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POPDC3 Gene

protein-coding   GIFtS: 50
GCID: GC06M105605

Popeye Domain Containing 3

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Popeye Domain Containing 31 2
POP32 3 5
Popeye Protein 32 3
bA355M14.12
Popeye Domain-Containing Protein 32

External Ids:    HGNC: 176491   Entrez Gene: 642082   Ensembl: ENSG000001324297   OMIM: 6058245   UniProtKB: Q9HBV13   
ORGUL members:         

Export aliases for POPDC3 gene to outside databases

Previous GC identifers: GC06M105651 GC06M105712 GC06M103048


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. An important paralog of this gene is POPDC2.

UniProtKB/Swiss-Prot: POPD3_HUMAN, Q9HBV1
Function: May play an important role in heart development

Gene Wiki entry for POPDC3 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000006.11  NC_018917.2  NT_025741.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the POPDC3 gene promoter:
         Pbx1a   ATF-2   HSF2   STAT3   Nkx2-5   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPOPDC3 promoter sequence
   Search Chromatin IP Primers for POPDC3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat POPDC3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6q21   Ensembl cytogenetic band:  6q21   HGNC cytogenetic band: 6q21

POPDC3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
POPDC3 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M105605:  view genomic region     (about GC identifiers)

Start:
105,605,775 bp from pter      End:
105,627,870 bp from pter
Size:
22,096 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: POPD3_HUMAN, Q9HBV1 (See protein sequence)
Recommended Name: Popeye domain-containing protein 3  
Size: 291 amino acids; 33870 Da
Secondary accessions: B2RA98 Q5T3Y8 Q8TBW6

Explore the universe of human proteins at neXtProt for POPDC3: NX_Q9HBV1

Explore proteomics data for POPDC3 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn4
  • Modification sites at PhosphoSitePlus

  • See POPDC3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_071756.2  
    ENSEMBL proteins: 
     ENSP00000254765   ENSP00000414409  

    POPDC3 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for POPDC3

     
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    antibodies-online proteins for POPDC3 (2 products) 

     
    antibodies-online peptides for POPDC3

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    antibodies-online antibodies for POPDC3 (16 products) 

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    antibodies-online kits for POPDC3 (6 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR018490 cNMP-bd-like
     IPR006916 Popeye_prot

    Graphical View of Domain Structure for InterPro Entry Q9HBV1

    ProtoNet protein and cluster: Q9HBV1

    UniProtKB/Swiss-Prot: POPD3_HUMAN, Q9HBV1
    Similarity: Belongs to the popeye family


    Find genes that share domains with POPDC3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: POPD3_HUMAN, Q9HBV1
    Function: May play an important role in heart development

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
         
    Find genes that share ontologies with POPDC3           About GenesLikeMe


    Phenotypes:
         3 GenomeRNAi human phenotypes for POPDC3:
     G0/1 arrest  Increased G1 DNA content  Increased cell size 

         1 MGI phenotypic allele for Popdc3 (no phenotypes)

    Find genes that share phenotypes with POPDC3           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for POPDC3

    miRNA
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    3 qRT-PCR Assays for microRNAs that regulate POPDC3:
    hsa-miR-3163 hsa-miR-340 hsa-miR-1272
    SwitchGear 3'UTR luciferase reporter plasmidPOPDC3 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat POPDC3

    Gene Editing
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    POPD3_HUMAN, Q9HBV1: Membrane; Multi-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    cytosol1
    nucleus1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016020membrane ----
    GO:0016021integral component of membrane NAS10882522

    Find genes that share ontologies with POPDC3           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for POPDC3
    Interactions:

        Search GeneGlobe Interaction Network for POPDC3

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--

    Find genes that share ontologies with POPDC3           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for POPDC3 (POPD3)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for POPDC3 gene: 
    NM_022361.4  

    Unigene Cluster for POPDC3:

    Popeye domain containing 3
    Hs.458336  [show with all ESTs]
    Unigene Representative Sequence: NM_022361
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000254765(uc003pra.3 uc003prb.3) ENST00000489134 ENST00000474760
    ENST00000429112
    miRNA
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    3 qRT-PCR Assays for microRNAs that regulate POPDC3:
    hsa-miR-3163 hsa-miR-340 hsa-miR-1272
    SwitchGear 3'UTR luciferase reporter plasmidPOPDC3 3' UTR sequence
    Inhib. RNA
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat POPDC3
    Primer
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    OriGene qPCR primer pairs and template standards for POPDC3
    OriGene qSTAR qPCR primer pairs in human, mouse for POPDC3
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat POPDC3
      QuantiTect SYBR Green Assays in human, mouse, rat POPDC3
      QuantiFast Probe-based Assays in human, mouse, rat POPDC3

    Additional mRNA sequence: 

    AF204171.1 AK225989.1 AK314101.1 BC022323.2 NR_024539.1 

    6 DOTS entries:

    DT.310711  DT.91712099  DT.100775199  DT.121384676  DT.95256618  DT.95355778 

    Selected AceView cDNA sequences (see all 49):

    BC022323 BM721545 CR591052 CK824801 CB115856 CA433204 CK005752 BX501538 
    NM_022361 BM800745 BQ005797 BP369262 BU156328 CK824800 BU627215 H84897 
    BX332531 BE670789 AF204171 AA861832 BX332532 AW188117 BF672934 BM264431 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for POPDC3 (see all 7)    About this scheme

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


    ECgene alternative splicing isoforms for POPDC3

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    POPDC3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    POPDC3 Expression
    About this image

    POPDC3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    POPDC3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.458336

    UniProtKB/Swiss-Prot: POPD3_HUMAN, Q9HBV1
    Tissue specificity: Expressed predominantly in skeletal muscle and detected in heart

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for POPDC3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for POPDC3 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Popdc31 , 5 popeye domain containing 31, 5 87.51(n)1
    89(a)1
      10 (23.35 cM)5
    789771  NM_024286.11  NP_077248.11 
     451780985 
    chicken
    (Gallus gallus)
    Aves POPDC31 popeye domain containing 3 76.09(n)
    79.86(a)
      395434  NM_204697.2  NP_990028.1 
    lizard
    (Anolis carolinensis)
    Reptilia POPDC36
    popeye domain containing 3
    72(a)
    1 ↔ 1
    GL343430.1(618670-624542)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.197272 Transcribed sequence with weak similarity to protein refNP_071756.1 (H.sapiens) popeye protein 3 [Homo sapiens] less 75.66(n)    AL960307.2 
    zebrafish
    (Danio rerio)
    Actinopterygii popdc31 popeye domain containing 3 64.77(n)
    61.22(a)
      415108  NM_001001848.1  NP_001001848.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta bves6
    bves
    17(a)
    1 → many
    X(20924990-20953418)


    ENSEMBL Gene Tree for POPDC3 (if available)
    TreeFam Gene Tree for POPDC3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for POPDC3 gene
    POPDC22  BVES2  
    2 SIMAP similar genes for POPDC3 using alignment to 2 protein entries:     POPD3_HUMAN (see all proteins):
    POPDC2    BVES

    Find genes that share paralogs with POPDC3           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for POPDC3 (see all 248)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs560608441,2
    C--103069371(+) ACACA-/CA/CAC
    ACACACACA
    GATTT
    1 -- int11NA 2
    rs1149239771,2
    C,F--105618397(+) ACCAGG/ATGGAC 2 -- int11Minor allele frequency- A:0.01WA 118
    rs11902981,2
    C,F,O,A,H--105618468(+) AGATAC/TCACGC 2 -- int123Minor allele frequency- T:0.40NS EA NA WA 2706
    rs607912581,2
    C,F--105618512(+) TTCTAC/TGCCAC 2 -- int11Minor allele frequency- T:0.04EA 120
    rs11902991,2
    C,H--105618761(+) TTGATC/ATTAAA 2 -- int115Minor allele frequency- A:0.01NS EA NA WA CSA 652
    rs1931526691,2
    --105618791(+) AGGGAA/GGTGGA 2 -- int10--------
    rs12126851,2
    H--105618879(+) AAATCC/ATAGAA 2 -- int15Minor allele frequency- A:0.00NS EA NA 414
    rs1457471751,2
    --105618882(+) TCCTAC/GAATGA 2 -- int10--------
    rs94860461,2
    C,F,A,H--105618976(+) AGCTGG/ATAGAT 2 -- int122Minor allele frequency- A:0.12NS EA NA WA CSA 2020
    rs1167749551,2
    C,F--105618982(+) TAGATG/ATTTGA 2 -- int11Minor allele frequency- A:0.01WA 118

    HapMap Linkage Disequilibrium report for POPDC3 (105605775 - 105627870 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for POPDC3:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2665928CNV Deletion23128226
    nsv886529CNV Loss21882294
    essv19736CNV CNV17122850
    dgv2000e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 605824    OMIM disorders: --


    Find genes that share disorders with POPDC3           About GenesLikeMe

    Genetic Association Database (GAD): POPDC3
    Human Genome Epidemiology (HuGE) Navigator: POPDC3 (5 documents)

    Export disorders for POPDC3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for POPDC3 gene, integrated from 10 sources (see all 15):
    (articles sorted by number of sources associating them with POPDC3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation and characterization of the novel popeye gene family expressed in skeletal muscle and heart. (PubMed id 10882522)1, 2, 3, 9 Andree B.... Brand T. (Dev. Biol. 2000)
    2. Genome-wide association study of severity in multiple sclerosis. (PubMed id 21654844)1, 4 (Genes Immun. 2011)
    3. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. (PubMed id 20546612)1, 4 Zhao J....Grant S.F. (BMC Med. Genet. 2010)
    4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    5. Genome-wide association study identifies sequence variants on 6q21 associated with age at menarche. (PubMed id 19448622)1, 4 Sulem P....Stefansson K. (Nat. Genet. 2009)
    6. Many sequence variants affecting diversity of adult human height. (PubMed id 18391951)1, 4 Gudbjartsson D.F....Stefansson K. (Nat. Genet. 2008)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    8. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (Nature 2003)
    9. Reduced Popdc3 expression correlates with high risk and poor survival in patients with gastric cancer. (PubMed id 22654436)1 Luo D....Luo J.B. (World J. Gastroenterol. 2012)
    10. Frequent silencing of popeye domain-containing genes, BVES and POPDC3, is associated with promoter hypermethylation in gastric cancer. (PubMed id 20627872)1 Kim M....Kim Y.S. (Carcinogenesis 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 64208 HGNC: 17649 AceView: POPDC3 Ensembl:ENSG00000132429 euGenes: HUgn64208
    ECgene: POPDC3 H-InvDB: POPDC3

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for POPDC3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for POPDC3 gene:
    Search GeneIP for patents involving POPDC3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from genOway)
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