Special

MmuINT0040455 @ mm9

Intron Retention

Gene
ENSMUSG00000032572 | Col6a4
Description
collagen, type VI, alpha 4 [Source:MGI Symbol;Acc:MGI:1915803]
Coordinates
chr9:105899456-105903226:-
Coord C1 exon
chr9:105902543-105903226
Coord A exon
chr9:105899553-105902542
Coord C2 exon
chr9:105899456-105899552
Length
2990 bp
Sequences
Splice sites
5' ss Seq
ATAGTGAGT
5' ss Score
6.97
3' ss Seq
AAAAATTGTTTTACTTTCAGGTG
3' ss Score
9.19
Exon sequences
Seq C1 exon
ACAAGTGCCGACCAGCCCTGGGGTGCCAGCTGCGTGCTCCTGGGCCTCAGAAGTTGGACATGGACTTGGTATTCCTGGTGGACAGCTCCCAGGGTGTCAGCAGGGACATATACCTTGGGGCTTTGCGGCTAGTGGATTCAGTGCTCAAGGACCTGGAGGTGGCTGCGCAGCCTGGCACATCCTGGCACGGGGCGCGCGCAGCCCTGTTGACACACACAACCCCAGGCTTTTGGCCTGGTGTGGATCAAGCCCCTGTGCTTGAGTACTTCCACCTGACCTCCCACGGCCACCGGACAGAAATGCAAAGGCAGATTCGGGAGGCTGCGAGTGGCCTGCTACAGGGAGGCCCCGCCCTGGGCCACGCCCTGGAGTGGACGCTGGAAAACGTGCTTCTGACAGCCGTACTGCCTCGGAGGTCACGGGTCCTCTATGCCATCGTGGCCAGCGAGACAAGCATCTGGGACAGAGAGAAGCTAAGGACTCTGTCCCAGGAGGCCAAGTGCAAGGGCATCGCATTATTCGTGCTCGCCGTGGGCCCTGGAGTGGGCGCCCAGGAGCTGGCTGAGCTGGCCAAAGTGGCCAGTGCGCCCTGGGAGCAGCACCTGCTACGCCTAGAGGGTGTCTCAGAGGCAGAGGTGGCCTATGCCAGCAGATTCACGGAGGCCTTCCTGAACCTTCTAAATA
Seq A exon
GTGAGTGGCCAAGGGGGTGGGTATGGAAGTGGGTTGGGGGTGTAGGCAGGTGGGGTGGGTAGGGACTGGGTTATCCTAGGTGCTGTTGGCCGCAGATGTTTTTTTTCTAAAACACCTTATTTTATTTTATTTTCAATGTCATTTTATTTGATAGTTGAAAGCCTTTATATTCATTGTTAATTTCATACAGGAAAATAATATATTTAGATCATATCACTCTTCCTGTTTCAACTCTTCTTGAACCTTCCCCCACATCCTCCTCCCAACTTCATTTCCTCCTCCTCCTCCTCTTCCTTCTTCCTCCTCCTCCCCTTCCTCCTCTTTTTTCCCCCTCCTCCTGCTCTTCTTTGCCACTGAGTTCATTTAGTGTTGTCAGTTGGCCGTGGGTTTAGGAACCATGGGCCATTTGCTTTAGGAACATGGGCAACCTACCATGGGGCACACCACAAAAGAAAACCGACTGTCCCTCCCTCCGCAGCTGTCACCTGTATATGGCTGTGTTTCAGGATACCGTTTCCAGCAATCTGCTCCAAATTCCTTGTCATTCTCTCCTCACCCGGTGGCCCCAGGCTTCCACACAGTTTCTCCATTTTTTTTCAGTTATCAAAATGAAAAATTTGGGATGTCTGTTCCCTGATCATTAAACCAGATGTTCATGGAGGGACTCAGCGCCAATACATGGGCGCTGCCGCCACACCCACTGCTCCTTTTCAGCAGTAGATGGCCATGCTTCTCAGATTTTAACTCACACACCCATCCTCTGGGCATCCTGGTCAGGTCTTGATCTAGTTCTGAGGTCTGGGCTGGGGTCTGAGGGTCTCGATTTCTCAACAGCTTCAGAATGACGCTGTTGGCCCACGGACCAAGGGGTTTGTTTGTTTGTTTGTTTTTTAGAGACAAGAGTCTTTCTTTACAGTCCAAGATGCCCTTAAACTGGCTGTAATCCTCCTGCCTCACCACCCTCTCCCCACAAAGTGGTGGGATTGCAGACATGTGCCACCATCTCAGAGTCATGGAACACATTTTAAGTAACAAGGGTAGAGAACTTTGTTCTTCTTTTGTTTACTTATTAAGTCAGCATTCAAAGCAGTGGTCTGATTATGGAACTTTAATACATATGTGTTGTTATACTTTCTCACTTAACCCCCCTCTCCTGCTGCCTCTCTTGAGGAACCACAGCTTCCTCTGGCTGTGCCCTTTCCTTCCCTGACAGCCCTTCTGCTTCCATTCACACACATTACATTCCAACATCCTCTTTTGCCTCCTCTCTTGTGATCTCTTCCTCACTTTTATGATCCTCTTTCTAGTTACATGATGTGCACATGCATATGCATGGGCACACATACATGCACATGTGTGCAGGCATGCACACACATTGCCTCCTTCACCATTTGAGACCTAAGCTCTGTACATTGGAGGAAGCAGGCAGGGTTTTGTCTTATTGCTTTAGAGCACAGGTTGAATTGGCAGCATGAGGTCAGAAGTCCTCAGAGACTTTCCAGGAAGCAAGGGTGACAGGTCAAGAGCTTGGGGTCTCCTTCAGGCGGGGTAGATTAAGCCAATGGTGACGATTAAAGAGTGGGGGCTGTGTCAGTGCATCCAGGCTGGGATTCTCCCCTTCATCCATGCCCCAGCAGCCTCACCTCCTATTACACCCAGATGAACCGAATTCATGAGCATCCAGGACCAAAGTGTACCCCCAACATAATAGTGGTGACTTAGCATAGGGTGGGGGTTTTAGCCTGGCCAATTCCAGGCATTTGTATTGCACTGGGTAATTAAAAATGAACCATGCTCAGGGCATGCTGTGAGGTCTGGGTGCTGCCTCCTCCCCCTCCATGCTGGAAGACATGAGTTCACAGCGGCTATGACGTCCCACTGTGGGTCTTGAGGGACATCTGCTCCTTCCCGACGCAGGAGGTAAAGGGATGCTGATGGACACCTTAGAAGCACTGGCGTGGAGTTTGCACCTTCCCGTTTGACAGATGCTTCATCACTGAGCTAATCTAGTCCTCGCTTTGTTACTCGGGAGCTGTGTGACAGAAAAAGCCACAGGCTTTCTTTCTCTGAGCCTTAGAGAGTAGTGGAGGTGGCTTAGAGCTCAGCGATTCTTTGAGGGAGAAGCTGAAAGACAATCGATTCTCTCATCTGTTTAATGTGGTTTTACTTTATTTTTGAGGTTTTTATTAGATTTGCACTTTATATTTTGTTGTCTTCCTTTATGTTGGGATATTATTTATCTAACAGAATGCGCTTTATGTTTTTGTTTTGCTTGCCTATGATTCAATTTTTATTGTTTTATTTGCATTTATTCTTACATTTGTTTTATGCTTTGTTCTAGTGCCTTTTATGAGTCTTTGATTTTACATCACAGACTTTTTTTTTGTTATTCTTACTGTTCAATTTGCCTCCTTTTTGCATTATTTTATTTTGTTTTATTCTAGATTTTGCCTTAATTTTCTGACTTTTGAGTTTGATGCAGTATTTTTGGCGGTGATGTTAGTGGCATTTTGTTTTCTTTTGTGCTGTTTTTTATTATTTTTTTTTATACACACAAGGTGTGGGGGGTGTCCACTGGAGCATGGATGACTACCAGTGGCCAACGCCCTTAAAGGAAACTGGTTTTTGTCTCCATGCGTACCAACCATCAGTATCTCCTCAGATAGGCATGTGGTTAGTGAGCCTCTTTCCCTCCTGCTAGAATATGGTGCTTCTCTGGTGCAGGTTTCTGGCACACCTACTGTGAGTTTGTGAGTGTGAGTGTAGGAGTGCTACCCTGTCAAGGAGACACTGCTTTGCTGTGCTGATTCCCACCCCTGGCTTCCACAGTCTTTGCATCTCTTCTTTCCTCAAGGTCCCCGAGCACTGCAGGGCTCCCAGTGGTGGTGATTAGATGTCCTGTTTGTGCTGGGCACACCTCGGACACTGTTTGCATTTTGATTATTTTTACATTCTTTATGATTTGATTTTAAAAATTGTTTTACTTTCAG
Seq C2 exon
GTGGAATAAACCAGTATCCACCCCCAGAGCTTGTTAAGGAGTGTGGAGGCCCAAACCGTGGGGACACCTTGCTGCATTTCTTCACTTCTGCCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032572-Col6a4:NM_026763:35
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.004 A=NA C2=0.273
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0009223=VWA=WD(100=82.5)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000035186





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000112472
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr3:130662309-130665002 
ALTERNATIVE
HsaINT0039610
(COL6A6)
Human
(hg19)
chr3:129983328-129985112 
LOW PSI
HsaINT0039532
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr1:153797387-153799109 
LOW PSI
BtaINT0004644
([1])
Chicken
(galGal4)
chr2:42174878-42175912 
GgaINT0094998
([2])
Chicken
(galGal3)
chr2:41594782-41595653 
LOW PSI
GgaINT0094998
([3])
Zebrafish
(danRer10)
chr16:36755805-36757810 
LOW PSI
DreINT0050263
(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"