Special

MmuINT0040490 @ mm9

Intron Retention

Gene
ENSMUSG00000043719 | Col6a6
Description
collagen, type VI, alpha 6 [Source:MGI Symbol;Acc:MGI:2444259]
Coordinates
chr9:105598043-105601662:-
Coord C1 exon
chr9:105600991-105601662
Coord A exon
chr9:105598137-105600990
Coord C2 exon
chr9:105598043-105598136
Length
2854 bp
Sequences
Splice sites
5' ss Seq
GGCGTAAGT
5' ss Score
9.39
3' ss Seq
GGAGCCTTTTCTCTTTCTAGATG
3' ss Score
8.48
Exon sequences
Seq C1 exon
ATCTATGCAAGCCGGATGCTTCGTGTGACCAAGCCAAACCACCCCCCATTCAGTCCTACCTGGACACTGCATTCCTACTGGATGGCTCTCGGCACGTGGGAAGTGCAGAGTTTGAAGACATGAGAGACTTTCTAGAGGCACTGCTAGATCACTTCGAAATCACTTCGGAGCCAGAGACATCTGTCACTGGAGACAGGGTGGCCCTGCTGAGCCATGCCCCCCTCGACTTCCTACCCAACACCCAGAGGAGTCCGGTTAGAACTGAGTTCAACCTAACCAGCTATAGCAGTAAGCGCCTCATGAAGAGACACGTGGATCAGGCAGTCCAGCAGCTGCATGGAGATGCTTTTCTTGGCCATGCCCTCGGGTGGGCACTGGACAACGTCTTTTTAAACACCCCCAATTTGAGACGAAACAAAGTCATATTTGTGATATCTGCTGGGGAAACCAGCCACCTGGATGCGGAAACCTTAAAGAAAGAGTCCCTACGAGCCAAATGTCATGGGTATGCCCTCTTTGTCTTTTCCTTGGGCCCTGACTGGGATGACAAGGAACTGGAAGACCTGGCCAGCCACCCCGTAGACCAGCACTTGATCCAGCTTGGCCGAATTCATAAACCTGACCACGGATACAGTGTGAAGTTTGTGAAGTCTTTTATAAACTCCATCAGGC
Seq A exon
GTAAGTCAGAAAACTGTTCCTGTACATAAGAGCCTGCTCCGTAATTCCCCAGAAGGGCAATGTGCTGGCGTGCATGCTTGGACACCTCTTGTTTGTCTTCAAGGGCATTGCAGGGTCAGAGAGGAAAATATGTAATAATGGATGGTGGAAGGGAGGACACTCTGGTTCCTAAGCATTTAATTTTCTGGCTCATCATATTTTTTTTTTATGCCTCTGGTTCCTATGGAGAAGCAATCATAACAAGCAGCTGTCCACACATCTGTCTGCACAGAGAGGTGTAGTCTGGGGGGTGTGAAATCACAGCCTGGACTCGGGCTCCCTTGCCATGTAACCCTAACAAGCTACCCTTTGGTAAGAGGTTTCTGCAGTTAACACAGAGAGAGAGAGAGAGAAGCCAGAGAAAAACAGAAACAATTCTTGGCTTTGCTTGGACAAGTTCCAAAGTCTGAGCTGGGAGTGTTAAAGAGATATCGTTTTTTATCGGTCAGAATGAAAGGCATGGCTTTGTATAACTTTCTCCCAACTCCATGACCTTGTAGGATTCACTCACGAGAATAACTGTGCCTGTAAGGAGACAAGCATGGGCTGTTTTTCTTGGCTGGGCGTCCTGAGAAATCTGCAGTCCATTTTGGATGCAGCAGGGATGGCCGAGGAGCCGTGTCCAGATATGAGGCTGAAGGCAGACAGGCAGTGGGTAACTATATCTGTTTTCAGAGCCTGCTGACTCTTGTCCAAGGGAGTGCAGATAAGGAGACAGGCATGCACAGGTTGAAGAAGGCATGTGCGAGTGCCTGGCTAATTCCTAAAGCTGTCATCGTATTGAAGAGTGAGGTGGGATGAGCCTGCAGATGTGCTGAGCAGTGCAGAGAGACTGCTGGTGGGGTTGATGGCAAATCCTACTCAGTGTGAGTCTAGGACCAGCACCAACTACCAGCTGGGGCTGGTTAGACGCAGGCTTCAGCCCCACCCGATGATGTATCTTACCCGAGCTCCCAGGATACACATATACAAGGTTTTAGAAACACGGGTATGGGAATAGTGAGCCCCCCAGAGTGAGATTCATTTCCATAGATTCTGGAACTGAAACCCCAAAGAGGAGTTTTGGGCAAGGGGTCACCCTGAAGGAAGTCTTTTATAAGGGTTGACCAAAAGACCACTTGGTAAGTCTCTGGTAAACTCGAAAAGAAGCTTGCTTGATGGCCCACAAGTGTGGGGGAGAGAGGGTAAGACTTGCCCTGAAATTTCCTTCCTGGTATTCCAGAATTCTTCCTGCTCTTCCCTGCCTGGGCATCCAGTCACATGATCAGATGCCAGTCACATGATCAGATGAGGCAGCCCCTCCCTCTTAGGACAAAAGCAGAAATGTTTTAAGCTAAGAGCAGGTGGGACTCACGGGAGACACAGAGAGTGTTCTGAACACTGAGCGTGATACAGCCGCCTACTCCATTTCCAAAGCTGTGATATCTAGAAAGTGCCATCTTTAAAACACAGCTGCAGGAAGTGAATTCTACCACAGGCCCATGGTCATGCCCATTCAACACAGTGTTCATTGCTGATCATCTACTCTGAGCCACTGGCTGCACCAGTGCTAGGCTTAAAGAATAGACTTGGCCAGATGCCCTCTGAAGCTTCGGATGCCTTCAAAGTGTCTGTGACTCATTTGGCGCACGACCACAAAGCAGACAGCAGGACATGGTCCACTTCAGAGCAGCACATTCCCTAAGGGAGGCAAAGCTGCTGAGTCAGCAACCTTCTACATACTGTTCAAATAAGAAAAGAAAACCCCAAGCCAGATCTGGTGGGCCCAGCACACACCTGTAATGTTTGCTTTGGAGAGGCAGAGACAGGAGGATTGCTGTAAGCCAGCCCAAGCCACTTAGTAAGACCCTACCTCAAAACAAAACTCCTATGTAAGACAAAAACCCTGAAGGCCATATGGTAGAGCATACTGCCCTTCTTGTAAGAGCAGTTTTGAACATATGCCCTGTTGTAGTCCAGGACATGCCTGTTAGTTGGAAGAACCTACTCAACCAGCAAGAGGCTCTGTGTGTGTGTGTGTGTGTTTGCGCGCGCGCGCGCGCATGTGTGCATGCATGTGCCACATGTACATGTGTGAGCCAGAGGACAGCCTCAGGTGTCACTCCTCAGGCACCGTCCTTTGGAGACAGAGATTCCCAGTGATGCAGAACTTGTCCAGCAGGCTAGGCTGGCTGGCCAGTATAACCCAGCATCACCAGTAAATCCTATCTTTTTGTCACCTCCCCAGTGCCAGGATTGTAAGTACTTGACACCAGGCCTGGCTTTTCCAGAAAGGTATTTGCTTAACAAATCTTTTTGACTTCACGCTTTCAGGCATGCATAACACATTTAAAAATTTTTCTCTGTTAAAAAAAAAAAGCTTTGCATTTTCAAATGGATTAAAGCATGCTTTATTGTTATGAAAAATTAATACTCTTCCAAATGAAGTGAATCGGTGAATTGAACCCAAAGGCATGTAGTGTGTTGCTAACATAAAGACCATAAAGGGACTACCCTGTTCCCTTCGCACTTGGATATGCCACAAAAACAAAAAATAAACTCTAATGAGCTCCTATCAAAGGCAAGAGCGTTATTAGGACTGCCTGCGTTTCATAATGGCTGACGACGTTAGGAGCTACAGGCATTTTAATGAAAAGTTGTTTGAATTCACCAACATATTCACTAGAGACTTCTTTCCCAAACTTGGTTTGGGGACTTCTCTGGGACATTTCTCATGCCCTGTGACCATCTTTGGATGGACATTGGCAACTGCTGTGGTACTGTACAGAACAGACAGACCAACGGAGAGCTTTATCGGAGCCTTTTCTCTTTCTAG
Seq C2 exon
ATGGGATAAACAAGTATCCACCGGTCAACCTCAAAGCCAAGTGCAACAGACTCGGCTCTAGGGATCTGAAGCCGCCCCCACGCCAGTTTCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043719-Col6a6:NM_001102607:35
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.013 A=NA C2=0.406
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0009223=VWA=WD(100=80.4)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000096040





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr3:130662309-130665002 
ALTERNATIVE
HsaINT0039610
(COL6A6)
Human
(hg19)
chr3:130381153-130383846 
ALTERNATIVE
HsaINT0039610
(COL6A6)
Rat
(rn6)
chr8:114360125-114363035 
LOW PSI
RnoINT0040289
(Col6a6)
Cow
(bosTau6)
chr1:153331650-153335682 
LOW PSI
BtaINT0042255
(COL6A6)
Chicken
(galGal4)
chr2:42174878-42175912 
GgaINT0094998
([1])
Chicken
(galGal3)
chr2:41594782-41595653 
LOW PSI
GgaINT0094998
([2])
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"