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

    Gene ID: 374659, updated on 10-Dec-2024

    Summary

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    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, Dec 2024]
    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

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    See HDDC3 in Genome Data Viewer
    Location:
    15q26.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (90929968..90932569, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (88689551..88694729, complement)
    RS_2024_09 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. MESH1 is a cytosolic NADPH phosphatase that regulates ferroptosis. Ding CC, et al. Nat Metab, 2020 Mar. PMID 32462112, Free PMC Article
    2. A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses. Sun D, et al. Nat Struct Mol Biol, 2010 Oct. PMID 20818390
    3. Analysis of the DNA sequence and duplication history of human chromosome 15. Zody MC, et al. Nature, 2006 Mar 30. PMID 16572171
    4. Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling. Zhai Y, et al. Nat Commun, 2022 Aug 20. PMID 35987950, Free PMC Article
    5. CFTR interactome mapping using the mammalian membrane two-hybrid high-throughput screening system. Lim SH, et al. Mol Syst Biol, 2022 Feb. PMID 35156780, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC45386

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanosine-3',5'-bis(diphosphate) 3'-diphosphatase 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
    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_001286451.2 → NP_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:4 → 137
      SpoT; (p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription]
      pfam13328
      Location:11 → 138
      HD_4; HD domain

    2. NM_198527.4 → NP_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:4 → 138
      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_2024_08

    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_054377892.1 → XP_054233867.1  guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1 isoform X1

      UniProtKB/Swiss-Prot
      Q8N4P3

    2. XM_054377893.1 → XP_054233868.1  guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1 isoform X2

      UniProtKB/TrEMBL
      H0YNP9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N4P3.3 GenPept UniProtKB/Swiss-Prot:Q8N4P3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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