGACTGATGTTGCGAAGGACGCTGTAGAAG
Seq A exon
GTAAGTAAACCTTGACCTTTGGCTATGTGTGTTACCAGGAAGTCACAGTGCATGAAGAAAACCTCGGGGCCTGGGGGTGTAGTTCAGTTGATAGGATAATTGCCTATCATGCATGAAGGCTTGGGTTTGGCGCCCAGCACCACACATAAGCTGGTGCAACCATGCATGCTTGTAGCCTTAGCACTCTGGGTGCAGAGAGGCAGGAGGAACTGAAGTTCATAAGCCAGCTTCATTAGTTACATACTGTGTTTGATGCCAGCGTCGCTCCTTGAAGCCATGTTATCTTATTTTATTTTCTAAAGGTAGAGGAGGAGGAGGAGGAGGGAGGAGGAGAAAGAGAAGGAGGAGGAGGGAGGAGGAGGAAGAGGAGGAGGAGAAAGAGGAGGAGGAGGAGGGAGGAAGAAATAGTTGGGAAAGAGCAGATGGGGTAGAGGAGGCATTCTGCATCCCTCAGTAGGAAAGACTTTCCCCTGTAGATAGGGAAGAGAAAGCAGACATGGGAATGCCTCAGTCAGACATCTTGAGGTACCCATGGCTACCACTACTATGCTGCTCAAGCCGTCTGTGTCAGTGGTTGGAAGTGATGACTTATCCTCACAGGTCTCGGTTAGCTGTAAAGTCCAGTGATGCCATCTGCTGACCTTAGCTGGGCTTATTAGCAGGTCTGAGGTTTAGCTGGCATTGGCTCTGCTTCTGACGTTATTCAGCCACTCTGAGCCAATTCTCCCTGTGGCAGTTGCGGAGACATAGAGAAATATCCAACTGTATAAGCTCTTTCCATATCTCTCCAGCACCTACTACATACTATTAGTGAGAGTAAGTCATGAGACTGTCAGCATCAGTGGAGGAAGAAAGTATATTGTTTCCACGGACATGAGGAGCAGGGAGTGACTAGTTTTGAATAATAGCCCAAGCTAACACATACCTTTTCTAGATGGACCATCAAGCTTTCATTCTAGTTTATGTGCATGGGTGTTTTGCCACATATGTGTCTGTGTACCACGTGTGTGCCTGGAGCCTGTGGATGCCACAAGAGGAAGTTGGACTGCGGTTACAGATGGCTGAGGGTCACCTGTGGGTACTGGGAATCAAATTTAGATCCTTTGGAAGAGTATCAAGTTCTTTCAACTAATGAGCCATCCTTCCAACCCTCTTGTTTATTTATTTTTATTTATATGTGTATGTACCTGTGTGAGTTTGTGTATACCACATACATGAAGGAGTCCCCAGAGGTCAGAAGAGAGCATCAGGTGATCCCTGGGTCTGGAATTACAGGTGGCTGTGAGCTGTCATGTGGATGTCTGGAACTGAGTCTAGGTCCTCTGTAAGAGCAGGAAGTGCTCTTAAGCACTGAGCCGTGTCTCTAGCCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTTCTTCTTCTTCTTCTTCTTCTTCTTTTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCCTCCTCCTCCTCCTTCTACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCGACCAAGATGACCTTGAACTTGTTACTCTCTGCCTCAGCCTTCCAAGGTCTGGGGTCATAGGCAAGCCTCACTGTGTCTAGTTAGCCCCATATTTGGGGAAAGATTTTCACAAAACTTGCAGAATTTCATTTTGTCTCTGTTGAAATTACATGAAGGGTGGGGGGAAGTGATGAAGTAAAGGATGTTTCAGACCCGTAGAGAGGATTTTGACTCAGAGTCTTCTTGAAGGTAGAAAAATGAAGGAAAAAGCCAGCCAATACCCCAAGCTTCTAAGATTGTTAGACAAATTGGAAGGTGATCTTGGGTGGTTTTATGGTGGGTGTCCATAACTTTTTTTTTTTTGAGAATTTTGGGATAGGCATGAATCTCTTAATGCATTTTGATTTTGATGTCCAAAAGAAAGAAAGAAAGAAAAAAAAAGACTTTCTCTAAATTCTAAAGCACCCAAGTAGAAGTTAGCATAATGTAACTTAAAGCCTTAGACACATTACTGTGGCAGATAGACCATGCCCCAGCAGTACCTTTATATTTGAGTATTTTCTTTATTCCTCCATTCTTAGGCTGGAACTCTCTGTGTCTTTTGGTTTTCAG
Seq C2 exon
AATGTCTAGTTCCCGTTCCAGCCGACCTGGTGTTCCTTGTTGAGGACTTTAGCAGTGCCAGGCAACCCAATTTCCAGCGAGTTGTCCATTTCTTGACGACCACTGTCCACTCTCTCAACATCCATCCTGATACCACAAGAGTCAGCTTGGTCTTTTACAGTGAGAAACCAAGGCTGGAGTTTTCCCTGGATATGTATCAAAGCGCTGCCCAAGTCTTACGCCATCTGGACAGGTTAACTTTCCGAGCAAGAAGAGGAAGGGCGAAGGCAGGTGCTGCTTTAGACTTCCTGAGGAAAGAAGTTTTCCTTCCAGAGAAGGGCAGCCGGCCCCATCGGGGCGTACAGCAGATAGCTGTGGTCATCATAGAAAGTCCTTCTCTAGACAATGTGTCTACACCTGCTTCCTACCTTCGCAGGGCGGGGGTCACCATCTATGCAGCGGGCACCCAGCCTGCCTCTGAGAGTAAGGACCTGGAGAAGATTGTCACATACCCTCCCTGGAAGCACGCCATCCGCCTAGAGTCCTTTCTGCAACTCAGTGTTGTAGGAAACAAACTTAAAAAGAAGCTCTGCCCTGAGATGTTGAGCGGAATGCCTCCTCTGATGAGCTTTATTCCAGAAAGCACACGACAAAGCACACAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032572-Col6a4:NM_026763:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.010 A=NA C2=0.037
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0009223=VWA=WD(100=83.3)

							
A:
NA

							
C2:
PF0009223=VWA=WD(100=83.8)

						

					

				








    
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)
chr3:15212085-15214962 
HsaINT0039517
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr1:153434100-153435371 
LOW PSI
BtaINT0042240
(COL6A6)
Chicken
(galGal4)
chr2:42140649-42141085 
GgaINT1001673
([1])
Chicken
(galGal3)
chr2:41558433-41559474 
GgaINT0095476
([2])
Zebrafish
(danRer10)
chr16:36722163-36724795 
LOW PSI
DreINT0050248
(col6a6)
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"