Special

MmuINT0180534 @ mm9

Intron Retention

Gene
ENSMUSG00000042446 | Zmym4
Description
zinc finger, MYM-type 4 [Source:MGI Symbol;Acc:MGI:1915035]
Coordinates
chr4:126588354-126592571:-
Coord C1 exon
chr4:126592316-126592571
Coord A exon
chr4:126588529-126592315
Coord C2 exon
chr4:126588354-126588528
Length
3787 bp
Sequences
Splice sites
5' ss Seq
AAAGTATAG
5' ss Score
-1.06
3' ss Seq
CATCTCTGTTATCATTTTAGAGA
3' ss Score
9.01
Exon sequences
Seq C1 exon
CTCCACAGTTGACTACTGGCTTTCAGCCTTCTCTGGCATCACCTGGCATGAATAAAATGCTTCCTTCAGTTCCAGCCACAGCTGTTCGAGTTTCTTGCTCTGGTTGTAAAAAAATCCTCCAGAAGGGGCAGACTGCTTATCAGAGGAAAGGGTCTACTCAGCTTTTCTGCTCTACCCTGTGCCTCACGGGATACACAGTTCCACCTGCCCGCCCACCGCCTCCCCTCACCAAGAAGACTTGTTCAAGTTGCTCAAA
Seq A exon
GTATAGCAGAGTTCTAAATTATCTTTTGTTTCTTTATTTCTTTTAATGCTTGTTTCTTAACCTGTGTATTATTACTTGCATTTCAACTTTGCTGTAGGTTTTTCTTGTAAAACAAAACAACAGTTAAAAAAAAAAAAAAACATTTAGTGCCCCATGTTGCTGCTTTCCATTTTTCTGGGAAGTACTCAATCTCTTTTAGCTCAACAAGTGATTTTTAAACCAATTCCTTCATATTTTTTAGTTAAGATTTCTTACATTCTACTAGTCTAGCACTGAAGCACTTTTCCAATAATTTTTCTGTGTAGCACACTGGCTGTTCTGGAATTCACTGAGTTACACCAGCCTGGCCTTGAGCTCATCTAGATGAGCCTGGGTCTGCCTCCCGCGTGCTGGGTTTAAAGGTGTGCGCCACGGCCATCCTGCTCTGCATTGTGTATGTACCATGTGTGAGCTTGGTGCCTTCAGGGGCCAGGAGTGGTAATGCATACTGTTAATTCCAACACTTGAGAAGCAGAGGCAGGTGGATCTTTTGAGTAGGAGGTCTACAGAGTGAGTTCCAGGACTGCCAGGGCTACACAGAGAAACCTTCTTGAGGAAAACAAAAAGAACTAAACCAAAGGAACCCCCCACCCACCGTCCCAATTCTGAGTTTATGTAAAGTATTGTTATAGCGAAAGTGACAACTGAGCAACTTTAGCCATTTCACCATGAAGATATACTTTAAAGCATTATATAAGTAAATATACAGTATTACCTGTCAGTGTTAAACAAAAATAATGTAGCAGTATATACTTTGTTGGGTTTACAACTATTAGTCTAATGGATACCTAATATTATTTATTGAATTATTTAATGACCTTAAATTTAGAGAAAAGCTATTAGTATTATAGCTACTAGTATTATGACTTAGGTAAGGTGACTATTAAATTGATTTTCCCGTACTTTTTTGGCTAAATTAATGTACCTAAAGCAGAGTTCTTTATTTCTACTGTTTTGTGATTTTAAAAATGAATACTTAGCTGTATTGTCTAAGCTTTTATATTTTAGTGCATGCACTATTAGGTTACTTTATGATTTGAGTTAGATTGAAAACTATGATTATTTTAGCTTTCTAGCTTGCTGTTTTATTGTGAAAAAGTTTGGATGGTTGATGTAATAGCTTTACTTGTTCATCTTTAACCATCTTAAGAATCAGGGATTTCTGAGACACCACTGATACTTTTTTCCCCATGAGAACCATAGATACATCTATAAAGATTTTTCATTTTTATCAATATAAGCTCACATAATTGTACAGAAATGTATCACCTTTCATGTATATATTCATAATAGTATGCTGATAGGGGAGGTCATGTGCGTACTCTGTATGCACATGTATATAGGTATATGTACATACATGCACATGAATATGAAAGACAGAGGATAACCTTATCCTCAGGAATATCAGGAATGCTATATGCCTTCTTTAAGACTAGACATCACGGGGGCTGGTGAGATGGCTCAGTTGGTAAGAGTACCCGACTGCTCTTCCAAAAGTCCAGAGTTCAAATCCCAGCGACCACATGGTGGCTCACAACCATCTGTAACGAGATCTGACTTCCTCTTCTGGAGTGTCTGAAGACAGCTACAGTGTACTTACATATAATAAATGAATAAATCTTAAAAAAAAAGACTAGACATCACTAATTCATTGACTTGGAGTTTAGCACTTACTCTAGACTGACTGGGATTTGCCTTAGGGATCCTTCTGGCTCTCTTAGGTATCCTCCAGTTTCAAGGATTCTCCTGTCTGGTCTTTTCTAGCATTGGTATTACAAGTGCTTATCACCATACCTGGTTGTCTTTATTTGGGTTCTAGGAATTGAACATAGGTCCTTATGCTGTCAAGGTTATACTTTACTGGCTGAACTGTATCCCAGCTACACCTTTTGGATGGATGGATATATATATATATGTGTGTGTGTATATATATATATATATATACATACACATATATATGTGTGTGTATATGTATATATATGCATATATGTGCACATATATGCACACATATATACATACACACATGTATGTATGTGTATTCGTATATATTACATTTTTGCATATGTATTAATTTTATATACACTTCTTATATTTTTTTTGTCCTTTGGTGGTTATTGCTGAGTTATCTGAAGACACATTATTTTTCTATACATGTCAGAAATAAGTGTTTAAGGGGCTGGAATGGTGACTCAGCAGTTAAGAGTACTTCTTGCTCTTTCAGAGGCCTTTAGTTCCGAGGACCCACATCATGCATCATAACCATTTGTAACTTCAGTTCCAGAGAATCCAATGCCTTCTAGTCTCCTCAGTACCAGGCATGCATATAGAGCATATATGTACCCAGAAGCAGATGTTCTTATAAATAAATCTTTAAAAGGATACCTAAAATTCAATGTTTGTGTTTTTCCCTCATCCATCAGGATTTCCAGTTTCACCTGTTCTCACTATTTTATCCCCTCATTCATTTATTCTTGTGTCCATTTTTTCTCTTTACTTTTCCGTTTCCTCTTTCTGTTACTTGGTAGCACTGTTTATTTACTTGCTTGTCTCCCCCTCCTCCTTCTTTTTTGGCTCTTTCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGAAGATGAAGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGAGCCACCACTGCCCGGTTGGGATTCATTCTTCTTTGTCTTCATTACTGATGCTTACATATTAAATTTTTTAGATGTGGACATCTAGATTTTTTTATAGCGATGCTTAAATATGTATCACACAGGACTAGGTAAATAGCTTATTTATAAAAATGATTGCCTTTTGAGCACGTAAGTTTAGATGCTCAGTACTGGGAAGGCAAAGAGTAGTAGATCCCTGTAGGTCAGTGGGGCACCTACTGTTTACTCTTTGAATTCCAGGTTCAGGGAGACCCTGTCTTGGAGGTTTGTAAGATGATTCAGTGAGTAAAGACTTAGTACCTGAATTCATTCCTGGAAGCCACAAGTTGTCGTCTGACATGCAGACATACAGACATACAAGATAAATAAACATGAAAGAGAAAAAAAGACAGAAAGAACAACACACCCCCCCCCACTGCAATACACACCACAAATGTATACGTGTACACTCACAAATTTAAACAGCTGTACACATGTACACCAACAAATTTAAGTTGCAATCTCTCCTGGGGGCTGGAGAGATTTAGTGGTTGAGAGCATTGATTAGTCTTTCAGAGGACCCTTGTGGTAGCTTATAGCCATCTAACTCCACTTCCAGGTGATTCAACTCCTTCTTCTGTTCCTTGACTGCACCAGAAACCCAAGTGGTGCACGGGCATTCATGTATGCAAAGTACTCATACACATAAAATTACAAATGTTTTTTTTTTTTTAAAGATTTATTTATTTATTTATTATATGTAAGTACACTGTAGCTGTCCTCAGACACTCCAGAAGAGGGAGTCAGATCTCGTTACGGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTTTGGACCTTCGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCCCAAAATTACAAATGTTTTAATTTTAAAAAGTTGCAATGCCCTTTATTATCAGCCTAGTTTTATTTGGTTCCTTTAATATACCAAGAGGGTGGTAAATGTAATATCCTGTGACTAATTTCATCTCTGTTATCATTTTAG
Seq C2 exon
AGACATTTTAAATCCAAAGGATGTGATCAGTGCCCAGTTTGAAAATAGTACCACCAGTAAGGATTTTTGCAGTCAATCATGCTTGTCAACATATGAACTGAAAAAAAAGCCCATTGTTACCATAAACACAAATAGCATTTCAACCAAATGCAGCATGTGCCAGAAGAACGCTGTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042446-Zmym4:NM_001114399:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.202 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF064679=zf-FCS=WD(100=47.7),PF064679=zf-FCS=PU(28.9=15.1)

							
A:
NA

							
C2:
PF064679=zf-FCS=PD(68.9=52.5),PF064679=zf-FCS=PU(40.0=27.1)

						

					

				








    
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)
chr1:35370628-35381258 
ALTERNATIVE
HsaINT0186048
(ZMYM4)
Human
(hg19)
chr1:35836229-35846859 
ALTERNATIVE
HsaINT0186048
(ZMYM4)
Rat
(rn6)
chr5:144924819-144931943 
RnoINT0169182
(Zmym4)
Cow
(bosTau6)
chr3:110974107-110978431 
BtaINT0164789
(ZMYM4)
Chicken
(galGal4)
chr23:4316229-4318032 
ALTERNATIVE
GgaINT0137482
([1])
Chicken
(galGal3)
chr23:4685829-4687632 
LOW PSI
GgaINT0137482
([2])
Zebrafish
(danRer10)
chr19:40490105-40493595 
LOW PSI
DreINT0181048
(zmym4)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
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"