CENPX centromere protein X [Homo sapiens (human)] - Gene

Summary

Official Symbol: CENPXprovided by HGNC
Official Full Name: centromere protein Xprovided by HGNC
Primary source: HGNC:HGNC:11422
See related: Ensembl:ENSG00000169689 MIM:615128; AllianceGenome:HGNC:11422
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: D9; MHF2; CENP-X; FAAP10; STRA13
Summary: Enables DNA binding activity. Contributes to double-stranded DNA binding activity. Involved in interstrand cross-link repair; replication fork processing; and resolution of meiotic recombination intermediates. Part of chromosome and nucleus. [provided by Alliance of Genome Resources, Oct 2024]
Expression: Ubiquitous expression in prostate (RPKM 17.1), colon (RPKM 14.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q25.3

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (82018703..82022878, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (82885862..82890037, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (79976579..79980754, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

MHF prefers branched DNA over dsDNA because it engages two duplex arms. MHF engages DNA forks or various four-way junctions independent of the junction-site structure. The DNA-binding interface of MHF is important for cellular resistance to DNA damage.
Title: The MHF complex senses branched DNA by binding a pair of crossover DNA duplexes.
The MHF complex, which is a heterotetramer that comprises two MHF1-MHF2 heterodimers, is remodeled by FANCM to favor recognition of branched DNA over dsDNA.
Title: The histone-fold complex MHF is remodeled by FANCM to recognize branched DNA and protect genome stability.
CENPX assembly in living human cells, revealing a window in S phase and G2 in which de novo assembly of the complex from a soluble precursor occurs through a dynamic exchange mechanism.
Title: A CENP-S/X complex assembles at the centromere in S and G2 phases of the human cell cycle.
It discusses current knowledge of the biological roles of CENP-S and CENP-X and how their dual existence may be a common feature of CCAN (constitutive centromere-associated network) proteins.
Title: Emerging roles for centromere-associated proteins in DNA repair and genetic recombination.
A long, positively charged patch exposed on the surface of the (MHF1-MHF2) complex plays a critical role in double-stranded DNA binding to chromatin.
Title: Structural peculiarities of the (MHF1-MHF2)4 octamer provide a long DNA binding patch to anchor the MHF-FANCM complex to chromatin: a solution SAXS study.
MHF1 and MHF2 form a compact tetramer to which FANCM-F binds through a 'dual-V' shaped structure.
Title: The structure of the FANCM-MHF complex reveals physical features for functional assembly.
provide biochemical evidence that MHF1 and MHF2 assemble into a heterodimer that binds DNA and enhances the DNA branch migration activity of FANCM.
Title: MHF1-MHF2, a histone-fold-containing protein complex, participates in the Fanconi anemia pathway via FANCM.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Identification of type 2 diabetes-associated combination of SNPs using support vector machine.
Results identified a centromere protein S (CENP-S)-containing subcomplex that includes the new constitutive kinetochore protein CENP-X [Stra13]
Title: The CENP-S complex is essential for the stable assembly of outer kinetochore structure.
Identification of human and mouse homologs of clone D9 of a murine promyelocyte cell line that was upregulated by retinoic acid.
Title: E3, a hematopoietic-specific transcript directly regulated by the retinoic acid receptor alpha.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in chromosome segregation	NAS Non-traceable Author Statement more info	PubMed
involved_in interstrand cross-link repair	IDA Inferred from Direct Assay more info	PubMed
involved_in kinetochore assembly	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein ubiquitination	TAS Traceable Author Statement more info	PubMed
involved_in replication fork processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in replication fork processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in resolution of meiotic recombination intermediates	IBA Inferred from Biological aspect of Ancestor more info
involved_in resolution of meiotic recombination intermediates	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of FANCM-MHF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of FANCM-MHF complex	IDA Inferred from Direct Assay more info	PubMed
part_of FANCM-MHF complex	IPI Inferred from Physical Interaction more info	PubMed
part_of Fanconi anaemia nuclear complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Fanconi anaemia nuclear complex	IDA Inferred from Direct Assay more info	PubMed
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
part_of inner kinetochore	IPI Inferred from Physical Interaction more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: centromere protein X

Names: FANCM associated histone fold protein 2; FANCM-interacting histone fold protein 2; Fanconi anemia-associated polypeptide of 10 kDa; retinoic acid-inducible gene D9 protein homolog; stimulated by retinoic acid 13 homolog; stimulated by retinoic acid gene 13 protein homolog

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_001271006.2 → NP_001257935.1 centromere protein X isoform 1

See identical proteins and their annotated locations for NP_001257935.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

BQ648002, HY110543

Consensus CDS

CCDS59303.1

UniProtKB/Swiss-Prot

A8MT69, O00281, O00282, Q96DD4, Q96F51

UniProtKB/TrEMBL

J3QR01

Related

ENSP00000376168.3, ENST00000392359.8

Conserved Domains (1) summary

pfam09415
Location:12 → 80

CENP-X; CENP-S associating Centromere protein X
NM_001271007.2 → NP_001257936.1 centromere protein X isoform 3

See identical proteins and their annotated locations for NP_001257936.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an exon in the coding region, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.

Source sequence(s)

AC137723, BC011610

Consensus CDS

CCDS59302.1

UniProtKB/Swiss-Prot

A8MT69

Related

ENSP00000462015.1, ENST00000580435.5

Conserved Domains (1) summary

pfam09415
Location:12 → 56

CENP-X; CENP-S associating Centromere protein X
NM_001330536.2 → NP_001317465.1 centromere protein X isoform 4

Status: VALIDATED

Source sequence(s)

BC011610, CB110145, HY070528, HY092955

Consensus CDS

CCDS82223.1

UniProtKB/TrEMBL

J3QRS1

Related

ENSP00000464357.1, ENST00000584347.1

Conserved Domains (1) summary

pfam09415
Location:12 → 46

CENP-X; CENP-S associating Centromere protein X
NM_144998.4 → NP_659435.2 centromere protein X isoform 2

See identical proteins and their annotated locations for NP_659435.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.

Source sequence(s)

BC009571, BC011610

Consensus CDS

CCDS32772.1

UniProtKB/Swiss-Prot

A8MT69

Related

ENSP00000302951.6, ENST00000306704.10

Conserved Domains (1) summary

pfam09415
Location:12 → 62

CENP-X; CENP-S associating Centromere protein X

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

82018703..82022878 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024450639.2 → XP_024306407.1 centromere protein X isoform X1

Conserved Domains (1) summary

pfam09415
Location:12 → 46

CENP-X; CENP-S associating Centromere protein X