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GHDC GH3 domain containing [ Homo sapiens (human) ]

Gene ID: 84514, updated on 27-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
  • 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

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