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GPN1 GPN-loop GTPase 1 [ Homo sapiens (human) ]

Gene ID: 11321, updated on 7-Apr-2024

Summary

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Official Symbol
GPN1provided by HGNC
Official Full Name
GPN-loop GTPase 1provided by HGNC
Primary source
HGNC:HGNC:17030
See related
Ensembl:ENSG00000198522 MIM:611479; AllianceGenome:HGNC:17030
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
XAB1; MBDIN; NTPBP; RPAP4; ATPBD1A
Summary
This gene encodes a guanosine triphosphatase enzyme. The encoded protein may play a role in DNA repair and may function in activation of transcription. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2009]
Expression
Ubiquitous expression in testis (RPKM 15.4), thyroid (RPKM 13.8) and 25 other tissues See more
Orthologs
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Genomic context

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See GPN1 in Genome Data Viewer
Location:
2p23.3
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (27628247..27651511)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (27671332..27694600)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (27851114..27874378)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 4379 Neighboring gene SPATA31 subfamily H member 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:27788766-27789965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15508 Neighboring gene zinc finger protein 512 Neighboring gene Sharpr-MPRA regulatory region 1109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15510 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15509 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15511 Neighboring gene coiled-coil domain containing 121 Neighboring gene small nucleolar RNA SNORA36 family Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:27875474-27876673 Neighboring gene SPT7 like, STAGA complex subunit gamma Neighboring gene solute carrier family 4 member 1 adaptor protein Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:27904532-27905731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11303 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11304 Neighboring gene long intergenic non-protein coding RNA 1460

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. A nuclear export sequence in GPN-loop GTPase 1, an essential protein for nuclear targeting of RNA polymerase II, is necessary and sufficient for nuclear export. Reyes-Pardo H, et al. Biochim Biophys Acta, 2012 Oct. PMID 22796641
  2. The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II. Forget D, et al. Mol Cell Proteomics, 2010 Dec. PMID 20855544, Free PMC Article
  3. 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
  4. 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
  5. 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

See all (60) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Results show that Gpn1-inhibitable, nuclear polyubiquitination on lysine 216 regulates the half-life of Gpn3 by tagging it for proteasomal degradation.
    Title: Gpn3 is polyubiquitinated on lysine 216 and degraded by the proteasome in the cell nucleus in a Gpn1-inhibitable manner.
  2. 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.
  3. GPN1 gene variation is associated with oral cavity and pharyngeal cancer.
    Title: Genome-wide association analyses identify new susceptibility loci for oral cavity and pharyngeal cancer.
  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. A highly active, evolutionarily conserved nuclear export sequences in XAB1/Gpn1, was identified.
    Title: A nuclear export sequence in GPN-loop GTPase 1, an essential protein for nuclear targeting of RNA polymerase II, is necessary and sufficient for nuclear export.
  6. 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.
  7. RPAP4/GPN1 is a member of a newly discovered GTPase family that contains a highly conserved GPN loop motif that is essential, along with its GTP-binding motifs, for nuclear localization of POLR2A/RPB1 in a process that also requires microtubule assembly
    Title: The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II.
  8. relieves MBD2-mediated transcriptional repression and reactivates transcription from methylated promoters
    Title: MBDin, a novel MBD2-interacting protein, relieves MBD2 repression potential and reactivates transcription from methylated promoters.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
A bivariate genome-wide approach to metabolic syndrome: STAMPEED consortium.
EBI GWAS Catalog
Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu
EBI GWAS Catalog
Genome-wide association study of chronic periodontitis in a general German population.
EBI GWAS Catalog

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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, GPN-loop GTPase 1 (GPN1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ51176

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
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
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
GPN-loop GTPase 1
Names
ATP(GTP)-binding protein
MBD2-interacting protein
RNA polymerase II associated protein 4
RNAPII-associated protein 4
XPA binding protein 1, GTPase
NP_001138519.1
NP_001138520.1
NP_001138521.1
NP_009197.3

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_001145047.2 → NP_001138519.1  GPN-loop GTPase 1 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, contains two alternate exons in the 5' coding region and uses an alternate start codon, compared to variant 1. The encoded isoform (b) has a shorter, distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AC074091, AJ010842, AK298827, AK310340
    Consensus CDS
    CCDS46248.1
    UniProtKB/Swiss-Prot
    Q9HCN4
    Related
    ENSP00000384255.3, ENST00000407583.7
    Conserved Domains (2) summary
    COG1100
    Location:23 → 217
    Gem1; GTPase SAR1 family domain [General function prediction only]
    pfam03029
    Location:23 → 249
    ATP_bind_1; Conserved hypothetical ATP binding protein

  2. NM_001145048.2 → NP_001138520.1  GPN-loop GTPase 1 isoform c

    See identical proteins and their annotated locations for NP_001138520.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a segment of the 5' coding region, and uses a downstream start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AC074091, AJ010842, AK298827
    Consensus CDS
    CCDS46250.1
    UniProtKB/Swiss-Prot
    Q9HCN4
    Related
    ENSP00000398115.1, ENST00000424214.5
    Conserved Domains (2) summary
    COG1100
    Location:1 → 150
    Gem1; GTPase SAR1 family domain [General function prediction only]
    pfam03029
    Location:1 → 182
    ATP_bind_1; Conserved hypothetical ATP binding protein

  3. NM_001145049.2 → NP_001138521.1  GPN-loop GTPase 1 isoform d

    See identical proteins and their annotated locations for NP_001138521.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has multiple coding region differences compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (d) with a shorter N-terminus compared to isoform a.
    Source sequence(s)
    AC074091, AJ010842, AK316404
    Consensus CDS
    CCDS46249.1
    UniProtKB/Swiss-Prot
    Q9HCN4
    Related
    ENSP00000412170.2, ENST00000458167.6
    Conserved Domains (2) summary
    COG1100
    Location:22 → 160
    Gem1; GTPase SAR1 family domain [General function prediction only]
    pfam03029
    Location:5 → 166
    ATP_bind_1; Conserved hypothetical ATP binding protein

  4. NM_007266.4 → NP_009197.3  GPN-loop GTPase 1 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC074091, AJ010842, AK298866, BC007451
    Consensus CDS
    CCDS1760.3
    UniProtKB/Swiss-Prot
    B4DQJ5, B4DQM4, B4DXU4, B5MBZ5, O76004, Q9HCN4
    UniProtKB/TrEMBL
    Q53RZ9
    Related
    ENSP00000476446.1, ENST00000610189.2
    Conserved Domains (1) summary
    pfam03029
    Location:24 → 261
    ATP_bind_1; Conserved hypothetical ATP binding protein

RNA

  1. NR_026735.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC074091, AJ010842, AK302131

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    27628247..27651511
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    27671332..27694600
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9HCN4.1 GenPept UniProtKB/Swiss-Prot:Q9HCN4

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