Smchd1 SMC hinge domain containing 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Smchd1provided by MGI
Official Full Name: SMC hinge domain containing 1provided by MGI
Primary source: MGI:MGI:1921605
See related: Ensembl:ENSMUSG00000024054 AllianceGenome:MGI:1921605
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: MommeD1; mKIAA0650; 4931400A14Rik
Summary: Enables ATP hydrolysis activity and protein homodimerization activity. Acts upstream of or within inactivation of paternal X chromosome by genomic imprinting. Located in Barr body. Is expressed in several structures, including blastocyst and genitourinary system. Human ortholog(s) of this gene implicated in facioscapulohumeral muscular dystrophy 2. Orthologous to human SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 9.1), placenta adult (RPKM 7.4) and 24 other tissues See more
Orthologs: human all
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Genomic context

Location:: 17 E1.3; 17 41.87 cM

Exon count:: 48

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	17	NC_000083.7 (71651484..71782361, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	17	NC_000083.6 (71344489..71475366, complement)

Chromosome 17 - NC_000083.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease.
Title: SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease.
SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice.
Title: SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice.
Maternal SMCHD1 regulates Hox gene expression and patterning in the mouse embryo.
Title: Maternal SMCHD1 regulates Hox gene expression and patterning in the mouse embryo.
Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation.
Title: Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation.
The chromosomal protein SMCHD1 regulates DNA methylation and the 2c-like state of embryonic stem cells by antagonizing TET proteins.
Title: The chromosomal protein SMCHD1 regulates DNA methylation and the 2c-like state of embryonic stem cells by antagonizing TET proteins.
Crystal structure of the hinge domain of Smchd1 reveals its dimerization mode and nucleic acid-binding residues.
Title: Crystal structure of the hinge domain of Smchd1 reveals its dimerization mode and nucleic acid-binding residues.
consistent with a role for SMCHD1 in promoting exit from the EGA1 state
Title: SMCHD1 terminates the first embryonic genome activation event in mouse two-cell embryos and contributes to a transcriptionally repressive state.
our study demonstrates preservation of XCI in arhinia and FSHD2, and implicates SMCHD1 in the regulation of the 3D organization of select autosomal gene clusters
Title: Role of the Chromosome Architectural Factor SMCHD1 in X-Chromosome Inactivation, Gene Regulation, and Disease in Humans.
This work adds Smchd1 to the PRC1 silencing pathway for X chromosome inactivation.
Title: Smchd1 Targeting to the Inactive X Is Dependent on the Xist-HnrnpK-PRC1 Pathway.
data suggest that Smchd1 is able to insulate chromatin, thereby limiting access to other chromatin-modifying proteins
Title: Smchd1 regulates long-range chromatin interactions on the inactive X chromosome and at Hox clusters.

Submit: New GeneRIF Correction See all GeneRIFs (23)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (3) 1 citation
Endonuclease-mediated (3) 1 citation
Gene trapped (1) 1 citation
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW554188 (e-PCR)
- UniSTS:181061

D17Wsu164e (e-PCR), detects polymorphism
- UniSTS:142173

AW549786 (e-PCR)
- UniSTS:209334

ATP5B (e-PCR)
- UniSTS:262101

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IDA Inferred from Direct Assay more info	PubMed
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromosome organization	IEA Inferred from Electronic Annotation more info
involved_in dosage compensation by inactivation of X chromosome	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within inactivation of paternal X chromosome by genomic imprinting	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of double-strand break repair via homologous recombination	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of double-strand break repair via homologous recombination	ISS Inferred from Sequence or Structural Similarity more info
involved_in nose development	ISO Inferred from Sequence Orthology more info
involved_in nose development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA repair	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of double-strand break repair via nonhomologous end joining	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of double-strand break repair via nonhomologous end joining	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in Barr body	IBA Inferred from Biological aspect of Ancestor more info
located_in Barr body	IDA Inferred from Direct Assay more info	PubMed
located_in Barr body	ISO Inferred from Sequence Orthology more info
located_in chromosome, telomeric region	IEA Inferred from Electronic Annotation more info
colocalizes_with chromosome, telomeric region	ISO Inferred from Sequence Orthology more info
located_in site of double-strand break	ISO Inferred from Sequence Orthology more info
located_in site of double-strand break	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: structural maintenance of chromosomes flexible hinge domain-containing protein 1

Names: SMC hinge domain-containing protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_028887.4 → NP_083163.3 structural maintenance of chromosomes flexible hinge domain-containing protein 1

See identical proteins and their annotated locations for NP_083163.3

Status: VALIDATED

Source sequence(s)

AC107664, AC126942

Consensus CDS

CCDS28958.2

UniProtKB/Swiss-Prot

Q6P5D8, Q6PDM8, Q6PE93, Q6ZQ78, Q811H3, Q8BP09, Q9D4M7

Related

ENSMUSP00000121835.2, ENSMUST00000127430.2

Conserved Domains (2) summary

smart00968
Location:1721 → 1847

SMC_hinge; SMC proteins Flexible Hinge Domain

cl00075
Location:143 → 275

HATPase_c; Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000083.7 Reference GRCm39 C57BL/6J

Range

71651484..71782361 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030250119.1 → XP_030105979.1 structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X1

Conserved Domains (2) summary

smart00968
Location:1470 → 1596

SMC_hinge; SMC proteins Flexible Hinge Domain

COG1196
Location:1368 → 1709

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]