HDGFL2 HDGF like 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HDGFL2provided by HGNC
Official Full Name: HDGF like 2provided by HGNC
Primary source: HGNC:HGNC:14680
See related: Ensembl:ENSG00000167674 MIM:617884; AllianceGenome:HGNC:14680
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HRP2; HDGF2; HRP-2; HDGF-2; HDGFRP2
Summary: This gene encodes a member of the hepatoma-derived growth factor (HDGF) family. The protein includes an N-terminal PWWP domain that binds to methyl-lysine-containing histones, with specific binding of this protein to tri-methylated lysines 36 and 79 of histone H3, and di- and tri-methylated lysine 20 of histone H4. The protein functions in LEDGF/p75-independent HIV-1 replication by determining HIV-1 integration site selection. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2014]
Expression: Ubiquitous expression in testis (RPKM 20.4), brain (RPKM 10.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19p13.3

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (4472297..4502207)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (4455746..4485666)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (4472294..4502219)

Chromosome 19 - NC_000019.10 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?

Epigenomic reprogramming via HRP2-MINA dictates response to proteasome inhibitors in multiple myeloma with t(4;14) translocation.
Title: Epigenomic reprogramming via HRP2-MINA dictates response to proteasome inhibitors in multiple myeloma with t(4;14) translocation.
Unlike Its Paralog LEDGF/p75, HRP-2 Is Dispensable for MLL-R Leukemogenesis but Important for Leukemic Cell Survival.
Title: Unlike Its Paralog LEDGF/p75, HRP-2 Is Dispensable for MLL-R Leukemogenesis but Important for Leukemic Cell Survival.
LEDGF and HDGF2 colocalize with Histone H3 lysine 36 methylation 2/3 at genomic regions containing active genes.
Title: LEDGF and HDGF2 relieve the nucleosome-induced barrier to transcription in differentiated cells.
HDGFRP2 promotes DNA repair by homologous recombination.
Title: Hepatoma-derived growth factor-related protein 2 promotes DNA repair by homologous recombination.
HRP-2 is frequently overexpressed in human hepatocellular carcinoma tissues at mRNA and protein levels. HRP-2 can promote hepatocellular carcinoma cells growth in vitro and xenograft tumors in vivo.
Title: HDGF-related protein-2 (HRP-2) acts as an oncogene to promote cell growth in hepatocellular carcinoma.
Authors show that HRP-2 functions as a co-factor of HIV-1 IN in LEDGF/p75-depleted cells.
Title: HRP-2 determines HIV-1 integration site selection in LEDGF/p75 depleted cells.
Here, we show that recombinant HDGF2 host cell factor efficiently reconstitutes the in vitro activity of HIV-1 preintegration complexes.
Title: Biochemical and genetic analyses of integrase-interacting proteins lens epithelium-derived growth factor (LEDGF)/p75 and hepatoma-derived growth factor related protein 2 (HRP2) in preintegration complex function and HIV-1 replication.

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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)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
HIV-1 NL4-3 replication is restricted by HDGFRP2 as enhanced replication was discovered when HDGFRP2 is deleted through CRISPR/Cas9 genome editing in primary CD4+ T cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Vpr	vpr	Hepatoma-derived growth factor 2 (HRP2) restores salt-stripped HIV-1 preintegration complex (PIC) activity in vitro	PubMed
integrase	gag-pol	Hepatoma-derived growth factor 2 (HRP2) restores salt-stripped HIV-1 preintegration complex (PIC) activity in vitro	PubMed
	gag-pol	Knockdown of HRP-2 by siRNA in LEDGF/p75-depleted cells reduces integration frequency in transcription units and shifts the integration distribution towards random	PubMed
	gag-pol	HRP-2 functions as a co-factor of HIV-1 IN in LEDGF/p75-depleted cells. HRP-2 overexpression rescues HIV-1 replication and restored integration in genes to wild-type levels	PubMed
	gag-pol	Hepatoma-derived growth factor-related protein 2 translocates HIV-1 integrase from the cytoplasm to the nucleus where both proteins co-localize	PubMed
matrix	gag	Hepatoma-derived growth factor 2 (HRP2) restores salt-stripped HIV-1 preintegration complex (PIC) activity in vitro	PubMed
reverse transcriptase	gag-pol	Hepatoma-derived growth factor 2 (HRP2) restores salt-stripped HIV-1 preintegration complex (PIC) activity in vitro	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D1S1423 (e-PCR)
- UniSTS:149619

D11S3114 (e-PCR)
- UniSTS:152207

D16S325 (e-PCR)
- UniSTS:147089

RH80135 (e-PCR)
- UniSTS:90516

RH91513 (e-PCR)
- UniSTS:92903

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables H3K27me3 modified histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables H3K27me3 modified histone binding	IDA Inferred from Direct Assay more info	PubMed
enables H3K9me3 modified histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables H3K9me3 modified histone binding	IDA Inferred from Direct Assay more info	PubMed
enables histone reader activity	IDA Inferred from Direct Assay more info	PubMed
enables methylated histone binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA recombination	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA repair-dependent chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in muscle cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in muscle organ development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell growth	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 skeletal muscle tissue regeneration	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity 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 2

Names: HDGF-related protein 2

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_001001520.3 → NP_001001520.1 hepatoma-derived growth factor-related protein 2 isoform 1

See identical proteins and their annotated locations for NP_001001520.1

Status: REVIEWED

Description

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

Source sequence(s)

AF294267

Consensus CDS

CCDS42472.1

UniProtKB/Swiss-Prot

I3L080, K7EQZ6, Q7Z4V5, Q96GI5, Q9BW08

Related

ENSP00000483345.1, ENST00000616600.5

Conserved Domains (2) summary

cd05834
Location:3 → 87

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, ...

pfam11467
Location:472 → 576

LEDGF; Lens epithelium-derived growth factor (LEDGF)
NM_001348169.2 → NP_001335098.1 hepatoma-derived growth factor-related protein 2 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate 5' exon resulting in a novel 5' UTR and 5' coding region compared to variant 1. The encoded isoform (3) has a longer and distinct N-terminus compared to isoform 1.

Source sequence(s)

AC011498, BU738961, KF573697

Conserved Domains (2) summary

PTZ00121
Location:232 → 651

PTZ00121; MAEBL; Provisional

cl02554
Location:49 → 111

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
NM_032631.4 → NP_116020.1 hepatoma-derived growth factor-related protein 2 isoform 2

See identical proteins and their annotated locations for NP_116020.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in an isoform (2) that is 1 aa shorter than isoform 1.

Source sequence(s)

AF294267, AW054790, BC000755

Consensus CDS

CCDS59336.1

UniProtKB/Swiss-Prot

Q7Z4V5

Related

ENSP00000483702.1, ENST00000621835.4

Conserved Domains (3) summary

cd05834
Location:3 → 87

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, ...

pfam11467
Location:472 → 576

LEDGF; Lens epithelium-derived growth factor (LEDGF)

cl26511
Location:208 → 627

Neuromodulin_N; Gap junction protein N-terminal region

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_000019.10 Reference GRCh38.p14 Primary Assembly

Range

4472297..4502207

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047439547.1 → XP_047295503.1 hepatoma-derived growth factor-related protein 2 isoform X3
XM_047439548.1 → XP_047295504.1 hepatoma-derived growth factor-related protein 2 isoform X4
XM_011528377.4 → XP_011526679.1 hepatoma-derived growth factor-related protein 2 isoform X1

Conserved Domains (2) summary

pfam11467
Location:496 → 600

LEDGF; Lens epithelium-derived growth factor (LEDGF)

cl02554
Location:49 → 111

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
XM_011528376.4 → XP_011526678.1 hepatoma-derived growth factor-related protein 2 isoform X2

Conserved Domains (2) summary

pfam11467
Location:495 → 599

LEDGF; Lens epithelium-derived growth factor (LEDGF)

cl02554
Location:49 → 111

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

4455746..4485666

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054322402.1 → XP_054178377.1 hepatoma-derived growth factor-related protein 2 isoform X3
XM_054322403.1 → XP_054178378.1 hepatoma-derived growth factor-related protein 2 isoform X4
XM_054322400.1 → XP_054178375.1 hepatoma-derived growth factor-related protein 2 isoform X1
XM_054322401.1 → XP_054178376.1 hepatoma-derived growth factor-related protein 2 isoform X2