Special

MmuINT0174338 @ mm9

Intron Retention

Gene
ENSMUSG00000025082 | Vwa2
Description
von Willebrand factor A domain containing 2 [Source:MGI Symbol;Acc:MGI:2684334]
Coordinates
chr19:56980880-56983873:+
Coord C1 exon
chr19:56980880-56981452
Coord A exon
chr19:56981453-56983321
Coord C2 exon
chr19:56983322-56983873
Length
1869 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
TATTTTGCTTGCTCCTCCAGGCT
3' ss Score
9.21
Exon sequences
Seq C1 exon
CCCCGAAGCTGAGCCTGGAATGCAGAATCGATGTCCTCTTCCTGCTGGACAGTTCTGCAGGCACCACATTGGGGGGCTTCCGGAGGGCCAAGGCCTTTGTCAAGCGCTTTGTGCAGGCCGTGCTGAGGGAGGACTCCCGAGCCCGCGTTGGGATAGCCAGTTATGGCAGGAATCTAATGGTGGCGGTGCCCGTCGGGGAGTACCAGCATGTGCCGGACCTGATCAGGAGCCTTGACAGCATTCCCTTCAGCGGTGGCCCGACCCTAACCGGGAGTGCCTTGCTCCAGGTGGCAGAGCACGGCTTTGGGAGTGCCAGCAGGACTGGTCAGGACAGGCCACGCAGAGTAGTAGTTCTGCTCACTGAATCACGCTCCCAGGATGAGGTGTCTGGGCCAGCAGCTCACGCAAGGGCTCGGGAGCTACTCCTCCTGGGCGTGGGCAGTGAGATCCTGCAGGCGGAGCTGGTGAAGATCACCGGTAGCCCGAAGCATGTGATGGTCCACACAGACCCTCAGGACCTGTTCAGCCAAATCCCAGAGCTGCAGAGGAGGCTATGCAGCCAGCCACGGCCAG
Seq A exon
GTAAAACTCTGCAGCCTAACCTAGGGCTGGCTTGTCAGTAGACAGGTCCGTCTGTCTGTCTTCTTGGCACCACCAGCCATTCTTTCCTTCAGTGCCTGTGCTGGGAACTAGGATCGGGGCCTGAGTGTAGAACTCTGTGGGGACTTCTTGTGAGGACCAGATAAGACAAGCCTAAGCAAGTACACTCAGCATGTCTAAGCGTGCACCTGATTATAGGTACTGTTACTAATCACACTTGATCATTGTTATTAGTCTTAAGGAGTTCTGAGTCAGAGACGTGTATTCTTAGAACACACACATGTACACATGCACACACACACTTGTTGCTGCACACTCGAACACAACCAAAGCGAACATGCTGTGATACCTTCTCTACTTCTCTGCTCATTCTGTTTCCTTTCCTATGAGGCTGAGCTTGTGAGCAGCACTCAGTGGGGAAATGGTAGCCCTGGGACTAAGCAGGGCCATGCAGCGGCTGGGCTAGTACCCGAGATGTCAGAGCTGGAACACATCGGTAAGAGGGCACTTCAGTGCTTCCCTGGGGAGCTAAGTGGAAGAGCCTCATGTGGGACTTAGCATCCCCAAACCGCGTTACTGGCGATGGTCCCCAGAGGTGAGAGTCCCCCTTCTGTAAAATGGTGATGAGGCTTGTCATGCCCCTTGTATCCTGTCCTCTAGGCCAGTCTCCTATGGCAGATATATATATATAACGGACTTGCCAATTGCAGAGAGTTCCATTATGTATCCATCCATTAGGATAGGTCATTGTTGCATTTAACAAACCAAAATCGATACATTGTTACTTAGTACAGTCTACCTTTGCTCAGATTTCCTTAGCTTTTACTTGATGTCTTCCTGTTCCCAACGCCAGAAATTGCCCTCACAGGGGAGTTAGCAGGCCTGTCTCCCCAGGGGGTTGTGGCAGGTTCTCTATTTTCCTTGTGTCCAGTGTGGTTTTTAAAAGCTAACATTATCAGACCACCAGACCCTTTGACTCCGTATTTAAACCATCCCAGTGGCTCTCCATGTGGCTGAAAGAAACCCGAGCCCCTTCCACCAGCTTCTGAGTACTTCCTGTCTGGCTGCTGCTCTCGCACACACTGGAAGACTGAGGAAGCTGCCTCCCTGCTAAGAAGCATCCTGCCTGCCAGTTAGCTTCACCTCTCTCCTCCCCAGGGTTCCCTGAGCACCTTCCTAGTCACATCTTGTCTTGCTGTCCCTTTAGCCCCTTCTTTCCCATGGTGTTGCTGGCTCTATTCCACATTTGTGTTCATTTCCTACCCATATGTCCTAAATCACCACTCCATAGATGGCAGGTATCAGCCTATTTGATATAATAGCAGAGCCCTGTGCACAGTGGGCAGGCACTGCGTGATGTAAGGAGGCAGGCGAAAGTACAGCCGCACCTGCTGCTGTTAGGGCCTTCAAAATCCCATATGCTGGGTCCTTCTTTCAAAGATCAAAGGTGAGTGACCTGGCTTCGCATGGCTTCAGAGCTGCGGCCCAAGGTCACCATTTCTAAGCCAGCAAGGATTTAAAAAAAAGATGAGGGAGGGAGGCTGAGGTCAAGCAGCTCCCACTGACACGTTAGAATTTATAGTTTCAAGCTTAGAAACTACATTCCCTTCGATTGGGACTACAGCACGGCCACCCCCTAGTGGCCATTCTCAGCAGGAAGCTGGGAATGTCATCAGGGCAGCCACTTGTATTCATGTCTATATTCTAAGGAAGGATGAAGTGTGATTGTAAGGAGGGTGGATGCTACATGGGCAGTCAGCACACTGGCTGGCCTGGACTCTGTCCAGCCCAGAACAGCCCTGCTGTACCAGCCAGATCTAGACAAGGGACCTATTTTGCTTGCTCCTCCAG
Seq C2 exon
GCTGCCAGGCACAGTCACTGGACCTGGTCTTCCTGTTGGATGCCTCTGCCTCTGTGGGACGTGAGAACTTTGCCCAAATGCAGAGCTTCATCAGGAAATGCACCCTCCGGTTTGATGTGAATCCTGATGTGACACAGGTTGGCCTGGTGGTATATGGCAGCCGGGTGCAGACTGCCTTCGGGCTAGACACCCATCCCACCCGGGCTGCCGTGTTGCGGGCCATGAGCCAGGCTCCCTACCTAGGGGGTGTGGGTTCTGCTGGTACAGCCTTGCTGCACATTGAGGACAAGGTGATGACGGTCCAGAGGGGTGCCCGCCCCGGTGTCCCCAAGGCCGTGGTGATGCTCACAGGCGGGAGTGGGGCAGAAGATGCAGCTGTCCCTGCCCAGAAGCTGAGAGGCAATGGCATCTCAGTCTTGGTTATGAGCGTGGGAGCCGTCCTCAGGGAGGCAGTACGGAGGCTTGCCGGTCCACGCGACTCCCTGATCCATGTGGCAGCTTACACAGACCTTCCGTACCATCAGGACATGCTCATCGAGTGGCTATGTAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025082-Vwa2:NM_172840:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.073 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0009223=VWA=WD(100=89.6)

							
A:
NA

							
C2:
PF0009223=VWA=WD(100=93.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000026068





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000107219
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr10:114286512-114288937 
ALTERNATIVE
HsaINT0181152
(VWA2)
Human
(hg19)
chr10:116046271-116048696 
ALTERNATIVE
HsaINT0181152
(VWA2)
Rat
(rn6)
chr1:277724974-277727200 
LOW PSI
RnoINT0163998
(Vwa2)
Cow
(bosTau6)
chr26:35041009-35044750 
LOW PSI
BtaINT0160598
(VWA2)
Chicken
(galGal4)
chr6:27280834-27281135 
ALTERNATIVE
GgaINT0044701
(VWA2)
Chicken
(galGal3)
chr6:29207063-29207364 
LOW PSI
GgaINT0044701
(VWA2)
Zebrafish
(danRer10)
chr12:30200224-30202028 
LOW PSI
DreINT0174581
(vwa2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CAAATCCCAGAGCTGCAGAGG

				
R: 
ACCGTCATCACCTTGTCCTCA

				
Band lengths: 
347-2216

			

		

	





	
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"