Special

MmuINT0180549 @ mm9

Intron Retention

Gene
ENSMUSG00000042408 | Zmym6
Description
zinc finger, MYM-type 6 [Source:MGI Symbol;Acc:MGI:106505]
Coordinates
chr4:126797672-126801538:+
Coord C1 exon
chr4:126797672-126797816
Coord A exon
chr4:126797817-126799592
Coord C2 exon
chr4:126799593-126801538
Length
1776 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
GATTCACATATTTCCTTTAGATT
3' ss Score
7.04
Exon sequences
Seq C1 exon
GGAAGTGCACAGGCACCTGCTGAGAGACTTCAGCCTCTGCAGCCCCCCAAGCTTCTGAAGAACAAAGGCATATTGTGCAAGCCAGTCACCCAGACCAAGGCCACCTCTTGCAGGCCACATACCCACCATGCTGCATGCCAGACAG
Seq A exon
GTAAGGAAGTGTCCTGGCACCTTGTATAAGCTTTGTTTTCTGCTTTGTTTTATTATGAAAAGGTAAAGGCAGTAATTTTCAGTGTAAAGTATTAATTCCTGGATTATATACTTCAAATCCATATGCATACAAAGTATTATATGTAGAGGTGAACATTTTATATGTGTACACATTACTTTTTCAAATGTATAAATAAGCCATTATAATTACTGATATATATCATATTTGCTTAAAAGCATTACCAGTTGAGCCTTAGTTCATCCAAATTTTTTTTCTTCTTTTCTTCCTTCCTTTCTTTTAAACTCTGCACTTAATTATTTAATTATAGGTTATTGAAATAATAGATAATAGGTCTGGGGTGTTGGTGATAGAAAGTTGAACTCCTACATGGAAAAGCTATAAAGTGTTGCCCCAATCAATGGTAATGCCTTAATCTCATATTCCTTGCATTTTTCAGTTATTTTAGTAGCCGGCTCTGCCCAAGGTGTGTGTGTGTATGTGATGCCGATGTGTCAATTTAGAGCTTTGCATTTTGCCACAGAGCTACAGTCCCAGTTTCTTTTGTTGTTAAGCATAACTTTATTCCATAGACTAACATATAAGTAAAAAACCTAGTCTGTGCCTGGGTGTTATGGTGAGCTACTATAGTCCCAGCTATTTGGGAGAATGAGGCAGAAAAGTCTTGAGTTTAAAGCCATTTTGGGCTGAATAGCAAGAGCCTGTCTCTAAATAAACAAACAGATAAAGCTTACTCTGGTAAAAGTAATATTGACATTTTAATAGGGTTCCTTTCCTTTGGTAGGAGTCAGAGATTTCTTTTTGTTTTGTTTTGTTTTGTTTGTTTGGTTTTTTGTTTTTCGAGACAGGGTTTCTCTGCGTAGCTCTGGCTGTCCTGGAGCTCACTCTGTAGCCCAGGCTGGCCTTGAACTCAGAAATCCACCTGCCTCTGCCTCCCGAGTGCTGGGATCAAAGGTGTGGGCCACCACCACTGCCCGGCCAGAGAATTCTTTCTTCAGGAAACTTGATTGTTTTATATTTCTGTGGAAAATGATACTCTTATCTGCTACATGAACTTCTGAAACCTTTCTTTTCATGTAAACAGTAGTAAAGGGTCTGTGGACATCTGGGATGTTTATGTTTCATTTTCATTTTGTTTTGTATTATTGGGTCTTTGGGTCTTTTTGTTTTTTGAGTTAAGATTTCTCTGTGTAGCCCTGGCTATCGAGGAACTTATTCTGTAGACCAGGCTGGCCTCTAACTCATTAGATATCCACCTGCCTCTGCCTCCTGAGTGCTGGGCTTAGATTCTAGTGTACACAACACAGCCAAACTCCAGGACTGGCCTTAGAGTTTACATGTGGTTGATTTGTCTGTCTTGGTGCTGAGCATTGGCTGCAGGGTGTCACACATCCCAAGTAAAGTGCCCTACCACTGAGCTGTACTCTAGCTCCTAAGTGTTCTTTTCAACGGCTAGATTTGATTTTTTTGGGGGGTGGGGAGGGGGTTTCGAGACAGGATTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGATCAGGCTGGCCTCGAACTCAGAAATCCACCTGCCTCTGCCTCCTGAGTGCTGGGATTAAAGGTGTGCGCCACCACTGCCCACCTAGATTTTAAATTTTCTAGGCAGCATTGGTTCAAGCTGTGTTAATAGATCTTTATCCAGTTTTTCATAACACATTTGTTCATATCATATTATACATGTTCATATTGTAACAGTGATTCACATATTTCCTTTAG
Seq C2 exon
ATTTACCTCTGCCAGAATGGAAGAGTGAAGAACCTGAGTCTCCACCGGCAAAAAGAAGAAGAGTAGACTTTTCCCAGACTTACAATGCAGAGTATATCAGATTCGGTTTCATTATCTGTTCTGGATCAGAGGAAAGTTCACCAAGCCCACAGTGTGTCATTTGTGGAGAGGTCTTACCTAGTGAAAGTGTGATGCCAGTAAGTCTTTCTAACCATTTGAAGGCAAAACATTCAGACTTAGAGAACAAGCCTGTAGACTTTTTTGAGGAAAAGTCACTTGAAATGGAATGTCAAAATAGTTCTTTAAAAAAGTGTTTACTAGTTGAAGAGTCACTTGTGAAAGCTTCTTATTTAATCGCTTTCCAAATTGCCGCCAGGAATAAGCCATTCTCGATTGCTGAAGAATTAATTAAACCATATTTAGTAGAAATGTGTTCAGAAGTTTTAGGTTCAAGTGCTGGAGAAAAAATGAAAACCATCCCTCTTTCTAATAGCACAATTGGGTGCAGGATCAAGAAACTGTCTGATGACATCGAAGATCAGCTGCTGCAGAAGGTCAGGGAGTCCAGGTGGTTTGCCCTTCAGGTGGACGAGTCGTCTGAGGCCACAGAGGTGCCGCTTCTCCTCTGCTATGTCCGCTTCATCGACTATGACCGTGGAGATGTGAAAGAAGAATTACTTTTTTGCACTGAAATGCCTTCTCCGAGCACAGATCTTGAAGTGTTTGAATTAATAAATAAATATATTGATAGCAGATCTCTGAATTGGAACCATTGTGTTGGTTTCTGTACTGATGGGGCCGCAAGCATGACTGACAGGTATTTTCGTTTAAGGTCAAAAATTCAAGAAATTGCCAAGAATACAGTGACATTTACACATTGTTTCATTCACCGTGAACACTTAGCAGCCAAAAAGCTATCTCCATGCTTACATGAAATTCTTTTGCAGTCATCACAAATTTTAAGCTTTGTAAAGAACAGTGCTTCAGATTCACAAATGTTGACAATTTTGTGTGAAGAGATGGGATCTGAGCATGTGAATTTACCACTTAATGCTGAAGTACGCTGGCTGTCGAGAGGGAGAATTTTAACAAGATTATTTGAACTGAGACATGAAATTGAAATATTTTTAAATCAAAAGCATTCAGATTTGGCCAGGTATTTCCATGATGAGGAATGGATTGCAAAGCTAGCCTATCTAGCAGATATATTTTCACTTATAAATAAATTAAATTCAAGTCTCCAAGGAACCATGACTACTTTTTTCAATTTGTATAATAAAGTTGACGTATTTCAGAAAAGGCTAAAAATGTGGTTGAAGCGTGCACAGGAGAATGATTACGGCATGTTCCCTCTGTTTTCTGAGTTCTTGGACTCATCAGATGTAAGTGTGAAAAACATTGCTAGCATCATTTTTGAGCACCTGGAAGGACTTTCTCAGATATTCCATGCCTGTTACCCACCAGAAGAGGACTTGCGTTCCGGAAACCTGTGGCTCACAGATCCTTTTGCCACTTACCACAGTAACAATCTCACTGACTCCGAGGAAGAGAAACTCGCCGTGTTATCTGCCGATACGGGATTTCAGTCAGTTCACAAGTCAATGTCTGTCACACAGTTTTGGGTCAATGCAAAGACAAGTTATCCCAAGCTCCATGAAAAGGCATTGAAGCTGCTGCTGCCCTTCTCAAGCACCTGTCTGTGCGATGCCACCTTTTCAGCCTTGACTGCATCCAAACAGAGAGACCTTCGGACTTGCGGTCCCACCCTAAGACTGGCAGTCACATCATTAGTTCCAAGGATAGAAAAGTTAGCAAAGGAGAAAGAGTAGTATCCGTATTGCTTATCATCAGAGTGTATAATTTTGTGTTAAATTTTGTATAAGTATCCTAAAATACAATTTGCTAATGTATCTGTATTTTCAGTGATTAAATGTTTTAATATTTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042408-Zmym6:NM_177462:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.469 A=NA C2=0.038
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000045366





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000092303, ENSMUSP00000101703
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:34988936-34992233 
ALTERNATIVE
HsaINT0186063
(ZMYM6)
Human
(hg19)
chr1:35454537-35457834 
ALTERNATIVE
HsaINT0186063
(ZMYM6)
Rat
(rn6)
chr5:145182753-145184339 
LOW PSI
RnoINT0169195
(Zmym6)
Cow
(bosTau6)
chr3:111272431-111274313 
ALTERNATIVE
BtaINT0164806
(ZMYM6)
Chicken
(galGal4)
chr23:4308607-4309009 
ALTERNATIVE
GgaINT0137493
([1])
Chicken
(galGal3)
chr23:4678207-4678609 
LOW PSI
GgaINT0137493
([2])
Zebrafish
(danRer10)
chr17:14743394-14743483 
LOW PSI
DreINT0139550
(si:ch211-266o15.1)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCACCTGCTGAGAGACTTCAG

				
R: 
AGAAAGACTTACTGGCATCACACT

				
Band lengths: 
342-2118

			

		

	





	
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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