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    GHDC GH3 domain containing [ Homo sapiens (human) ]

    Gene ID: 84514, updated on 14-Nov-2024

    Summary

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    Official Symbol
    GHDCprovided by HGNC
    Official Full Name
    GH3 domain containingprovided by HGNC
    Primary source
    HGNC:HGNC:24438
    See related
    Ensembl:ENSG00000167925 MIM:608587; AllianceGenome:HGNC:24438
    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
    LGP1; D11LGP1
    Summary
    Predicted to enable acid-amino acid ligase activity. Located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 16.7), spleen (RPKM 13.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GHDC in Genome Data Viewer
    Location:
    17q21.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (42189087..42194494, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (43045561..43050968, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (40341105..40346512, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:40311466-40312136 Neighboring gene RAB5C antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 11697 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:40330401-40330902 Neighboring gene potassium voltage-gated channel subfamily H member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:40331553-40332120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8517 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:40333316-40333591 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:40336245-40337046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:40345000-40345530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12191 Neighboring gene hypocretin neuropeptide precursor Neighboring gene signal transducer and activator of transcription 5B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8519 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:40439573-40440073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12192 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8520 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12193 Neighboring gene signal transducer and activator of transcription 5A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12194 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8522 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8523 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8524 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:40480835-40481564 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:40481565-40482295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12195 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12196 Neighboring gene signal transducer and activator of transcription 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12197 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8525 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8527 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8528

    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 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. The Stat3/5 locus encodes novel endoplasmic reticulum and helicase-like proteins that are preferentially expressed in normal and neoplastic mammary tissue. Cui Y, et al. Genomics, 2001 Dec. PMID 11735219
    2. Structure of the mouse Stat 3/5 locus: evolution from Drosophila to zebrafish to mouse. Miyoshi K, et al. Genomics, 2001 Jan 15. PMID 11161808
    3. Regulation of membrane fluidity by RNF145-triggered degradation of the lipid hydrolase ADIPOR2. Volkmar N, et al. EMBO J, 2022 Oct 4. PMID 35993436, Free PMC Article
    4. Cytoplasmic Metadherin (MTDH) provides survival advantage under conditions of stress by acting as RNA-binding protein. Meng X, et al. J Biol Chem, 2012 Feb 10. PMID 22199357, Free PMC Article
    5. Global proteomics of Ubqln2-based murine models of ALS. Whiteley AM, et al. J Biol Chem, 2021 Jan-Jun. PMID 33277362, Free PMC Article

    See all (28) 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables acid-amino acid ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane HDA PubMed 
    located_in nuclear envelope IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in secretory granule lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in specific granule lumen TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    GH3 domain-containing protein
    Names
    homolog of mouse LGP1

    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_001142623.2 → NP_001136095.1  GH3 domain-containing protein isoform 3 precursor

      See identical proteins and their annotated locations for NP_001136095.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site, resulting in a frameshifted and alternate 3' coding region, compared to variant 1. The encoded isoform (3) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK075277, BC022784, DB084267
      Consensus CDS
      CCDS45682.1
      UniProtKB/TrEMBL
      K7ESN3
      Related
      ENSP00000399952.2, ENST00000414034.7
      Conserved Domains (2) summary
      cl21606
      Location:249 → 410
      PLN02247; indole-3-acetic acid-amido synthetase
      pfam03321
      Location:54 → 420
      GH3; GH3 auxin-responsive promoter

    2. NM_032484.5 → NP_115873.1  GH3 domain-containing protein isoform 1 precursor

      See identical proteins and their annotated locations for NP_115873.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      BC022784, DB084267
      Consensus CDS
      CCDS11422.1
      UniProtKB/Swiss-Prot
      B4DQS4, E9PDB5, Q8N2G8, Q9BXM6
      UniProtKB/TrEMBL
      B3KVB0
      Related
      ENSP00000467585.1, ENST00000587427.6
      Conserved Domains (2) summary
      cl21606
      Location:89 → 530
      PLN02247; indole-3-acetic acid-amido synthetase
      pfam03321
      Location:54 → 490
      GH3; GH3 auxin-responsive promoter

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      42189087..42194494 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      43045561..43050968 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001142622.1: Suppressed sequence

      Description
      NM_001142622.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, which appears to be a cloning artifact.

    2. NR_024573.1: Suppressed sequence

      Description
      NR_024573.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, which may partially retain intron sequence at its 5' end.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N2G8.2 GenPept UniProtKB/Swiss-Prot:Q8N2G8

    Gene LinkOut

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

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