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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

FREM2 Gene

protein-coding   GIFtS: 51
GCID: GC13P039261

FRAS1 related extracellular matrix protein 2

 Explore 5 diseases affiliated with
FREM2 via our new
 Human Malady Compendium 
Biological research products
for FREM2
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
FRAS1 Related Extracellular Matrix Protein 21 2
ECM3 Homolog2 3
DKFZp686J08111
FRAS1-Related Extracellular Matrix Protein 22

External Ids:    HGNC: 253961   Entrez Gene: 3416402   Ensembl: ENSG000001508937   OMIM: 6089455   UniProtKB: Q5SZK83   

Export aliases for FREM2 gene to outside databases

Previous GC identifers: GC13P038159 GC13P020059


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for FREM2:
This gene encodes a membrane protein that belongs to the FRAS1 family. This extracellular matrix protein is thought to
be required for maintaining the integrity of the skin epithelium and the differentiated state of renal epithelia. The
protein localizes to the basement membrane, forming a ternary complex that plays a role in epidermal-dermal
interactions during morphogenetic processes. Mutations in this gene are associated with Fraser syndrome. (provided by
RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: FREM2_HUMAN, Q5SZK8
Function: Extracellular matrix protein required for maintenance of the integrity of the skin epithelium and for
maintenance of renal epithelia. May be required for epidermal adhesion

Gene Wiki entry for FREM2


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000013.10  NC_018924.1  NT_024524.14  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the FREM2 gene promoter:
         p53   GCNF   NRSF form 1   Nkx2-5   NRSF form 2   GATA-1   SRY   GCNF-1   GCNF-2   RSRFC4   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): FREM2 promoter sequence
   Search SABiosciences Chromatin IP Primers for FREM2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat FREM2


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

Entrez Gene cytogenetic band: 13q13.3   Ensembl cytogenetic band:  13q13.3   HGNC cytogenetic band: 13q13.3

FREM2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FREM2 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13P039261:  view genomic region     (about GC identifiers)

Start:
39,261,173 bp from pter      End:
39,461,268 bp from pter
Size:
200,096 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: FREM2_HUMAN, Q5SZK8 (See protein sequence)
Recommended Name: FRAS1-related extracellular matrix protein 2 precursor  
Size: 3169 amino acids; 351157 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein; Extracellular side (Potential)
Sequence caution: Sequence=BAC87040.1; Type=Erroneous initiation;
Secondary accessions: Q4QQG1 Q5H9N8 Q5T6Q1 Q6N057 Q6ZSB4 Q7Z305 Q7Z341
Alternative splicing: 2 isoforms:  Q5SZK8-1   Q5SZK8-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for FREM2: NX_Q5SZK8

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q5SZK8

  • FREM2 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_997244.3  
    ENSEMBL proteins: 
     ENSP00000280481  

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    Uscn Proteins for FREM2

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005604basement membrane IEA--
    GO:0005886plasma membrane IEA--
    GO:0016021integral to membrane IEA--


    FREM2 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    FREM2 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR003644 Calx_beta
     IPR002126 Cadherin

    Graphical View of Domain Structure for InterPro Entry Q5SZK8

    ProtoNet protein and cluster: Q5SZK8

    UniProtKB/Swiss-Prot: FREM2_HUMAN, Q5SZK8
    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 5 Calx-beta domains
    Similarity: Contains 12 CSPG (NG2) repeats


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: FREM2_HUMAN, Q5SZK8
    Function: Extracellular matrix protein required for maintenance of the integrity of the skin epithelium and for
    maintenance of renal epithelia. May be required for epidermal adhesion

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    hsa-miR-607 hsa-let-7d hsa-miR-429 hsa-miR-29a hsa-miR-628-3p hsa-let-7g hsa-miR-9 hsa-let-7a
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--


    FREM2 for ontologies           About GeneDecksing


    Animal Models:
         15 MGI mutant phenotypes (inferred from 5 alleles(MGI details for Frem2):
     cardiovascular system  craniofacial  embryogenesis  growth/size  hearing/vestibular/ear 
     integument  limbs/digits/tail  mortality/aging  nervous system  pigmentation 
     renal/urinary system  reproductive system  respiratory system  skeleton  vision/eye 

    FREM2 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for FREM2

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    3 Interacting proteins for FREM2 (Q5SZK83 ENSP000002804814) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RYKP349253, ENSP000002960844I2D: score=1 STRING: ENSP00000296084
    GRIP1Q9Y3R03I2D: score=1 
    STK3Q131883I2D: score=1 
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002009morphogenesis of an epithelium IEA--
    GO:0007154cell communication IEA--
    GO:0007156homophilic cell adhesion IEA--
    GO:0048839inner ear development IEA--


    FREM2 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for FREM2

    1 HMDB Compound for FREM2    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--
    Search CenterWatch for drugs/clinical trials and news about FREM2 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for FREM2 gene: 
    NM_207361.4  

    Unigene Cluster for FREM2:

    FRAS1 related extracellular matrix protein 2
    Hs.253994  [show with all ESTs]
    Unigene Representative Sequence: NM_207361
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000280481(uc001uwv.3 uc001uww.3) ENST00000482551

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    hsa-miR-607 hsa-let-7d hsa-miR-429 hsa-miR-29a hsa-miR-628-3p hsa-let-7g hsa-miR-9 hsa-let-7a
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat FREM2
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    Additional cDNA sequence: 

    AK127571.1 BX538150.1 BX538304.1 BX640686.1 CR933724.1 

    4 DOTS entries:

    DT.75169242  DT.101956127  DT.95073344  DT.101957386 

    24/30 AceView cDNA sequences (see all 30):

    NM_207361 BF431464 AW612422 AI289430 BQ719838 AI913099 AK127571 AI274791 
    AW194836 AI375575 AW303485 AL708377 BF476132 AI370601 BX640686 BX538150 
    CD655887 BX538304 BG484526 AA448605 AW858448 BM983495 AW242548 AL119393 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    FREM2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TATGTAGTTC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    FREM2 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    6 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    OvaryAntral FollicleMature Granulosa CellsOvary
    Spinal CordSpinal Ventral ColumnsVentral Spinal Cord Progenitor CellsMotor Neurons
    BrainMedulla OblongataBrain
    KidneyMetanephrosKidney
    Neural TubeMetencephalonNeural Tube
    Spinal CordSpinal Ventral ColumnsSpinal Cord
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Nkx2-1 GFP+ cells (Efficient derivation...)

    See FREM2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for FREM2

    SOURCE GeneReport for Unigene cluster: Hs.253994
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FREM2

    (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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for FREM2 gene from 2/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves FREM21 FRAS1 related extracellular matrix protein 2 73.63(n)
    77.47(a)
      418893  XM_417087.3  XP_417087.3 
    zebrafish
    (Danio rerio)
    Actinopterygii frem2b6
    frem2a6
    Fras1 related extracellular matrix protein 2a
    69(a)
    67(a)
    1 ↔ many
    1 ↔ many
    15(33278548-33437985)
    10(26616760-26746559)


    ENSEMBL Gene Tree for FREM2 (if available)
    TreeFam Gene Tree for FREM2 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for FREM2 gene
    CSPG42  FREM12  FREM32  FRAS12  
    2 SIMAP similar genes for FREM2 using alignment to 1 protein entry:     FREM2_HUMAN:
    FREM3    FRAS1

    FREM2 for paralogs           About GeneDecksing


    2 Pseudogenes.org Pseudogenes for FREM2
    PGOHUM00000248518 PGOHUM00000245716


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/3748 NCBI SNPs in FREM2 are shown (see all 3748    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1144093051,2
    C,other33529841(+) TTATTC/TGTTAT 2 R C mis11Minor allele frequency- T:0.01EA 208
    rs734578911,2
    C,F,--20058048(+) TTAAAT/CTGATC 1 -- us2k14Minor allele frequency- C:0.37WA CSA 124
    rs170584301,2
    C,F,H,--20058096(+) TATGAT/ATCCTG 1 -- us2k19Minor allele frequency- A:0.10NA NS EA CSA WA 662
    rs740481161,2
    C,--20058339(+) AAAAAG/CACATT 1 -- us2k12Minor allele frequency- C:0.18WA 120
    rs749167391,2
    F,--20058547(+) AAGTTT/CAAATT 1 -- us2k11Minor allele frequency- C:0.05WA 118
    rs1138183011,2
    --20058808(+) GAAGAG/CAACAG 1 -- us2k11Minor allele frequency- C:0.50CSA 2
    rs1125648711,2
    --20059334(+) ACAGCC/AGTGTG 1 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs24964211,2
    C,F,A,--20059477(+) CCCCGC/TAGTTT 1 -- us2k13Minor allele frequency- T:0.22WA 122
    rs79978381,2
    C,F,H,--20059652(+) AGTGGA/GGGGAT 1 -- ut5112Minor allele frequency- G:0.12NS EA NA CSA WA 1309
    rs170584331,2
    C,H--20063045(+) GAGAAT/GTGGTG 2 /S /I mis19Minor allele frequency- G:0.00NA NS EA 544

    HapMap Linkage Disequilibrium report for FREM2 (39261173 - 39461268 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for FREM2
         2 CNVs: 58624 43565
    Human Gene Mutation Database (HGMD): FREM2

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    FREM2 for disorders           About GeneDecksing

    OMIM gene information: 608945   
    OMIM disorders: 219000  
    UniProtKB/Swiss-Prot: FREM2_HUMAN, Q5SZK8
  • Defects in FREM2 are a cause of Fraser syndrome (FRASS) [MIM:219000]. Fraser syndrome is a multisystem
  • malformation usually comprising cryptophthalmos, cutaneous syndactyly, ear abnormalities, renal agenesis and
    congenital heart defects

    5 diseases for FREM2:    About MalaCards
    fraser syndrome    cryptophthalmos    macrostomia    renal agenesis
    syndactyly

    2 diseases from the University of Copenhagen DISEASES database for FREM2:
    Syndactyly     Renal agenesis

    1 Novoseek disease relationship for FREM2 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    fraser syndrome 93.3 2 17596926 (1), 18563433 (1), 18155042 (1), 17251066 (1) (see all 7)


    Export disorders for FREM2 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)
    About This Section

    PubMed articles for FREM2 gene, integrated from 9 sources (see all 26):
    (articles sorted by number of sources associating them with FREM2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PubMed id 16335952)1, 2 Liu T.... Smith R.D. (2005)
    2. Identification of a new gene mutated in Fraser syndrome and mouse myelencephalic blebs. (PubMed id 15838507)1, 2 Jadeja S....Scambler P.J. (2005)
    3. The DNA sequence and analysis of human chromosome 13. (PubMed id 15057823)1, 2 Dunham A.... Ross M.T. (2004)
    4. The extracellular matrix gene Frem1 is essential for the normal adhesion of the embryonic epidermis. (PubMed id 15345741)1, 3 Smyth I.... Jackson I.J. (2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    6. Molecular study of 33 families with Fraser syndrome new data and mutation review. (PubMed id 18671281)1, 9 van Haelst M.M....Scambler P.J. (2008)
    7. Identification of two novel CAKUT-causing genes by mas sively parallel exon resequencing of candidate genes in patients with unilateral renal agenesis. (PubMed id 21900877)1 Saisawat P....Hildebrandt F. (2012)
    8. Amplification of the STOML3, FREM2, and LHFP genes is associated with mesenchymal differentiation in gliosarcoma. (PubMed id 22538188)1 Nagaishi M....Ohgaki H. (2012)
    9. Genome-wide association study does not reveal major ge netic determinants for anti-cytomegalovirus antibody response. (PubMed id 21993531)1 Kuparinen T....Hurme M. (2012)
    10. Mindbomb 1, an E3 ubiquitin ligase, forms a complex w ith RYK to activate Wnt/I^-catenin signaling. (PubMed id 21875946)1 Berndt J.D....Moon R.T. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 341640 HGNC: 25396 AceView: FREM2 Ensembl:ENSG00000150893 euGenes: HUgn341640
    ECgene: FREM2 H-InvDB: FREM2

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for FREM2 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/FREM2

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for FREM2 gene:
    Search GeneIP for patents involving FREM2

    GeneCards and IP:
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