HDGFL3 HDGF like 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HDGFL3provided by HGNC
Official Full Name: HDGF like 3provided by HGNC
Primary source: HGNC:HGNC:24937
See related: Ensembl:ENSG00000166503 MIM:616643; AllianceGenome:HGNC:24937
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: HDGF2; HRP-3; HDGF-2; CGI-142; HDGFRP3
Summary: Predicted to enable double-stranded DNA binding activity; microtubule binding activity; and transcription coregulator activity. Predicted to be involved in several processes, including microtubule polymerization; negative regulation of microtubule depolymerization; and neuron projection development. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in testis (RPKM 18.5), brain (RPKM 17.0) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q25.2

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (83112738..83207823, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (80976764..81071906, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (83796505..83876575, complement)

Chromosome 15 - NC_000015.10 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
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?

Bulk RNA-Seq Combined with Single-Cell Transcriptome Sequencing Reveals the Possible Mechanisms by Which HDGFL3 Involves in Prostate Cancer Growth and Metastasis.
Title: Bulk RNA-Seq Combined with Single-Cell Transcriptome Sequencing Reveals the Possible Mechanisms by Which HDGFL3 Involves in Prostate Cancer Growth and Metastasis.
HDGFRP3 interaction with 53BP1 promotes DNA double-strand break repair.
Title: HDGFRP3 interaction with 53BP1 promotes DNA double-strand break repair.
A novel function of HRP-3 in regulating cell cycle progression via the HDAC-E2F1-Cyclin E pathway in lung cancer.
Title: A novel function of HRP-3 in regulating cell cycle progression via the HDAC-E2F1-Cyclin E pathway in lung cancer.
The study observed higher expression levels of HDGFRP3 and ID2 in bipolar disorder (BD) patients who favourably respond to lithium. Both of these genes are involved in neurogenesis, and HDGFRP3 has been suggested to be a neurotrophic factor.
Title: RNA sequencing of bipolar disorder lymphoblastoid cell lines implicates the neurotrophic factor HRP-3 in lithium's clinical efficacy.
HRP3 PWWP is a new family of minor groove-specific DNA-binding proteins
Title: The HRP3 PWWP domain recognizes the minor groove of double-stranded DNA and recruits HRP3 to chromatin.
Glucose deprivation-induced HRP-3 up-regulation potentially plays a major role in protecting hepatocellular carcinoma cells against apoptosis caused by energy pressure.
Title: HRP-3 protects the hepatoma cells from glucose deprivation-induced apoptosis.
Depletion of HRP-3 induces apoptosis of radio- and chemoresistant A549 cells. HRP-3 is essential for regulating reactive oxygen species-dependent, p53-induced cell death.
Title: Depletion of hepatoma-derived growth factor-related protein-3 induces apoptotic sensitization of radioresistant A549 cells via reactive oxygen species-dependent p53 activation.
Hepatoma-derived growth factor-related protein-3 interacts with microtubules and promotes neurite outgrowth in mouse cortical neurons
Title: Hepatoma-derived growth factor-related protein-3 interacts with microtubules and promotes neurite outgrowth in mouse cortical neurons.
LEDGF/p75 and HRP2 IBDs avidly bind HIV-1 Integrase, share a similar domain organization and have an evident evolutionary and likely functional relationship
Title: Identification of an evolutionarily conserved domain in human lens epithelium-derived growth factor/transcriptional co-activator p75 (LEDGF/p75) that binds HIV-1 integrase.

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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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Markers

STS-AA035142 (e-PCR)
- UniSTS:65668

SHGC-35969 (e-PCR)
- UniSTS:63665

RH47317 (e-PCR)
- UniSTS:22749

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables growth factor activity	IEA Inferred from Electronic Annotation more info
enables microtubule binding	ISS Inferred from Sequence or Structural Similarity more info
enables tubulin binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in microtubule polymerization	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of microtubule depolymerization	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron projection development	ISS Inferred from Sequence or Structural Similarity more info
involved_in signal transduction	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
located_in extracellular region	HDA more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay 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: hepatoma-derived growth factor-related protein 3

Names: hepatoma-derived growth factor 2; hepatoma-derived growth factor, related protein 3

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_016073.4 → NP_057157.1 hepatoma-derived growth factor-related protein 3

See identical proteins and their annotated locations for NP_057157.1

Status: VALIDATED

Source sequence(s)

AA725615, AC024270, AC103876, BC015483, BC040554

Consensus CDS

CCDS32314.1

UniProtKB/Swiss-Prot

Q9Y3E1

Related

ENSP00000299633.4, ENST00000299633.7

Conserved Domains (1) summary

cd05834
Location:7 → 91

HDGF_related; The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000015.10 Reference GRCh38.p14 Primary Assembly

Range

83112738..83207823 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006720554.5 → XP_006720617.1 hepatoma-derived growth factor-related protein 3 isoform X1

See identical proteins and their annotated locations for XP_006720617.1

Conserved Domains (1) summary

cd05834
Location:7 → 91

HDGF_related; The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, ...