Khdc3 KH domain containing 3, subcortical maternal complex member [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Khdc3provided by MGI
Official Full Name: KH domain containing 3, subcortical maternal complex memberprovided by MGI
Primary source: MGI:MGI:1914241
See related: Ensembl:ENSMUSG00000092622 AllianceGenome:MGI:1914241
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: FILIA; OEEP48; 2410004A20Rik
Summary: Predicted to enable RNA binding activity. Involved in several processes, including positive regulation of dendrite development; positive regulation of double-strand break repair via homologous recombination; and positive regulation of embryonic development. Acts upstream of or within mitotic spindle assembly; mitotic spindle assembly checkpoint signaling; and protein phosphorylation. Located in several cellular components, including apical cortex; centrosome; and mitochondrion. Part of subcortical maternal complex. Is expressed in cranial ganglion; dorsal root ganglion; early conceptus; ovary; and vibrissa. Human ortholog(s) of this gene implicated in gestational trophoblastic neoplasm. Orthologous to human KHDC3L (KH domain containing 3 like, subcortical maternal complex member). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in ovary adult (RPKM 4.8), stomach adult (RPKM 0.3) and 1 other tissue See more
Orthologs: human all
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Genomic context

Location:: 9 D; 9 40.08 cM

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (73008660..73013915)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (73101381..73106631)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

Acute deletion of TET enzymes results in aneuploidy in mouse embryonic stem cells through decreased expression of Khdc3.
Title: Acute deletion of TET enzymes results in aneuploidy in mouse embryonic stem cells through decreased expression of Khdc3.
Genome integrity and neurogenesis of postnatal hippocampal neural stem/progenitor cells require a unique regulator Filia.
Title: Genome integrity and neurogenesis of postnatal hippocampal neural stem/progenitor cells require a unique regulator Filia.
Mouse embryonic stem cells utilize a unique Filia-Floped protein complex-dependent mechanism to efficiently promote the restart of stalled replication forks, therefore maintaining genomic stability.
Title: Mouse embryonic stem cells have increased capacity for replication fork restart driven by the specific Filia-Floped protein complex.
the identification of Filia as a specific regulator of genomic stability in mouse embryonic stem cells, is reported.
Title: Filia Is an ESC-Specific Regulator of DNA Damage Response and Safeguards Genomic Stability.
FILIA is part of the subcortical maternal complex (SCMC). SCMC is required for formation of the cytoplasmic F-actin meshwork that controls the central position of the spindle and ensures symmetric division.
Title: The subcortical maternal complex controls symmetric division of mouse zygotes by regulating F-actin dynamics.
FILIA and FILIA-N could sequester specific RNA components, supporting the critical roles of FILIA in regulation of RNA transcripts during mouse oogenesis and early embryogenesis.
Title: The N-terminus of FILIA forms an atypical KH domain with a unique extension involved in interaction with RNA.
High-quality diffraction data were collected from the two crystal forms of FILIA to resolutions of 1.8 and 2.2 A, respectively, using synchrotron radiation
Title: Preliminary crystallographic analysis of the N-terminal domain of FILIA, a protein essential for embryogenesis.
Filia is central to integrating the spatiotemporal localization of regulators that helps ensure euploidy and high-quality cell cycle progression in preimplantation mouse development.
Title: Role of Filia, a maternal effect gene, in maintaining euploidy during cleavage-stage mouse embryogenesis.
Results describe a subcortical maternal complex, containing Mater, Floped, TLE6, and Filia, that is essential for preimplantation mouse embryogenesis.
Title: A subcortical maternal complex essential for preimplantation mouse embryogenesis.
The plasticity of the FILIA-MATER complex localization may reflect the regulative nature of preimplantation mouse development.
Title: Maternally derived FILIA-MATER complex localizes asymmetrically in cleavage-stage mouse embryos.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Variation

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Alleles

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

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

AI467128 (e-PCR)
- UniSTS:165647

NoName (e-PCR)
- UniSTS:492913

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in actin filament organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell cycle	IEA Inferred from Electronic Annotation more info
involved_in establishment of organelle localization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mitotic spindle assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mitotic spindle assembly checkpoint signaling	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of dendrite development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of double-strand break repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of double-strand break repair via homologous recombination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of double-strand break repair via homologous recombination	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neurogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein localization	ISO Inferred from Sequence Orthology more info
involved_in replication fork processing	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cell cortex	IDA Inferred from Direct Assay more info	PubMed
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	IBA Inferred from Biological aspect of Ancestor more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of subcortical maternal complex	IDA Inferred from Direct Assay more info	PubMed
part_of subcortical maternal complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: KH domain-containing protein 3

Names: protein Filia

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_001311106.1 → NP_001298035.1 KH domain-containing protein 3 isoform 2

See identical proteins and their annotated locations for NP_001298035.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses alternate splice sites in the 3' coding region that result in a frame-shift compared to variant 1. It encodes isoform 2, which is shorter than and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AK010377, AK145595

Consensus CDS

CCDS81036.1

UniProtKB/Swiss-Prot

Q9CWU5

Related

ENSMUSP00000133915.2, ENSMUST00000173734.9

Conserved Domains (1) summary

cd12795
Location:12 → 124

FILIA_N_like; FILIA-N KH-like domain
NM_025890.3 → NP_080166.1 KH domain-containing protein 3 isoform 1

See identical proteins and their annotated locations for NP_080166.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AK010377, AK145595, BY756270

Consensus CDS

CCDS23336.1

UniProtKB/Swiss-Prot

A7YIL2, Q9CRD6, Q9CWU5

Related

ENSMUSP00000034737.7, ENSMUST00000034737.13

Conserved Domains (1) summary

cd12795
Location:12 → 124

FILIA_N_like; FILIA-N KH-like domain

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_000075.7 Reference GRCm39 C57BL/6J

Range

73008660..73013915

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006511374.5 → XP_006511437.1 KH domain-containing protein 3 isoform X2

Conserved Domains (2) summary

PRK10811
Location:122 → 336

rne; ribonuclease E; Reviewed

cd12795
Location:12 → 124

FILIA_N_like; FILIA-N KH-like domain
XM_006511372.5 → XP_006511435.1 KH domain-containing protein 3 isoform X1

Conserved Domains (2) summary

PRK10811
Location:121 → 335

rne; ribonuclease E; Reviewed

cd12795
Location:12 → 118

FILIA_N_like; FILIA-N KH-like domain