Special

MmuINT0180458 @ mm9

Intron Retention

Gene
ENSMUSG00000043872 | Zmym1
Description
zinc finger, MYM domain containing 1 [Source:MGI Symbol;Acc:MGI:1915560]
Coordinates
chr4:126724338-126727845:-
Coord C1 exon
chr4:126727808-126727845
Coord A exon
chr4:126727151-126727807
Coord C2 exon
chr4:126724338-126727150
Length
657 bp
Sequences
Splice sites
5' ss Seq
AGCGTAAGT
5' ss Score
10.07
3' ss Seq
ATTTTACCATTTGTCCTAAGAAC
3' ss Score
5.05
Exon sequences
Seq C1 exon
GTACACTTTCTTCTCTACCGACAGATGTCATCATGAGC
Seq A exon
GTAAGTTTTATCCTGATTTTTAAAATTAATTAATTTATTTATATGCGTACACCATAGCTGACATCAGACACCCTAGAAGAGGGCATTAGATCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCACTGAGCCATCTCTCTGATTGACCTTTTGTGGGTTTTTGTTGTTGTTGTTGTTTGTTTGTTTGTTTGTTTGTTGGGTTTTTGTTTTGTTTTGTTTTGTTTTCGAGACGGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTTGAACTCACAGAAATCCACCTGCCTCTGCCTCTAGAGTGCTAGGACTAAAGGTGCATGCCACCACGCCCAGCTTCCTTTTGAGTGAATAGTTCTAATCATCTGAGTAATAAAAATATTTCTCTGCTGTTATATACCTAGAGCTCCTTTAAACACTGAATGCTGAATTTAGATGGCAAATAATTATGTTAGTGCTGCTTATAGAGAATCCTATACTATAACTTGTTCATTTTACTGTGTTATTGCAATGGATATGTTTTGATATTTTTATTATTTGAAAACTGCTTAAACAAGTATTATTTTACCATTTGTCCTAAG
Seq C2 exon
AACTCAGCCAGTGAGTCCAGCAGTGGTGTTGGTAATAGTGCGGACCAGCCAGGCCTCCTCCCACCTTGCTCGGTGCTCTGTGAGGACACAGCTGCTCCCGGTGAGGGAGTAGAGAACAACAGTGAGAAATCCATGGAAGGAAATGATAGGCTGTGTCTCTCAAAGTCCACATTAACAGAACAGAACATTAAGACAGAGCCTCCGGGAGAGCCCTGGAGCCCAGCTCTCCAGCATCTGCATCCCAGCCCTGCAGACAATATCGCATTCTGCTATTCTTGCTACTTGTTCTTCCAGAAAAAATTTAGCTGTCGGAGAGAAGCTTTTGCAACCCAAGGAACTGCTGACTGGGAGAAAATGCTGGGAAATTTCAGAAAGCATGAAGAAAGTGACGTGCACTTAAAGTCACTGCAATTTTGGAGGCAATACCAGTTTCTCGATGCTATTCCGTGTGACAATTCATCTGTTTATTCAAAACAGATTGAAGGAAATAAAAAGTACCTAAGGCTCATCATTGAGAACATTTTATTTCTTGGAAAACAGTGCTTGCTGTTAAAAGGAAATGACCAGTCTGTTTCACCCATGAATAAAGGCAGTTTTTTGGAATTGCTAGAACTTAGAGCAAGAGATAGAGGAGAGGTATTTCAGCTCATGAGTTCCCACGTGGACTTCTATAGCAGCACGCTTGTCCAGGAGGAGATTATTGAAATGATAAAGGATGAAATGTTGCAAGACATCGTGAGTGAGATCAACGCCTCCTCAGCCTTTTCAATAATCTGCGAGGAGATAGCTGGTAGTGCCGCTGAGAGACAGCTTTCCGTGTGTGTGAGGTACCCACAAAAGACGCCAAGTGCTGTCTTGGTTAAGGAAAGGTTCCTGGGGTTTGTGACTGCCGAGGAGGTGACTGGGGTCCACGTGCATGGGCGGATCAAAGCTTACCTGCAGCAGGTTGGAGTTGATTTTAATAAAATATGTGGCCAAGCCTATGATAGTGCCACAAATTTTACGGTAAAATTGAATGAAGTTGTAGCAGAATTCAAGAAGGAAGAGCCAAGAGCTCTCTATGTGCATTGTCACGCCCATTTTTTGGAGTTAGCGGTGATTAGCTTCTGTAAGGAGGTGAAGGAGCTCCGCGAGGCACTACACACTCTCTGCTCTTTGTTCAACACAGTTCATGTGTCTGAAGAAATGTTGGCAAGTTTGCAAACCATGTGTAAGCTAAGTCTAAATAAAACTTGTAAGAAACACACGTCACAGTCGTGTTGGCCAGCCCACGACCATTTGCTGCTGGCCGTGACGGACTGCCTTCCGGAGGTCGTTGAGGTGCTGGCGTCAGTGTCACGCCGGTGCGCAGGCACAGCTGTGGCTGCCGAGCTGGAGGACCTGTTGGCCATGGTTACCAAGTTTGAATTTATATTTTGTTTGAAATTTCTTTATCGAGTACTCAGTATCACAGGGATTCTTTCTAGAGAGTTTCAAAGTGAAACTGTTGACATCTTTTCTTTGTTTTCAAAAATAGAAGCAATTTTGGAATGTTTATCTTCTGAAAGGAATGATACATACTTTAAAAATATCTGGGATGGAGCAGATGAAATATGTAAAAAGATAACCAGTAAGGGTTTTGATGTTGAGAAACCCTCTTTTCAAAAAAGAAGAAAAGTTCAAAGAACAGTAGATCCTGGCAACTCAGAGCATATGTTTTTTCCTACTTCAGCAGATGAACAATATAAATTTAATATTTACTACCAAGGTCTGGACACGGTATTAAAACATTTAAAGTTATATTTTTCAGAGTTTGACTATTGTAAAATGAAACAAATTTCAGAGCTGTTACTTAAGTGGAATGAGCCATTAAATGAAGCAACAGCCAAGCACATCCAGGAATTCTATAAGCTTGATGCAGACATCATTCCCGAGCTCCGATTTTACCGGCAGTATGCAGGTTTCAACTTCATCGCAGAGGATGGGTCCTTAAGCTTCATTGACCTAGGCTCTTTGTTTATTCAGCATGCTCTCCACAATAATATTCCTTGTATCACGAAGCTGTTGCATATTGCTTTATCTTGGCCAATTACTTCAGCAAATAATGAGAAGTCATTTTCCACGCTGTCTCATCTTAAAACATACTTACTTCGTACCATGGGACAAGAGAAACTTAGTAGCCTGGCTCTGATAGCTGTTGAGCAGGAACTGGTAAATAAACTGATGGAACCTGAAAGACTGGGGGGAATTGTCGAAAAGTTCATTAGTCAAATGAAAGATACGTGAGACAAACTTGCAACTTTGAGCTTAATTAAAAGAATTCTGTGGTTTTATTAGAATCCTAATGAAGTTTTGTTTGTTGGAGGTTCTTTGAGACAGATAGGGATCTTGCTCTGTAGCCTAGGCTAGTCTTGAATTTGTAAGCTCTTGAGACTGATTGACCCTCTTACCTGACTCTTCTCCTTTAAAGTATTCCAGTTGACGTATTGTGTCGTAGGCACATCTACATTTAATACATTTACTGAGCAACTACTATATGCCAGATAGTATGATATGTGCTGGAGGTATAGCAGAGAATTAGGAGCCTAGAGTCAATTGAACATAGTTTTTTCTAATATAGAAATCTAGTAAGCCTGGCACAGCGGCACACTTTCCTCCAGGACTGTGACTCATTGGTAACATACTTAACGTCCCTAGAATGCATAAGGCCCAGATTCAATTCCCAGTGCCAAGGAAGTCCTGTAATACCATCATAGCTGCTAGTGACCGTGTGCATTGTTAAATAAAATTTTAACTAAAAACCATTGCTGGGAAGAGAATAGTTCTACAGAAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043872-Zmym1:NM_026670:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.154 A=NA C2=0.062
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF142911=DUF4371=WD(100=31.1),PF056999=Dimer_Tnp_hAT=WD(100=11.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000050669





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000101705, ENSMUSP00000101708
  



Associated events






Conservation


Human
(hg38)
chr1:35112131-35112976 
LOW PSI
HsaINT0185971
(ZMYM1)
Human
(hg19)
chr1:35577732-35578577 
LOW PSI
HsaINT0185971
(ZMYM1)
Rat
(rn6)
chr5:145108879-145110079 
ALTERNATIVE
RnoINT0169110
(Zmym1)
Cow
(bosTau6)
chr3:111182450-111183059 
ALTERNATIVE
BtaINT0164718
(ZMYM1)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr23:4678755-4679957 
LOW PSI
GgaINT0137492
([1])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
ACCGACAGATGTCATCATGAGC

				
R: 
TGCAAAAGCTTCTCTCCGACA

				
Band lengths: 
349-1006

			

		

	





	
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"