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FREM3 Gene

protein-coding   GIFtS: 42
GCID: GC04M144498

FRAS1 Related Extracellular Matrix 3

  See FREM3-related disease
at  

(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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Aliases
FRAS1 Related Extracellular Matrix 31 2
FRAS1-Related Extracellular Matrix Protein 32

External Ids:    HGNC: 251721   Entrez Gene: 1667522   Ensembl: ENSG000001830907   OMIM: 6089465   UniProtKB: P0C0913   

Export aliases for FREM3 gene to outside databases

Previous GC identifers: GC04M144849 GC04M144717 GC04M140228


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for FREM3 Gene:
FREM3 (FRAS1 related extracellular matrix 3) is a protein-coding gene. Diseases associated with FREM3 include fraser syndrome. An important paralog of this gene is FREM2.

UniProtKB/Swiss-Prot: FREM3_HUMAN, P0C091
Function: Extracellular matrix protein which may play a role in cell adhesion (By similarity)




(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_000004.11  NC_018915.2  NT_016354.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the FREM3 gene promoter:
         STAT5B   ISGF-3   AML1a   MIF-1   CUTL1   Nkx2-5   LCR-F1   C/EBPalpha   CHOP-10   Cart-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for FREM3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FREM3


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

Entrez Gene cytogenetic band: 4q31.21   Ensembl cytogenetic band:  4q31.21   HGNC cytogenetic band: 4q31.21

FREM3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FREM3 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M144498:  view genomic region     (about GC identifiers)

Start:
144,498,455 bp from pter      End:
144,621,828 bp from pter
Size:
123,374 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, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: FREM3_HUMAN, P0C091 (See protein sequence)
Recommended Name: FRAS1-related extracellular matrix protein 3 precursor  
Size: 2139 amino acids; 238179 Da

Explore the universe of human proteins at neXtProt for FREM3: NX_P0C091

Explore proteomics data for FREM3 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn846, Asn1368, Asn1374, Asn1588
  • Modification sites at PhosphoSitePlus

  • See FREM3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001161707.1  
    ENSEMBL proteins: 
     ENSP00000332886  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR003644 Calx_beta

    Graphical View of Domain Structure for InterPro Entry P0C091

    ProtoNet protein and cluster: P0C091

    UniProtKB/Swiss-Prot: FREM3_HUMAN, P0C091
    Domain: The Calx-beta domains bind calcium with high affinity and undergo a major conformational shift upon
    binding (By similarity)
    Similarity: Belongs to the FRAS1 family
    Similarity: Contains 3 Calx-beta domains
    Similarity: Contains 12 CSPG (NG2) repeats


    Find genes that share domains with FREM3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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: FREM3_HUMAN, P0C091
    Function: Extracellular matrix protein which may play a role in cell adhesion (By similarity)

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding ----
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with FREM3           About GenesLikeMe


    Animal Models:
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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
    FREM3_HUMAN, P0C091: Secreted, extracellular space, extracellular matrix (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular2
    cytosol1
    endoplasmic reticulum1
    golgi apparatus1
    lysosome1
    mitochondrion1
    peroxisome1
    plasma membrane1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005604basement membrane IEA--
    GO:0005615extracellular space IDA--
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--
    GO:0031012colocalizes with extracellular matrix TAS--

    Find genes that share ontologies with FREM3           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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    Interactions:

        Search GeneGlobe Interaction Network for FREM3

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007154cell communication IEA--
    GO:0007155cell adhesion IEA--

    Find genes that share ontologies with FREM3           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 FREM3

    1 HMDB Compound for FREM3    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--



    (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 FREM3 gene: 
    NM_001168235.1  

    Unigene Cluster for FREM3:

    FRAS1 related extracellular matrix 3
    Hs.252714  [show with all ESTs]
    Unigene Representative Sequence: NM_001168235
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000329798(uc021xsj.1) ENST00000508899
    miRNA
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    hsa-miR-4265 hsa-miR-1258 hsa-miR-4296
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    Inhib. RNA
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    2 DOTS entries:

    DT.436368  DT.439230 

    10 AceView cDNA sequences:

    Z43936 AA350251 BE223071 AW953229 T33332 R44016 H09749 R19029 
    R44783 R19117 

    GeneLoc Exon Structure


    (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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    FREM3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    FREM3 Expression
    About this image

    FREM3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    FREM3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.252714
        Custom PCR Arrays for FREM3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FREM3

    (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 chordates.

    Orthologs for FREM3 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Frem31 , 5 Fras1 related extracellular matrix protein 31, 5 76.96(n)1
    69.13(a)1
      8 (38.35 cM)5
    3333151  NM_001167898.11  NP_001161370.11 
     806110805 
    chicken
    (Gallus gallus)
    Aves --
    Uncharacterized protein
    15(a)
    many ↔ many
    Z(16411044-16453742)
    lizard
    (Anolis carolinensis)
    Reptilia FREM36
    FRAS1 related extracellular matrix 3
    42(a)
    1 ↔ 1
    5(118414608-118507635)
    zebrafish
    (Danio rerio)
    Actinopterygii frem36
    Fras1 related extracellular matrix 3
    40(a)
    1 ↔ 1
    1(35322204-35361675) ENSDARG00000074677


    ENSEMBL Gene Tree for FREM3 (if available)
    TreeFam Gene Tree for FREM3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for FREM3 gene
    FREM22  CSPG42  FREM12  FRAS12  
    2 SIMAP similar genes for FREM3 using alignment to 2 protein entries:     FREM3_HUMAN (see all proteins):
    FREM2    FREM1

    Find genes that share paralogs with FREM3           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 FREM3 (see all 2451)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2016085011,2
    C--144498291(-) CTTTTA/GTAAAA 1 -- int10--------
    rs1442903281,2
    C--144498367(+) AAAATC/TGAAGA 1 -- int10--------
    rs1487407801,2
    --144498376(+) GAATTA/CGCTAA 1 -- int10--------
    rs1923423591,2
    C--144498472(+) AACTTC/TTGATT 1 -- int10--------
    rs1843497051,2
    --144498526(+) AAAACA/CAAATA 1 -- int10--------
    rs1412946001,2
    --144498612(+) AGTCAA/TATAAA 1 -- ut310--------
    rs1462371321,2
    C--144498675(+) TGATAC/TCCCAG 1 -- ut310--------
    rs1891237391,2
    --144498678(+) TATCCC/TAGAAT 1 -- ut310--------
    rs1815150791,2
    --144498691(+) CTAAGA/TTCTAT 1 -- ut310--------
    rs14976221,2
    C,F,H--144498768(-) CTTTGA/GTTGAA 2 D G mis112Minor allele frequency- G:0.02MN NS EA NA WA 1402

    HapMap Linkage Disequilibrium report for FREM3 (144498455 - 144621828 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for FREM3 (see all 12):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2728475CNV Deletion23290073
    esv4609CNV Deletion18987735
    esv2669991CNV Deletion23128226
    nsv4533CNV Insertion18451855
    esv9197CNV Loss19470904
    nsv428452CNV Loss18775914
    nsv830103CNV Loss17160897
    nsv293188CNV Loss16902084
    dgv1684e1CNV Complex17122850
    dgv1683e1CNV Complex17122850

    Human Gene Mutation Database (HGMD): FREM3
    Site Specific Mutation Identification with PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for FREM3

    (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: 608946    OMIM disorders: --

    1 disease for FREM3:    
    About MalaCards
    fraser syndrome

    2 diseases from the University of Copenhagen DISEASES database for FREM3:
    Renal agenesis     Syndactyly

    Find genes that share disorders with FREM3           About GenesLikeMe


    Export disorders for FREM3 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 FREM3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with FREM3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The extracellular matrix gene Frem1 is essential for the normal adhesion of the embryonic epidermis. (PubMed id 15345741)1, 2, 3 Smyth I.... Jackson I.J. (Proc. Natl. Acad. Sci. U.S.A. 2004)
    2. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)1, 2 Hillier L.W.... Wilson R.K. (Nature 2005)
    3. A study of the combined effects of the EHD3 and FREM3 genes in patients with major depressive disorder. (PubMed id 22337703)1 Shi C....Xu Q. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2012)
    4. Basement membrane localization of Frem3 is independent of the Fras1/Frem1/Frem2 protein complex within the sublamina densa. (PubMed id 17596926)9 Petrou P....Chalepakis G. (Matrix Biol. 2007)
    5. The Fras1/Frem family of extracellular matrix proteins: structure, function, and association with Fraser syndrome and the mouse bleb phenotype. (PubMed id 18661360)9 Petrou P....Chalepakis G. (Connect. Tissue Res. 2008)
    6. Ultrastructural localization of Fras1 in the sublamina densa of embryonic epithelial basement membranes. (PubMed id 17576586)9 Dalezios Y....Chalepakis G. (Arch. Dermatol. Res. 2007)

    (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: 166752 HGNC: 25172 AceView: FREM3.1 Ensembl:ENSG00000183090 euGenes: HUgn166752
    ECgene: FREM3 H-InvDB: FREM3

    (According to HUGE)
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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 FREM3 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 FREM3 gene:
    Search GeneIP for patents involving FREM3

    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, LSBio, 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 inGenious Targeting Laboratory, genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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