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HDGFL2 HDGF like 2 [ Homo sapiens (human) ]

Gene ID: 84717, updated on 5-Jan-2022

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
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
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Genomic context

See HDGFL2 in Genome Data Viewer
Location:
19p13.3
Exon count:
17
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (4472297..4502220)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (4472294..4502219)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985297 Neighboring gene chromatin assembly factor 1 subunit A Neighboring gene microRNA 4746 Neighboring gene UBX domain protein 6 Neighboring gene perilipin 4 Neighboring gene perilipin 5 Neighboring gene leucine rich alpha-2-glycoprotein 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC2641

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables H3K27me3 modified histone binding IDA
Inferred from Direct Assay
more info
PubMed 
enables H3K9me3 modified histone binding IDA
Inferred from Direct Assay
more info
PubMed 
enables double-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
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 
enables transcription coregulator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

  1. NM_001001520.3NP_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
    Q7Z4V5
    Related
    ENSP00000483345.1, ENST00000616600.5
    Conserved Domains (2) summary
    cd05834
    Location:387
    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:472576
    LEDGF; Lens epithelium-derived growth factor (LEDGF)
  2. NM_001348169.2NP_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:232651
    PTZ00121; MAEBL; Provisional
    cl02554
    Location:49111
    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 ...
  3. NM_032631.4NP_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:387
    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:472576
    LEDGF; Lens epithelium-derived growth factor (LEDGF)
    cl26511
    Location:208627
    Neuromodulin_N; Gap junction protein N-terminal region

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    4472297..4502220
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011528377.3XP_011526679.1  hepatoma-derived growth factor-related protein 2 isoform X1

    Conserved Domains (2) summary
    pfam11467
    Location:496600
    LEDGF; Lens epithelium-derived growth factor (LEDGF)
    cl02554
    Location:49111
    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 ...
  2. XM_011528376.3XP_011526678.1  hepatoma-derived growth factor-related protein 2 isoform X2

    Conserved Domains (2) summary
    pfam11467
    Location:495599
    LEDGF; Lens epithelium-derived growth factor (LEDGF)
    cl02554
    Location:49111
    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 ...
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