Special

MmuINT0040458 @ mm9

Intron Retention

Gene
ENSMUSG00000032572 | Col6a4
Description
collagen, type VI, alpha 4 [Source:MGI Symbol;Acc:MGI:1915803]
Coordinates
chr9:105977153-105979790:-
Coord C1 exon
chr9:105979203-105979790
Coord A exon
chr9:105977762-105979202
Coord C2 exon
chr9:105977153-105977761
Length
1441 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGC
5' ss Score
7.31
3' ss Seq
TCTCCTTTCTTTACTTTTAGAGT
3' ss Score
11.44
Exon sequences
Seq C1 exon
CGTGCTCAGAAGCATCCCCGGCTGACATTGTGTTTTTGGTGGACAGTTCAACTAGCATCGGACTCCAGAACTTCCAGAAAGTGAAGCATTTCCTCCACTCTGTTGTCTCGGGGCTCGACGTCAGAAGCGATCAGGTGCAAGTGGGGCTGGTCCAGTACAGTGACAACATTTACCCAGCCTTTCCGCTGAAGCAGTCCTCTCTGAAGAGCGCCGTCCTGGATCGGATCCGGAATCTGCCCTACAGCATGGGGGGCACAAGTACCGGAAGCGCCCTGGAGTTCATCAGGGCCAACTCCTTGACTGAGATGAGTGGCAGCCGTGCCAAGGATGGGGTTCCTCAGATAGTTGTCCTGGTGACAGATGGGGAGTCCAGTGATGAGGTCCAGGATGTGGCTGACCAGCTGAAAAGAGACGGGGTCTTTGTGTTTGTGGTAGGGATCAATATTCAAGATGTCCAAGAGTTGCAGAAAATAGCCAACGAGCCGTTTGAGGAGTTTCTCTTCACCACAGAAAACTTCAGCATCTTGCAGGCGCTCTCAGGAACCCTCCTTCAGGCCCTGTGTTCCACGGTGGAGAGGCAGATGAAAA
Seq A exon
GTAAGCCCCGTTCAATCATCTACCACTGAACTGCAATGTAGCAGTGTGCTTCCGAAGGGGAAGGGTGGCCTATAATCACGGGAGCATCTGGGGATGTCTCCTAGAGGAGAGGAAGTCCGAGCTGGCCTTGAAGGATGAGTAGAGAGCTCATAGGTAGAAAAGAAAAGAGAAGACACGCTGTTGGGTTGTTTAGAAGAAACAGCATGGGCTCTGGGGTAGAGAAGTCATACTTTTAAAATCGTACATCTGCCACTTATCAGTTACTTTCAGATCCAAAGGAAACTCTAATCCCCTGAACTCCAAAAGGCGGTCCACATATCCAGAATGAGCTCAACCTGGACTATAGACAGATTACTGGCAGTTAGATAAAAGCCAGCATTCTCCAGGAATTGGTTCCCATCTGCCAAAATGAGTCATCTCCCTTACCTCTGGCAGAAGGGACAGATGGCTGGCTACTTGTGGCACCTATTCGTGTATCAAAGCTTATGCTGTCCTCCAGACTCCCTCTGTATCATAAGCACCTGTTAAACATTTCAAAGTCCGTGCATCCTAGCCCTTGCCACCCCTCCCCTCCCCTCCCCTCTCTCTGGCTCATGGGCTTCCATTCCCCAGCTACTCGTCCTTCTTATAATCAACTGTTTTTACTTCTCTGTGCTCCGGCTAGTCTATTCACTACCTATCTCCTAGCTCCATGGTCTCACTATCTCCACTATTCTCTCCTACTCTCTGCTTCCATAGCCCCGGGCATGTCAGGTCTGCTGGACATGTCCGGTCTACTTCTTTCTCCCTCTGCTCTGGATTCTTCCAGATGCCTCTAGATATTTTCTCTCTCTTATATCCAGTAGAATCCTTCCCCTTAGCCACACCAACAAAGCAGATCATTTTGGTAGTTATATGAGCATTGGAATGGCTTCACTTCTCTTCAGTATCTTCACCTGCATGAGGGAGACAATATGCTTGTAGAAGAATGACGTATATGGATCAGATGAGACAAAGTGTTTAAAGAGCTGTGGTTCACAGAAGCCACGCATTAGGGGATGCCTTCTCCATTGGAGGAAGATTAAAAAAAAAAAGAGAAGGATAATAAAGAAGCAGGCCAGAAGAGGAGGAAGAGAAGAGAGAGGTAGAGAAGAAAGGAAGAAAGGAAGAAGTGGTAGAGGAAGGAAGGGAGGGAGGGAGGGAAGGAGGGAGGGAGGGAGGGAGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATATTATGCCTGTGACAGAGTCTTATGCAGAGAAAGGGCAAGTCCTGGGTGTACTATTGTGTAAATACACTGGCCATCTCTCTCATCACCCACACCAAACCATGCTTGTACTCTGTTTCTTCACAAGAGCTTAATTTGATTCATCTTTTCCTGTCTTCTCCTCCCATCTCCTTTCTTTACTTTTAG
Seq C2 exon
AGTCTACCAAGACCTACGCAGACGTGGTCTTTCTTATTGACACCTCCCAGGGGACATCACAGGCTAGTTTCCAGTGGATGCAGAATTTCATCTCTAGAATTATTGGCATCCTGGAGGTCGGCCAGGACAAATACCAGATTGGGCTGGCTCAGTATAGCGATCAAGGTCACACTGAGTTTTTGTTCAATACCCACAAGACCCGGAATGAGATGGTCGCACACATCCATGAACTCTTGGTGTTCCAAGGTGGCTCCAGGAAGACTGGCCAAGGCCTTCGGTTTCTTCATCGGACTTTCTTCCAGGAGGCAGCAGGAAGCCGGCTCTTACAGGGTGTCCCTCAGTATGTGGTAGTCATTACTTCAGGGAAATCTGAGGACGAGGTCGGAGAGGTCGCACAGATCCTGAGGAAGAGAGGCGTGGACATCGTGTCTGTGGGCTTGCAGGACTTTGACAGGGCAGAACTGGAGGGGATAGGGCCTGTAGTGCTTGTGTCTGACCTGCAGGGAGAAGATAGAATCAGACAGCTAATGCTGGATGTGAATATGTTCATCCAGGGGAGTCCAAAGCCTCCACGGGTCATGACTGATGTTGCGAAGGACGCTGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032572-Col6a4:NM_026763:4
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=0.010
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0009223=VWA=WD(100=90.9)

							
A:
NA

							
C2:
PF0009223=VWA=WD(100=83.3)

						

					

				








    
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)
chr3:15215569-15216269 
HsaINT0039517
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr1:153434100-153435371 
LOW PSI
BtaINT0042240
(COL6A6)
Chicken
(galGal4)
chr7:4778013-4779053 
LOW PSI
GgaINT0050808
(COL6A3)
Chicken
(galGal3)
chr2:41559508-41559962 
GgaINT0095477
([1])
Zebrafish
(danRer10)
chr16:36722163-36724795 
LOW PSI
DreINT0050248
(col6a6)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTCCAGTGATGAGGTCCAGGA

				
R: 
CTGGTATTTGTCCTGGCCGAC

				
Band lengths: 
358-1799

			

		

	





	
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"