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    HDDC3 HD domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 374659, updated on 17-Jun-2024

    Summary

    Official Symbol
    HDDC3provided by HGNC
    Official Full Name
    HD domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:30522
    See related
    Ensembl:ENSG00000184508 AllianceGenome:HGNC:30522
    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
    MESH1; MYNRL15; (ppGpp)ase
    Summary
    Predicted to enable guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in fat (RPKM 9.9), kidney (RPKM 7.9) and 25 other tissues See more
    Orthologs
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    Genomic context

    See HDDC3 in Genome Data Viewer
    Location:
    15q26.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (90929968..90932569, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (88689551..88694729, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (91473198..91475799, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10099 Neighboring gene FES proto-oncogene, tyrosine kinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10100 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6831 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6832 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10101 Neighboring gene mannosidase alpha class 2A member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6833 Neighboring gene unc-45 myosin chaperone A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:91496471-91496971 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:91497796-91498350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6834 Neighboring gene RCCD1 and UNC45A antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6835 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6836 Neighboring gene RCC1 domain containing 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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General protein information

    Preferred Names
    guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1
    Names
    HD domain-containing protein 3
    metazoan SpoT homolog 1
    myeloid leukemia noncoding regulatory locus on chromosome 15
    penta-phosphate guanosine-3'-pyrophosphohydrolase
    NP_001273380.1
    NP_940929.1
    XP_054233867.1
    XP_054233868.1

    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_001286451.2NP_001273380.1  guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1 isoform 1

      See identical proteins and their annotated locations for NP_001273380.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the shortest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC068831
      Consensus CDS
      CCDS66866.1
      UniProtKB/Swiss-Prot
      Q8N4P3
      Related
      ENSP00000377814.4, ENST00000394272.8
      Conserved Domains (2) summary
      COG0317
      Location:4137
      SpoT; (p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription]
      pfam13328
      Location:11138
      HD_4; HD domain
    2. NM_198527.4NP_940929.1  guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1 isoform 2

      See identical proteins and their annotated locations for NP_940929.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AW138983, BC033794, BI833873, BQ187342
      Consensus CDS
      CCDS10366.1
      UniProtKB/TrEMBL
      H0YNP9
      Related
      ENSP00000330721.3, ENST00000330334.7
      Conserved Domains (1) summary
      COG0317
      Location:4138
      SpoT; (p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription]

    RNA

    1. NR_104447.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' terminal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC068831, AW138983, BQ777217, BU633661, CA450487

    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

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      90929968..90932569 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      88689551..88694729 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377892.1XP_054233867.1  guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1 isoform X1

      UniProtKB/Swiss-Prot
      Q8N4P3
    2. XM_054377893.1XP_054233868.1  guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1 isoform X2

      UniProtKB/TrEMBL
      H0YNP9