Special

MmuINT0103196 @ mm9

Intron Retention

Gene
ENSMUSG00000056328 | Myh1
Description
myosin, heavy polypeptide 1, skeletal muscle, adult [Source:MGI Symbol;Acc:MGI:1339711]
Coordinates
chr11:67015344-67015819:+
Coord C1 exon
chr11:67015344-67015587
Coord A exon
chr11:67015588-67015675
Coord C2 exon
chr11:67015676-67015819
Length
88 bp
Sequences
Splice sites
5' ss Seq
ACTGTGAGT
5' ss Score
7.94
3' ss Seq
TATCTCTTGTTTATGGACAGACT
3' ss Score
5.59
Exon sequences
Seq C1 exon
GCAGGCTCTCTCACTGGGCTGCAACCAATAGCCCGCAGCCATGAGTTCCGACGCCGAGATGGCCGTTTTCGGGGAGGCTGCTCCTTACCTCCGGAAGTCTGAAAAGGAGCGAATCGAGGCTCAGAACAAGCCTTTTGACGCCAAGTCATCGGTGTTTGTGGTGGATGCTAAGGAGTCTTTTGTAAAAGCAACGGTGCAGAGCAGGGAAGGGGGGAAGGTGACAGCCAAGACCGAAGGCGGAACT
Seq A exon
GTGAGTAAAAACATCTAGAGCTGGGGACACTACACTGCGGGGCTAGTTTGACTTAGTTCCTAACTTAATATCTCTTGTTTATGGACAG
Seq C2 exon
ACTGTAACAGTAAAAGATGATCAGGTCTACCCCATGAACCCTCCCAAGTACGACAAGATCGAGGACATGGCCATGATGACCCACCTGCATGAGCCCGCTGTGCTGTACAACCTCAAAGAGCGTTATGCAGCCTGGATGATCTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000056328-Myh1:NM_030679:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.235 A=NA C2=0.113
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0236813=Big_2=PU(85.3=94.1),PF027119=Pap_E4=PU(90.3=82.4),PF0273614=Myosin_N=PU(78.6=48.5)

							
A:
NA

							
C2:
PF0236813=Big_2=PD(12.0=18.8),PF0273614=Myosin_N=PD(16.7=14.6),PF0006316=Myosin_head=PU(4.1=58.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000018637





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000075147, ENSMUSP00000115583, ENSMUSP00000117569, ENSMUSP00000131057
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr17:10419660-10419755 
HsaINT0107441
(MYH1)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr19:30132593-30132691 
Chicken
(galGal4)
chr18:448713-448802 
Chicken
(galGal3)
chr18:453994-454083 
GgaINT0127769
([1])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCGAATCGAGGCTCAGAACAA

				
R: 
AGGGTTCATGGGGTAGACCTG

				
Band lengths: 
178-266

			

		

	





	
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"