Aliases for GPN3 Gene

Aliases for GPN3 Gene

  • GPN-Loop GTPase 3 2 3 4 5
  • ATP-Binding Domain 1 Family Member C 3 4
  • ATPBD1C 3 4
  • ATP Binding Domain 1 Family, Member C 2
  • Protein X 0004 3

External Ids for GPN3 Gene

Previous HGNC Symbols for GPN3 Gene

  • ATPBD1C

Previous GeneCards Identifiers for GPN3 Gene

  • GC12M109374
  • GC12M110890
  • GC12M107908

Summaries for GPN3 Gene

GeneCards Summary for GPN3 Gene

GPN3 (GPN-Loop GTPase 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include nucleotide binding and hydrolase activity. An important paralog of this gene is GPN2.

UniProtKB/Swiss-Prot Summary for GPN3 Gene

  • Small GTPase required for proper localization of RNA polymerase II (RNAPII). May act at an RNAP assembly step prior to nuclear import.

Gene Wiki entry for GPN3 Gene

Additional gene information for GPN3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GPN3 Gene

Genomics for GPN3 Gene

GeneHancer (GH) Regulatory Elements for GPN3 Gene

Promoters and enhancers for GPN3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J110466 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas 536.8 +0.9 947 3.8 HNRNPK ZNF217 EP300 CTCF SIN3A NRF1 TCF12 MYC USF1 POLR2G GPN3 FAM216A lnc-GPN3-1 IFT81 ARPC3 RNU4-32P ANAPC7 UBE3B RPL31P49
GH12J110449 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 36.9 +19.3 19303 2.7 EP300 ZBTB40 CTCF POLR2G SP1 GTF2E2 PHF8 ZFX POLR2A ZBTB10 ARPC3 lnc-ARPC3-2-001 GPN3 ANAPC7 GLTP FAM216A ENSG00000258210
GH12J110280 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 26 +186.0 185969 8.2 HNRNPK EP300 ZSCAN5C SIN3A NRF1 POLR2G SP1 PHF8 ZFX ZIC2 ATP2A2 RNU4-32P GPN3 ARPC3 KCTD10 ANAPC7 IFT81 ENSG00000255655 FAM216A GLTP
GH12J110589 Enhancer 1.7 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 29.8 -121.6 -121633 6.6 EP300 ZBTB40 USF1 NCOR1 KDM6A TCF7 ZNF623 REST TOE1 SKI GPN3 FAM216A ARPC3 TCTN1 PPTC7 PPP1CC IFT81 HVCN1 lnc-TCTN1-1
GH12J110454 Promoter/Enhancer 1.1 Ensembl ENCODE 41.4 +12.7 12711 3.5 PBX2 ZNF384 GABPA NBN ZNF395 NRF1 HDGF TBX21 MEIS2 POLR2A RF00017-1264 GPN3 HE856252
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GPN3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for GPN3

Top Transcription factor binding sites by QIAGEN in the GPN3 gene promoter:
  • AP-2gamma
  • ATF6
  • c-Ets-1
  • E2F
  • E2F-1
  • GR-alpha
  • HSF1 (long)
  • HSF1short
  • MRF-2
  • Nkx2-5

Genomic Locations for GPN3 Gene

Genomic Locations for GPN3 Gene
chr12:110,452,486-110,469,268
(GRCh38/hg38)
Size:
16,783 bases
Orientation:
Minus strand
chr12:110,890,289-110,907,073
(GRCh37/hg19)
Size:
16,785 bases
Orientation:
Minus strand

Genomic View for GPN3 Gene

Genes around GPN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GPN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GPN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GPN3 Gene

Proteins for GPN3 Gene

  • Protein details for GPN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UHW5-GPN3_HUMAN
    Recommended name:
    GPN-loop GTPase 3
    Protein Accession:
    Q9UHW5
    Secondary Accessions:
    • B2RC54
    • D4YWV1
    • F5H759
    • Q53FS3
    • Q6UVZ6
    • Q7Z3D3
    • Q8NEI2
    • Q96HK9

    Protein attributes for GPN3 Gene

    Size:
    284 amino acids
    Molecular mass:
    32761 Da
    Quaternary structure:
    • Heterodimer with GPN1 (PubMed:21768307). Binds to RNA polymerase II (RNAPII) (PubMed:20864038, PubMed:21768307). Interacts directly with subunits RPB4 and RPB7 and the CTD of RPB1 (PubMed:21768307).
    SequenceCaution:
    • Sequence=CAD97937.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for GPN3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GPN3 Gene

Post-translational modifications for GPN3 Gene

  • Ubiquitination at Lys16 and Lys216
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for GPN3 Gene

Domains & Families for GPN3 Gene

Gene Families for GPN3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for GPN3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for GPN3 Gene

GenScript: Design optimal peptide antigens:
  • GPN-loop GTPase 3 (D4YWV1_HUMAN)
  • ATP-binding domain 1 family member C (GPN3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UHW5

UniProtKB/Swiss-Prot:

GPN3_HUMAN :
  • Belongs to the GPN-loop GTPase family.
Family:
  • Belongs to the GPN-loop GTPase family.
genes like me logo Genes that share domains with GPN3: view

Function for GPN3 Gene

Molecular function for GPN3 Gene

UniProtKB/Swiss-Prot Function:
Small GTPase required for proper localization of RNA polymerase II (RNAPII). May act at an RNAP assembly step prior to nuclear import.

Phenotypes From GWAS Catalog for GPN3 Gene

Gene Ontology (GO) - Molecular Function for GPN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003924 GTPase activity IBA 21873635
GO:0005515 protein binding IPI 25241168
GO:0005525 GTP binding IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with GPN3: view
genes like me logo Genes that share phenotypes with GPN3: view

Animal Model Products

CRISPR Products

miRNA for GPN3 Gene

miRTarBase miRNAs that target GPN3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GPN3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for GPN3 Gene

Localization for GPN3 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GPN3 gene
Compartment Confidence
nucleus 3
cytosol 3
plasma membrane 1
extracellular 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GPN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032991 protein-containing complex IDA --
genes like me logo Genes that share ontologies with GPN3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for GPN3 Gene

Pathways & Interactions for GPN3 Gene

PathCards logo

SuperPathways for GPN3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for GPN3 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for GPN3 Gene

Drugs & Compounds for GPN3 Gene

No Compound Related Data Available

Transcripts for GPN3 Gene

mRNA/cDNA for GPN3 Gene

3 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GPN3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GPN3 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9
SP1: - -
SP2: -
SP3:
SP4:

Relevant External Links for GPN3 Gene

GeneLoc Exon Structure for
GPN3

Expression for GPN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GPN3 Gene

Protein differential expression in normal tissues from HIPED for GPN3 Gene

This gene is overexpressed in Bone (16.5), Peripheral blood mononuclear cells (11.1), and Testis (10.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GPN3 Gene



Protein tissue co-expression partners for GPN3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for GPN3

SOURCE GeneReport for Unigene cluster for GPN3 Gene:

Hs.634680

Evidence on tissue expression from TISSUES for GPN3 Gene

  • Adrenal gland(4.2)
  • Bone marrow(4.2)
  • Liver(4.2)
  • Lung(4.2)
  • Spleen(4.2)
  • Eye(4.1)
genes like me logo Genes that share expression patterns with GPN3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for GPN3 Gene

Orthologs for GPN3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for GPN3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GPN3 31 30
  • 99.88 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GPN3 31 30
  • 93.08 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GPN3 31 30
  • 92.72 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GPN3 31
  • 90 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia GPN3 31
  • 88 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Gpn3 30
  • 86.62 (n)
mouse
(Mus musculus)
Mammalia Gpn3 17 31 30
  • 85.21 (n)
chicken
(Gallus gallus)
Aves GPN3 31 30
  • 78.4 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GPN3 31
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gpn3 30
  • 78.17 (n)
Str.15832 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.10460 30
zebrafish
(Danio rerio)
Actinopterygii gpn3 31 30
  • 75.27 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG2656 31 30
  • 60.71 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001152 30
  • 58.03 (n)
worm
(Caenorhabditis elegans)
Secernentea CELE_Y75B8A.14 30
  • 56.39 (n)
Y75B8A.14 31
  • 50 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GPN3 33 30
  • 54.01 (n)
-- 31
  • 40 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGL117C 30
  • 53.94 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D18557g 30
  • 53.87 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G12790 30
  • 59.97 (n)
rice
(Oryza sativa)
Liliopsida Os03g0337700 30
  • 59.16 (n)
Os.11878 30
barley
(Hordeum vulgare)
Liliopsida Hv.2697 30
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2812 31
  • 55 (a)
OneToOne
Cin.4433 30
bread mold
(Neurospora crassa)
Ascomycetes NCU02658 30
  • 54.81 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes fet5 30
  • 53.41 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4433 30
Species where no ortholog for GPN3 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for GPN3 Gene

ENSEMBL:
Gene Tree for GPN3 (if available)
TreeFam:
Gene Tree for GPN3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GPN3: view image

Paralogs for GPN3 Gene

Paralogs for GPN3 Gene

(2) SIMAP similar genes for GPN3 Gene using alignment to 5 proteins:

  • GPN3_HUMAN
  • F8W1F4_HUMAN
  • H0YHZ5_HUMAN
  • H0YI19_HUMAN
  • S4R3M7_HUMAN

Pseudogenes.org Pseudogenes for GPN3 Gene

genes like me logo Genes that share paralogs with GPN3: view

Variants for GPN3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GPN3 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
rs17850320 - p.Val244Ala
rs17856906 - p.Ala52Val

Additional dbSNP identifiers (rs#s) for GPN3 Gene

Structural Variations from Database of Genomic Variants (DGV) for GPN3 Gene

Variant ID Type Subtype PubMed ID
nsv973114 CNV duplication 23825009

Variation tolerance for GPN3 Gene

Residual Variation Intolerance Score: 30.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.58; 30.52% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GPN3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
GPN3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GPN3 Gene

Disorders for GPN3 Gene

Additional Disease Information for GPN3

No disorders were found for GPN3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for GPN3 Gene

Publications for GPN3 Gene

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4 54
  2. Human GTPases associate with RNA polymerase II to mediate its nuclear import. (PMID: 21768307) Carré C … Shiekhattar R (Molecular and cellular biology 2011) 3 4 54
  3. BAP1 regulation of the key adaptor protein NCoR1 is critical for γ-globin gene repression. (PMID: 30463901) Yu L … Engel JD (Genes & development 2018) 3 54
  4. Mapping the Genetic Landscape of Human Cells. (PMID: 30033366) Horlbeck MA … Gilbert LA (Cell 2018) 3 54
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54

Products for GPN3 Gene

Sources for GPN3 Gene