Special

MmuINT0180523 @ mm9

Intron Retention

Gene
ENSMUSG00000042446 | Zmym4
Description
zinc finger, MYM-type 4 [Source:MGI Symbol;Acc:MGI:1915035]
Coordinates
chr4:126566759-126567419:-
Coord C1 exon
chr4:126567240-126567419
Coord A exon
chr4:126566854-126567239
Coord C2 exon
chr4:126566759-126566853
Length
386 bp
Sequences
Splice sites
5' ss Seq
CAGGTTTGT
5' ss Score
7.44
3' ss Seq
CTTTCTGCTGCTTTTTTCAGAAT
3' ss Score
10.86
Exon sequences
Seq C1 exon
ACCAAGGAAGTACATATAGTGGTGATCTTGAGTCAGAAGCAGTATCAACTCCACACAGCTGGGAAGAAGAGCTGAATCATTACGCATTAAAGTCGAATGCTGTGCAAGATGCTGATTCAGAACTGAAACCGTTTTCAAAAGGGGAAACAGAGCAGGATCTGGAGGCAGACTTCCCATCAG
Seq A exon
GTTTGTACCTCATAGACGGCTGAAGGTCGTCATAGACGGCTGAAGTCAGAAGATTGGGAGAGCTCCAAGTTTGCAGGGTTAAACGGTGTGAAGTGTTCGGGAGTCTTCTGCCTTTATAAATGTGAATATCTGTTGCAAGGTTCTTGTAAGTGGTTAATTTTATTGTTTGCAATTTTTAATGACCTTTTCAACAGTAACTATTTACGGATGGTTTCCTTGCTAACTGCCGTTTCATTCATGTGTTAAAATCCGTTGTGCATCTTAACTATATAAGCGGAGGTCTTTATCACGGAGACTGGACTGATGATTACTGATACTAGTCTTATGAGCTCTCTTAAGTCTGTGTGTTACATACCTCACACTGGGCTTTCTGCTGCTTTTTTCAG
Seq C2 exon
AATCTTTTGACCCACTTAATAAAGGACAGGGGATCCAGGCACGTTCTCGAACAAGACGAAGACACAGAGATGGATTCCCCCAGCCCAGACGGCGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042446-Zmym4:NM_001114399:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.896 A=NA C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000101714





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000030630, ENSMUSP00000120813
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:35399044-35399481 
ALTERNATIVE
HsaINT0186036
(ZMYM4)
Human
(hg19)
chr1:35864645-35865082 
ALTERNATIVE
HsaINT0186036
(ZMYM4)
Rat
(rn6)
chr5:144904320-144904718 
LOW PSI
RnoINT0169170
(Zmym4)
Cow
(bosTau6)
chr3:110946091-110946499 
LOW PSI
BtaINT0164779
(ZMYM4)
Chicken
(galGal4)
chr23:4306480-4306988 
ALTERNATIVE
GgaINT0137497
([1])
Chicken
(galGal3)
chr23:4676080-4676588 
LOW PSI
GgaINT0137497
([2])
Zebrafish
(danRer10)
chr19:40514925-40515242 
LOW PSI
DreINT0181037
(zmym4)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
ACCAAGGAAGTACATATAGTGGTGA

				
R: 
GTCTGGGCTGGGGGAATCC

				
Band lengths: 
270-656

			

		

	





	
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






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