Special

MmuINT0103502 @ mm9

Intron Retention

Gene
ENSMUSG00000057003 | Myh4
Description
myosin, heavy polypeptide 4, skeletal muscle [Source:MGI Symbol;Acc:MGI:1339713]
Coordinates
chr11:67054087-67054565:+
Coord C1 exon
chr11:67054087-67054329
Coord A exon
chr11:67054330-67054421
Coord C2 exon
chr11:67054422-67054565
Length
92 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
TATCCTTCCATTCTTAACAGACG
3' ss Score
9.82
Exon sequences
Seq C1 exon
GTGCACCTGGCCCTGAGCTGCCACCAATAGCCCGCAGCCATGAGTTCCGACGCTGAGATGGCCGTTTTCGGGGAGGCTGCTCCTTACCTCCGGAAGTCTGAAAAGGAGCGAATCGAGGCCCAGAACAAGCCTTTTGATGCCAAGTCATCGGTGTTTGTGGTGGATGCTAAGGAGTCCTATGTGAAAGCAACAGTGCAGAGCAGGGAAGGGGGGAAGGTGACAGCCAAGACCGAAGGCGGAGCT
Seq A exon
GTGAGTAAAAGCAAGACGTGGGAGAGGTTGGGAAGCATGAATACTCTTCTGCTAACTAGTTGGCACCAACTGTATCCTTCCATTCTTAACAG
Seq C2 exon
ACGGTCACCGTCAAGGATGATCAAGTCTTCTCCATGAACCCTCCCAAGTACGACAAGATTGAGGACATGGCCATGATGACCCACCTGCACGAGCCCGCTGTGCTGTACAACCTCAAAGAGCGTTATGCAGCCTGGATGATCTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057003-Myh4:NM_010855:2
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=0.191 A=NA C2=0.042
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0236813=Big_2=PU(82.1=94.1),PF0273614=Myosin_N=PU(78.6=48.5)

							
A:
NA

							
C2:
PF0236813=Big_2=PD(15.4=25.0),PF0273614=Myosin_N=PD(16.7=14.6),PF0006316=Myosin_head=PU(4.1=58.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000018632





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000127514, ENSMUSP00000129599
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr17:10369734-10369858 
HsaINT0107781
(MYH4)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr19:30103131-30103229 
Chicken
(galGal4)
chr18:398533-398620 
Chicken
(galGal3)
chr18:401226-401313 
GgaINT0129342
(MYH1)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CGGTGTTTGTGGTGGATGCTA

				
R: 
GGTCATCATGGCCATGTCCTC

				
Band lengths: 
176-268

			

		

	





	
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"