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    HDDC2 HD domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 51020, updated on 27-Nov-2024

    Summary

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    Official Symbol
    HDDC2provided by HGNC
    Official Full Name
    HD domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:21078
    See related
    Ensembl:ENSG00000111906 AllianceGenome:HGNC:21078
    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
    C6orf74; CGI-130; NS5ATP2; dJ167O5.2
    Summary
    Predicted to enable 5'-deoxynucleotidase activity. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in adrenal (RPKM 20.8), brain (RPKM 17.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HDDC2 in Genome Data Viewer
    Location:
    6q22.31
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (125275350..125301967, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (126463762..126490399, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (125596496..125623113, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901394 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:125444775-125445974 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:125475715-125476302 Neighboring gene TPD52 like 1 Neighboring gene uncharacterized LOC100126584 Neighboring gene MPRA-validated peak6105 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:125583541-125584054 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:125584055-125584568 Neighboring gene uncharacterized LOC124901395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17517 Neighboring gene CRISPRi-validated cis-regulatory element chr6.4553 Neighboring gene CRISPRi-validated cis-regulatory element chr6.4554 Neighboring gene uncharacterized LOC107986640 Neighboring gene uncharacterized LOC102723341 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:125711176-125711724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:125765831-125766344

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Identification of an FMNL2 Interactome by Quantitative Mass Spectrometry. Fox S, et al. Int J Mol Sci, 2024 May 23. PMID 38891874, Free PMC Article
    2. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. Lai CH, et al. Genome Res, 2000 May. PMID 10810093, Free PMC Article
    3. MAP4K Interactome Reveals STRN4 as a Key STRIPAK Complex Component in Hippo Pathway Regulation. Seo G, et al. Cell Rep, 2020 Jul 7. PMID 32640226, Free PMC Article
    4. Alterations in the brain interactome of the intrinsically disordered N-terminal domain of the cellular prion protein (PrPC) in Alzheimer's disease. Ulbrich S, et al. PLoS One, 2018. PMID 29791485, Free PMC Article
    5. Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling. Zhai Y, et al. Nat Commun, 2022 Aug 20. PMID 35987950, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    Submit: New GeneRIF Correction

    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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    Protein interactions

    Protein Gene Interaction Pubs
    integrase gag-pol HIV-1 IN is identified to have a physical interaction with HD domain containing 2 (HDDC2) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses 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

    Homology

    Clone Names

    • MGC87330

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 5'-deoxynucleotidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    5'-deoxynucleotidase HDDC2
    Names
    HCV NS5A-transactivated protein 2
    HD domain-containing protein 2
    hepatitis C virus NS5A-transactivated protein 2
    testicular tissue protein Li 83
    NP_057147.2
    XP_024302218.1
    XP_047274806.1
    XP_054211526.1

    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_016063.3 → NP_057147.2  5'-deoxynucleotidase HDDC2

      See identical proteins and their annotated locations for NP_057147.2

      Status: VALIDATED

      Source sequence(s)
      AL121938, BE743302, BP257644, DB447428
      Consensus CDS
      CCDS43503.1
      UniProtKB/Swiss-Prot
      Q5TDQ4, Q6NZ49, Q7Z4H3, Q9BTT2, Q9BV31, Q9Y3D1
      UniProtKB/TrEMBL
      A0A140VJK7
      Related
      ENSP00000381220.1, ENST00000398153.7
      Conserved Domains (1) summary
      pfam13023
      Location:24 → 183
      HD_3; HD domain

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      125275350..125301967 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024446450.2 → XP_024302218.1  5'-deoxynucleotidase HDDC2 isoform X1

      Conserved Domains (1) summary
      cl21469
      Location:1 → 131
      HDc; Metal dependent phosphohydrolases with conserved 'HD' motif

    2. XM_047418850.1 → XP_047274806.1  5'-deoxynucleotidase HDDC2 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      126463762..126490399 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355551.1 → XP_054211526.1  5'-deoxynucleotidase HDDC2 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z4H3.1 GenPept UniProtKB/Swiss-Prot:Q7Z4H3

    Gene LinkOut

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