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    GPN3 GPN-loop GTPase 3 [ Homo sapiens (human) ]

    Gene ID: 51184, updated on 5-Mar-2024

    Summary

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    Official Symbol
    GPN3provided by HGNC
    Official Full Name
    GPN-loop GTPase 3provided by HGNC
    Primary source
    HGNC:HGNC:30186
    See related
    Ensembl:ENSG00000111231 AllianceGenome:HGNC:30186
    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
    ATPBD1C
    Summary
    Predicted to enable GTPase activity. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 19.7), fat (RPKM 10.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GPN3 in Genome Data Viewer
    Location:
    12q24.11
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (110452486..110468721, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (110430179..110446415, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (110890291..110906526, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110866603-110867104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7002 Neighboring gene high mobility group AT-hook 1 pseudogene 3 Neighboring gene actin related protein 2/3 complex subunit 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:110886698-110887550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7003 Neighboring gene ribosomal protein L31 pseudogene 49 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7004 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7005 Neighboring gene uncharacterized LOC124903016 Neighboring gene family with sequence similarity 216 member A Neighboring gene uncharacterized LOC124903015 Neighboring gene small nucleolar RNA SNORD50 Neighboring gene VPS29 retromer complex component

    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. Gpn3 Is Essential for Cell Proliferation of Breast Cancer Cells Independent of Their Malignancy Degree. Lara-Chacón B, et al. Technol Cancer Res Treat, 2019 Jan 1. PMID 31431135, Free PMC Article
    2. Gpn3 is polyubiquitinated on lysine 216 and degraded by the proteasome in the cell nucleus in a Gpn1-inhibitable manner. Méndez-Hernández LE, et al. FEBS Lett, 2017 Nov. PMID 29029378
    3. The Gpn3 Q279* cancer-associated mutant inhibits Gpn1 nuclear export and is deficient in RNA polymerase II nuclear targeting. Barbosa-Camacho AA, et al. FEBS Lett, 2017 Nov. PMID 28940195
    4. Gpn1 and Gpn3 associate tightly and their protein levels are mutually dependent in mammalian cells. Méndez-Hernández LE, et al. FEBS Lett, 2014 Nov 3. PMID 25241168
    5. Parcs/Gpn3 is required for the nuclear accumulation of RNA polymerase II. Calera MR, et al. Biochim Biophys Acta, 2011 Oct. PMID 21782856

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. our analysis of public data revealed that Gpn3 overexpression was associated with a significant decrease in overall survival in patients with estrogen receptor-positive and Human epidermal growth factor receptor 2 (HER2+) breast cancer, supporting our proposal that targeting Gpn3 could potentially benefit patients with breast cancer.
      Title: Gpn3 Is Essential for Cell Proliferation of Breast Cancer Cells Independent of Their Malignancy Degree.
    2. Results indicate that polyubiquitination on lysine 216 is a regulatory process for proteasomal degradation of Gpn3 that is not in a complex with Gpn1, a critical partner of Gpn3 in human cells.
      Title: Gpn3 is polyubiquitinated on lysine 216 and degraded by the proteasome in the cell nucleus in a Gpn1-inhibitable manner.
    3. an acquired PDZ-binding motif in Gpn3 Q279* caused Gpn3 nuclear entry, and inhibited Gpn1 nuclear export and Gpn3-mediated RNAPII nuclear targeting.
      Title: The Gpn3 Q279* cancer-associated mutant inhibits Gpn1 nuclear export and is deficient in RNA polymerase II nuclear targeting.
    4. Gpn1-Gpn3 interaction was essential to maintain steady-state protein levels of both GTPases
      Title: Gpn1 and Gpn3 associate tightly and their protein levels are mutually dependent in mammalian cells.
    5. Data show that GPN1/GPN3 define a new family of small GTPases that are specialized for the transport of RNA polymerase II into the nucleus.
      Title: Human GTPases associate with RNA polymerase II to mediate its nuclear import.
    6. Parcs/Gpn3 plays a critical role in the nuclear accumulation of RNAP II, and this function explains the relative importance of Parcs/Gpn3 in cell proliferation.
      Title: Parcs/Gpn3 is required for the nuclear accumulation of RNA polymerase II.
    Submit: New GeneRIF Correction

    Phenotypes

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    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC14560, MGC32810

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    GPN-loop GTPase 3
    Names
    ATP-binding domain 1 family member C
    protein x 0004

    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_001164372.2 → NP_001157844.1  GPN-loop GTPase 3 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate 5' exon, resulting in a distinct 5' UTR and translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a longer and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK223209, BC008416, BI546381
      Consensus CDS
      CCDS53831.1
      UniProtKB/Swiss-Prot
      Q9UHW5
      Related
      ENSP00000442770.1, ENST00000543199.5
      Conserved Domains (2) summary
      COG1100
      Location:56 → 249
      Gem1; GTPase SAR1 family domain [General function prediction only]
      pfam03029
      Location:56 → 293
      ATP_bind_1; Conserved hypothetical ATP binding protein

    2. NM_001164373.2 → NP_001157845.1  GPN-loop GTPase 3 isoform 3

      See identical proteins and their annotated locations for NP_001157845.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. This results in a longer protein (isoform 3), compared to isoform 1.
      Source sequence(s)
      AK223209, BC008416, BX537973
      Consensus CDS
      CCDS53830.1
      UniProtKB/Swiss-Prot
      Q9UHW5
      Related
      ENSP00000443068.2, ENST00000537466.6
      Conserved Domains (1) summary
      pfam03029
      Location:8 → 264
      ATP_bind_1; Conserved hypothetical ATP binding protein

    3. NM_016301.4 → NP_057385.3  GPN-loop GTPase 3 isoform 1

      See identical proteins and their annotated locations for NP_057385.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the predominant isoform (1).
      Source sequence(s)
      AK223209, BC008416
      Consensus CDS
      CCDS9147.1
      UniProtKB/Swiss-Prot
      B2RC54, D4YWV1, F5H759, Q53FS3, Q6UVZ6, Q7Z3D3, Q8NEI2, Q96HK9, Q9UHW5
      Related
      ENSP00000228827.3, ENST00000228827.8
      Conserved Domains (1) summary
      cd17872
      Location:4 → 249
      GPN3; GPN-loop GTPase 3

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      110452486..110468721 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428936.1 → XP_047284892.1  GPN-loop GTPase 3 isoform X4

    2. XM_047428934.1 → XP_047284890.1  GPN-loop GTPase 3 isoform X2

    3. XM_047428935.1 → XP_047284891.1  GPN-loop GTPase 3 isoform X3

    4. XM_047428933.1 → XP_047284889.1  GPN-loop GTPase 3 isoform X1

    5. XM_017019394.2 → XP_016874883.1  GPN-loop GTPase 3 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      110430179..110446415 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372187.1 → XP_054228162.1  GPN-loop GTPase 3 isoform X4

    2. XM_054372185.1 → XP_054228160.1  GPN-loop GTPase 3 isoform X2

    3. XM_054372186.1 → XP_054228161.1  GPN-loop GTPase 3 isoform X3

    4. XM_054372184.1 → XP_054228159.1  GPN-loop GTPase 3 isoform X1

    5. XM_054372188.1 → XP_054228163.1  GPN-loop GTPase 3 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UHW5.2 GenPept UniProtKB/Swiss-Prot:Q9UHW5

    Gene LinkOut

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

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