U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    HDGFL2 HDGF like 2 [ Homo sapiens (human) ]

    Gene ID: 84717, updated on 9-Dec-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See HDGFL2 in Genome Data Viewer
    Location:
    19p13.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (4472297..4502207)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (4455746..4485666)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (4472294..4502219)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4365919-4366840 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4368989-4369938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4369939-4370886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4372431-4373164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4373165-4373898 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr19:4374633-4375365 and GRCh37_chr19:4375366-4376099 Neighboring gene SH3 domain containing GRB2 like 1, endophilin A2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4377567-4378299 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13773 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:4386482-4386982 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4389401-4390008 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4390009-4390615 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4390616-4391224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4394991-4395501 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4399905-4400734 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4402397-4403094 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4403095-4403790 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4408505-4409316 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4409317-4410128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4412803-4413801 Neighboring gene chromatin assembly factor 1 subunit A Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:4430727-4431490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4436676-4437176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4437177-4437677 Neighboring gene Sharpr-MPRA regulatory region 9621 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:4444373-4444541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4453327-4454026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9891 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13774 Neighboring gene microRNA 4746 Neighboring gene UBX domain protein 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9893 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4474209-4475158 Neighboring gene perilipin 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4534387-4534942 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

    Clone Names

    • MGC2641

    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

    Preferred Names
    hepatoma-derived growth factor-related protein 2
    Names
    HDGF-related protein 2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      I3L080, K7EQZ6, Q7Z4V5, Q96GI5, Q9BW08
      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: 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

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      4472297..4502207
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439547.1XP_047295503.1  hepatoma-derived growth factor-related protein 2 isoform X3

    2. XM_047439548.1XP_047295504.1  hepatoma-derived growth factor-related protein 2 isoform X4

    3. XM_011528377.4XP_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 ...
    4. XM_011528376.4XP_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 ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      4455746..4485666
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322402.1XP_054178377.1  hepatoma-derived growth factor-related protein 2 isoform X3

    2. XM_054322403.1XP_054178378.1  hepatoma-derived growth factor-related protein 2 isoform X4

    3. XM_054322400.1XP_054178375.1  hepatoma-derived growth factor-related protein 2 isoform X1

    4. XM_054322401.1XP_054178376.1  hepatoma-derived growth factor-related protein 2 isoform X2