This gene encodes a member of the POP family of proteins containing three putative transmembrane domains. This gene is expressed in cardiac and skeletal muscle and may play an important role in these tissues during development. Alternatively spliced transcript variants have been found. [provided by RefSeq, Nov 2008] See more...

Aliases for POPDC3 Gene

Aliases for POPDC3 Gene

  • Popeye Domain Containing 3 2 3 5
  • POP3 2 3 4
  • Popeye Domain-Containing Protein 3 3 4
  • Popeye Protein 3 3 4
  • BA355M14.1 2 3
  • MGC22671 2
  • LGMDR26 3
  • POPDC3 5

External Ids for POPDC3 Gene

Previous GeneCards Identifiers for POPDC3 Gene

  • GC06M105605
  • GC06M105651
  • GC06M105712
  • GC06M103048

Summaries for POPDC3 Gene

Entrez Gene Summary for POPDC3 Gene

  • This gene encodes a member of the POP family of proteins containing three putative transmembrane domains. This gene is expressed in cardiac and skeletal muscle and may play an important role in these tissues during development. Alternatively spliced transcript variants have been found. [provided by RefSeq, Nov 2008]

GeneCards Summary for POPDC3 Gene

POPDC3 (Popeye Domain Containing 3) is a Protein Coding gene. Diseases associated with POPDC3 include Muscular Dystrophy, Limb-Girdle, Autosomal Recessive 26 and Malignant Glioma. An important paralog of this gene is POPDC2.

UniProtKB/Swiss-Prot Summary for POPDC3 Gene

  • May play a role in the maintenance of heart function mediated, at least in part, through cAMP-binding.

Gene Wiki entry for POPDC3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for POPDC3 Gene

Genomics for POPDC3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for POPDC3 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
GH06J105177 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 614.2 +0.8 849 3.7 KDM1A ZSCAN4 EZH2 ZNF600 ZNF341 ZFX ZNF561 SCRT2 ZBTB20 ZXDB POPDC3 lnc-POPDC3-1 BVES RF00017-5692
GH06J105176 Promoter/Enhancer 1.1 EPDnew ENCODE dbSUPER 617.9 +3.4 3409 0.7 REST POLR2A NFYB FOXM1 CREM PRDM10 ATF1 ZBTB33 FOS MEIS2 POPDC3 RF00017-5692 BVES lnc-POPDC3-1
GH06J105136 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 23.6 +43.5 43513 3.4 PRDM1 ZIC2 CTCF EZH2 ZNF600 ZBTB20 ZNF639 ZXDB ZBTB48 ZBTB26 BVES BVES-AS1 POPDC3 PREP LIN28B
GH06J105160 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 19.1 +14.4 14399 10.4 ATF7 PRDM10 ZNF629 RFX1 ZNF600 ZBTB44 TCF7L2 CEBPB ZNF316 MAFF BVES POPDC3 PREP RF00017-5692 lnc-POPDC3-1 BVES-AS1
GH06J105209 Enhancer 1.1 Ensembl ENCODE dbSUPER 11.2 -30.9 -30887 3.4 GATAD2A ZNF24 SOX6 CEBPA ZBTB44 FOXA1 CEBPB NFE2 ZNF316 OSR2 POPDC3 ENSG00000231628 piR-55110-080 RF00994-935 PREP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around POPDC3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for POPDC3

Top Transcription factor binding sites by QIAGEN in the POPDC3 gene promoter:
  • ATF-2
  • HSF2
  • Nkx2-5
  • Pbx1a
  • STAT3

Genomic Locations for POPDC3 Gene

Genomic Locations for POPDC3 Gene
chr6:105,157,900-105,180,014
(GRCh38/hg38)
Size:
22,115 bases
Orientation:
Minus strand
chr6:105,605,775-105,627,870
(GRCh37/hg19)
Size:
22,096 bases
Orientation:
Minus strand

Genomic View for POPDC3 Gene

Genes around POPDC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
POPDC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for POPDC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for POPDC3 Gene

Proteins for POPDC3 Gene

  • Protein details for POPDC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HBV1-POPD3_HUMAN
    Recommended name:
    Popeye domain-containing protein 3
    Protein Accession:
    Q9HBV1
    Secondary Accessions:
    • B2RA98
    • Q5T3Y8
    • Q8TBW6

    Protein attributes for POPDC3 Gene

    Size:
    291 amino acids
    Molecular mass:
    33870 Da
    Quaternary structure:
    No Data Available

neXtProt entry for POPDC3 Gene

Post-translational modifications for POPDC3 Gene

  • Glycosylation at Asn4
  • Modification sites at PhosphoSitePlus

Other Protein References for POPDC3 Gene

No data available for DME Specific Peptides for POPDC3 Gene

Domains & Families for POPDC3 Gene

Gene Families for POPDC3 Gene

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

Protein Domains for POPDC3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for POPDC3 Gene

GenScript: Design optimal peptide antigens:
  • Popeye domain-containing protein 3 (POPD3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9HBV1

UniProtKB/Swiss-Prot:

POPD3_HUMAN :
  • Belongs to the popeye family.
Family:
  • Belongs to the popeye family.
genes like me logo Genes that share domains with POPDC3: view

Function for POPDC3 Gene

Molecular function for POPDC3 Gene

UniProtKB/Swiss-Prot Function:
May play a role in the maintenance of heart function mediated, at least in part, through cAMP-binding.

Phenotypes From GWAS Catalog for POPDC3 Gene

Gene Ontology (GO) - Molecular Function for POPDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003674 molecular_function ND --
GO:0030552 cAMP binding IBA,ISS --
genes like me logo Genes that share ontologies with POPDC3: view
genes like me logo Genes that share phenotypes with POPDC3: view

Animal Models for POPDC3 Gene

MGI Knock Outs for POPDC3:
  • Popdc3 Popdc3<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for POPDC3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for POPDC3 Gene

Localization for POPDC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for POPDC3 Gene

Membrane. Multi-pass membrane protein.

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 POPDC3 gene
Compartment Confidence
plasma membrane 4
nucleus 2
extracellular 1
endoplasmic reticulum 1
cytosol 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for POPDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA,IBA 21873635
GO:0016021 integral component of membrane NAS 10882522
GO:0042383 sarcolemma IBA 21873635
genes like me logo Genes that share ontologies with POPDC3: view

Pathways & Interactions for POPDC3 Gene

PathCards logo

SuperPathways for POPDC3 Gene

No Data Available

Interacting Proteins for POPDC3 Gene

STRING Interaction Network Preview (showing top 1 STRING interactants - click image to see details)
STRING Interaction Network
Selected Interacting proteins: ENSP00000254765 Q9HBV1-POPD3_HUMAN for POPDC3 Gene via STRING IID

Gene Ontology (GO) - Biological Process for POPDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007507 heart development IBA 21873635
GO:0007519 skeletal muscle tissue development IBA 21873635
GO:0008150 biological_process ND --
GO:0042391 regulation of membrane potential IEA,ISS --
GO:0051146 striated muscle cell differentiation IBA 21873635
genes like me logo Genes that share ontologies with POPDC3: view

No data available for Pathways by source and SIGNOR curated interactions for POPDC3 Gene

Drugs & Compounds for POPDC3 Gene

No Compound Related Data Available

Transcripts for POPDC3 Gene

mRNA/cDNA for POPDC3 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
4 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 POPDC3

Alternative Splicing Database (ASD) splice patterns (SP) for POPDC3 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c · 5d ^ 6a · 6b ^ 7a · 7b · 7c · 7d
SP1: - - -
SP2: - - - - - -
SP3: - - - - -
SP4:
SP5: - - -
SP6:
SP7: - - - -

Relevant External Links for POPDC3 Gene

GeneLoc Exon Structure for
POPDC3

Expression for POPDC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for POPDC3 Gene

mRNA differential expression in normal tissues according to GTEx for POPDC3 Gene

This gene is overexpressed in Muscle - Skeletal (x19.8) and Heart - Left Ventricle (x5.7).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for POPDC3

SOURCE GeneReport for Unigene cluster for POPDC3 Gene:

Hs.458336

mRNA Expression by UniProt/SwissProt for POPDC3 Gene:

Q9HBV1-POPD3_HUMAN
Tissue specificity: Expressed predominantly in skeletal muscle and detected in heart.

Evidence on tissue expression from TISSUES for POPDC3 Gene

  • Muscle(4.6)
  • Nervous system(4.3)
  • Heart(2.6)
genes like me logo Genes that share expression patterns with POPDC3: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for POPDC3 Gene

Orthologs for POPDC3 Gene

This gene was present in the common ancestor of animals.

Orthologs for POPDC3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia POPDC3 30 31
  • 99.77 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia POPDC3 30 31
  • 93.01 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia POPDC3 30 31
  • 91.41 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Popdc3 30 17 31
  • 87.51 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Popdc3 30
  • 85.15 (n)
Oppossum
(Monodelphis domestica)
Mammalia POPDC3 31
  • 82 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia POPDC3 31
  • 75 (a)
OneToOne
Chicken
(Gallus gallus)
Aves POPDC3 30 31
  • 76.09 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia POPDC3 31
  • 72 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia popdc3 30
  • 71.32 (n)
Str.19727 30
Zebrafish
(Danio rerio)
Actinopterygii popdc3 30 31
  • 64.77 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta bves 31
  • 17 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 27 (a)
OneToMany
Species where no ortholog for POPDC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • 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 (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for POPDC3 Gene

ENSEMBL:
Gene Tree for POPDC3 (if available)
TreeFam:
Gene Tree for POPDC3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for POPDC3: view image

Paralogs for POPDC3 Gene

Paralogs for POPDC3 Gene

(2) SIMAP similar genes for POPDC3 Gene using alignment to 2 proteins:

  • POPD3_HUMAN
  • Q5T554_HUMAN
genes like me logo Genes that share paralogs with POPDC3: view

Variants for POPDC3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for POPDC3 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
716895 Benign: not provided 105,161,515(-) C/T MISSENSE_VARIANT
778249 Benign: not provided 105,159,789(-) C/T NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
778250 Benign: not provided 105,161,898(-) A/G NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
869186 Pathogenic: MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 26 105,158,564(-) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
869187 Pathogenic: MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 26 105,161,446(-) A/T MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for POPDC3 Gene

Structural Variations from Database of Genomic Variants (DGV) for POPDC3 Gene

Variant ID Type Subtype PubMed ID
esv2665928 CNV deletion 23128226
esv2759461 CNV gain 17122850
esv3540257 CNV deletion 23714750
esv3610253 CNV loss 21293372
nsv604437 CNV loss 21841781

Variation tolerance for POPDC3 Gene

Residual Variation Intolerance Score: 48.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.45; 54.85% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for POPDC3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
POPDC3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for POPDC3 Gene

Disorders for POPDC3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for POPDC3 Gene - From: LncRNADisease, OMIM, ClinVar, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
muscular dystrophy, limb-girdle, autosomal recessive 26
  • lgmdr26
malignant glioma
  • glial cell tumor
autosomal recessive limb-girdle muscular dystrophy type 2x
  • muscular dystrophy, limb-girdle, type 2x
muscular dystrophy
  • muscular dystrophies
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for POPDC3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with POPDC3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for POPDC3 Gene

Publications for POPDC3 Gene

  1. Isolation and characterization of the novel popeye gene family expressed in skeletal muscle and heart. (PMID: 10882522) Andrée B … Brand T (Developmental biology 2000) 2 3 4 23
  2. Genome-wide association study of severity in multiple sclerosis. (PMID: 21654844) International Multiple Sclerosis Genetics Consortium (Genes and immunity 2011) 3 41
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41
  4. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. (PMID: 20546612) Zhao J … Grant SF (BMC medical genetics 2010) 3 41
  5. Genome-wide association study identifies sequence variants on 6q21 associated with age at menarche. (PMID: 19448622) Sulem P … Stefansson K (Nature genetics 2009) 3 41

Products for POPDC3 Gene

Sources for POPDC3 Gene