PHF13 PHD finger protein 13 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PHF13provided by HGNC
Official Full Name: PHD finger protein 13provided by HGNC
Primary source: HGNC:HGNC:22983
See related: Ensembl:ENSG00000116273 MIM:620054; AllianceGenome:HGNC:22983
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: PHF5; SPOC1
Summary: Enables chromatin binding activity; chromatin-protein adaptor activity; and methylated histone binding activity. Involved in mitotic chromosome condensation and regulation of DNA repair. Located in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in testis (RPKM 26.3), endometrium (RPKM 8.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p36.31

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (6613731..6624030)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (6139395..6149694)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (6673791..6684090)

Chromosome 1 - NC_000001.11 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?

PHF13 epigenetically activates TGFbeta driven epithelial to mesenchymal transition.
Title: PHF13 epigenetically activates TGFβ driven epithelial to mesenchymal transition.
High SPOC1 expression is associated with Cytomegalovirus infections.
Title: Chromatin-Remodeling Factor SPOC1 Acts as a Cellular Restriction Factor against Human Cytomegalovirus by Repressing the Major Immediate Early Promoter.
PHF13 has opposing effects throughout the HIV-1 replication cycle (figure 8). After viral entry and nuclear import of the PIC, PHF13 can increase the number of integrated HIV-1 proviral genomes. After integration, PHF13 acts as antiviral restriction factor and inhibits viral gene expression.
Title: Dual role of the chromatin-binding factor PHF13 in the pre- and post-integration phases of HIV-1 replication.
These experiments showed that PHF13 binds specifically to DNA and to two types of histone H3 methyl tags (lysine 4-tri-methyl or lysine 4-di-methyl) where it functions as a transcriptional co-regulator.
Title: PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3.
SPOC1-mediated restriction imposed upon Ad growth is relieved by its functional association with the Ad major core protein pVII that enters with the viral genome, followed by E1B-55K/E4orf6-dependent proteasomal degradation of SPOC1.
Title: SPOC1-mediated antiviral host cell response is antagonized early in human adenovirus type 5 infection.
SPOC1 modulates chromatin structure and that tight regulation of its expression levels and subcellular localization during mitosis are crucial for proper chromosome condensation and cell division.
Title: SPOC1: a novel PHD-containing protein modulating chromatin structure and mitotic chromosome condensation.

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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 chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin-protein adaptor activity	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	IDA Inferred from Direct Assay more info	PubMed
enables methylated histone binding	NAS Non-traceable Author Statement 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 chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromosome segregation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic chromosome condensation	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitotic chromosome condensation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA repair	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: PHD finger protein 13

Names: PHD zinc finger protein PHF5; survival time-associated PHD finger protein in ovarian cancer 1; survival time-associated PHD protein in ovarian cancer

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_153812.3 → NP_722519.2 PHD finger protein 13

See identical proteins and their annotated locations for NP_722519.2

Status: VALIDATED

Source sequence(s)

AK097715, AY069975, DB064673

Consensus CDS

CCDS85.1

UniProtKB/Swiss-Prot

B3KUQ7, Q59FB6, Q5TH65, Q86YI8, Q8N551, Q9UJP2

UniProtKB/TrEMBL

A0A158RFV6

Related

ENSP00000366876.4, ENST00000377648.5

Conserved Domains (1) summary

cd15632
Location:232 → 278

PHD_PHF13; PHD finger found in PHD finger protein 13 (PHF13)

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_000001.11 Reference GRCh38.p14 Primary Assembly

Range

6613731..6624030

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011540762.2 → XP_011539064.1 PHD finger protein 13 isoform X1

Conserved Domains (1) summary

cd15632
Location:241 → 287

PHD_PHF13; PHD finger found in PHD finger protein 13 (PHF13)