U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    Frem1 Fras1 related extracellular matrix protein 1 [ Mus musculus (house mouse) ]

    Gene ID: 329872, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Frem1provided by MGI
    Official Full Name
    Fras1 related extracellular matrix protein 1provided by MGI
    Primary source
    MGI:MGI:2670972
    See related
    Ensembl:ENSMUSG00000059049 AllianceGenome:MGI:2670972
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    heb; crf11; eyes2; qbrick; D430009N09; D630008K06; eye<m02Jus>
    Summary
    Predicted to enable carbohydrate binding activity and metal ion binding activity. Acts upstream of or within cell-matrix adhesion. Located in basement membrane. Is expressed in several structures, including alimentary system; bone; brain; sensory organ; and skin. Used to study Fraser syndrome; chromosome 9p deletion syndrome; and congenital diaphragmatic hernia. Human ortholog(s) of this gene implicated in congenital diaphragmatic hernia. Orthologous to human FREM1 (FRAS1 related extracellular matrix 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in limb E14.5 (RPKM 2.7), CNS E11.5 (RPKM 2.1) and 19 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Frem1 in Genome Data Viewer
    Location:
    4 C3; 4 39.4 cM
    Exon count:
    42
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (82816157..82970743, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (82897920..83052506, complement)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene zinc finger, DHHC domain containing 21 Neighboring gene VISTA enhancer mm56 Neighboring gene cerberus 1, DAN family BMP antagonist Neighboring gene predicted gene, 33260 Neighboring gene STARR-seq mESC enhancer starr_10628 Neighboring gene predicted gene, 24884 Neighboring gene predicted gene, 46887

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Head blebs: a new mutation on chromosome 4 of the mouse. Varnum DS, et al. J Hered, 1981 Jul-Aug. PMID 6793660
    2. Overlapping and divergent localization of Frem1 and Fras1 and its functional implications during mouse embryonic development. Petrou P, et al. Exp Cell Res, 2007 Mar 10. PMID 17240369
    3. FREM1 mutations cause bifid nose, renal agenesis, and anorectal malformations syndrome. Alazami AM, et al. Am J Hum Genet, 2009 Sep. PMID 19732862, Free PMC Article
    4. Manitoba-oculo-tricho-anal (MOTA) syndrome is caused by mutations in FREM1. Slavotinek AM, et al. J Med Genet, 2011 Jun. PMID 21507892, Free PMC Article
    5. Frem1 activity is regulated by Sonic hedgehog signaling in the cranial neural crest mesenchyme during midfacial morphogenesis. McLaughlin MT, et al. Dev Dyn, 2023 Apr. PMID 36495293, Free PMC Article

    See all (41) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Frem1 activity is regulated by Sonic hedgehog signaling in the cranial neural crest mesenchyme during midfacial morphogenesis.
      Title: Frem1 activity is regulated by Sonic hedgehog signaling in the cranial neural crest mesenchyme during midfacial morphogenesis.
    2. loss of FREM1 function promotes epidermal blistering in Fraser syndrome as a consequence of reduced PDGFC activity, in addition to its stabilising role in the basement membrane
      Title: Regulation of PDGFC signalling and extracellular matrix composition by FREM1 in mice.
    3. FREM1-deficient mice faithfully recapitulate many of the phenotypes seen in individuals with FREM1 deficiency and that variations in GATA4 and SLIT3 expression modulate some FREM1-related phenotypes in mice.
      Title: Novel frem1-related mouse phenotypes and evidence of genetic interactions with gata4 and slit3.
    4. We conclude that FREM1 plays a critical role in the development of the diaphragm and that FREM1 deficiency can cause CDH in both humans and mice.
      Title: Deficiency of FRAS1-related extracellular matrix 1 (FREM1) causes congenital diaphragmatic hernia in humans and mice.
    5. the loss of QBRICK significantly diminished The expression of nephronectin, an integrin alpha8beta1 ligand necessary for renal development.
      Title: Basement membrane assembly of the integrin α8β1 ligand nephronectin requires Fraser syndrome-associated proteins.
    6. Frem1 mutant mice is the first bona fide mouse model of human metopic craniosynostosis and a new model for midfacial hypoplasia.
      Title: Heterozygous mutations of FREM1 are associated with an increased risk of isolated metopic craniosynostosis in humans and mice.
    7. TILRR, an isoform encoded by an alternatively spliced FREM1 mRNA, is an IL-1RI co-receptor that associates with the signaling receptor complex to enhance recruitment of MyD88 and control Ras-dependent amplification of NF-kappaB and inflammatory responses.
      Title: TILRR, a novel IL-1RI co-receptor, potentiates MyD88 recruitment to control Ras-dependent amplification of NF-kappaB.
    8. The phenotypic variability reported for different Frem1 mouse mutants suggests that the apparently distinct phenotype of bifid nose and anorectal and renal anomalies syndrome in humans may represent a previously unrecognized variant of Fraser syndrome.
      Title: FREM1 mutations cause bifid nose, renal agenesis, and anorectal malformations syndrome.
    9. The localization pattern of Fras1 and Frem2 was indistinguishable, while both proteins along with Frem3 could be detected even in the absence of Frem1.
      Title: Differential localization profile of Fras1/Frem proteins in epithelial basement membranes of newborn and adult mice.
    10. in the absence of Fras1 the basement membrane localization of Frem3 remains unaffected in contrast to Frem1 and Frem2 which are completely abolished from the basement membrane.
      Title: Basement membrane localization of Frem3 is independent of the Fras1/Frem1/Frem2 protein complex within the sublamina densa.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    Phenotypes

    Go to the top of the page Help

    Associated conditions

    Description Tests
    head blebs
    GeneReviews: Not available

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Chemically induced (ENU) (4)  1 citation
    • Endonuclease-mediated (1) 
    • Spontaneous (1) 
    • Targeted (2)  1 citation

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in anatomical structure morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell communication IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within cell-matrix adhesion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in craniofacial suture morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in craniofacial suture morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in basement membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    FRAS1-related extracellular matrix protein 1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001198811.2 → NP_001185740.1  FRAS1-related extracellular matrix protein 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001185740.1

      Status: VALIDATED

      Source sequence(s)
      AB160986
      Consensus CDS
      CCDS57281.1
      UniProtKB/TrEMBL
      A2ADN1
      Related
      ENSMUSP00000102849.2, ENSMUST00000107230.9
      Conserved Domains (3) summary
      smart00034
      Location:2046 → 2168
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:1489 → 1596
      Cadherin_3; Cadherin-like
      cl02522
      Location:1746 → 1828
      Calx-beta; Calx-beta domain

    2. NM_177863.5 → NP_808531.2  FRAS1-related extracellular matrix protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_808531.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer protein (isoform 1).
      Source sequence(s)
      AL670958
      Consensus CDS
      CCDS38791.1
      UniProtKB/Swiss-Prot
      Q5H8C2, Q5M7B3, Q684R7, Q8C732
      Related
      ENSMUSP00000071627.6, ENSMUST00000071708.12
      Conserved Domains (3) summary
      smart00034
      Location:2065 → 2187
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:364 → 508
      Cadherin_3; Cadherin-like
      cl02522
      Location:1765 → 1847
      Calx-beta; Calx-beta domain

    RNA

    1. NR_154662.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AB160986, AL670958, BC145274

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000070.7 Reference GRCm39 C57BL/6J

      Range
      82816157..82970743 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006538013.5 → XP_006538076.1  FRAS1-related extracellular matrix protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006538076.1

      UniProtKB/TrEMBL
      A2ADN1
      Conserved Domains (3) summary
      smart00034
      Location:2046 → 2168
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:1489 → 1596
      Cadherin_3; Cadherin-like
      cl02522
      Location:1746 → 1828
      Calx-beta; Calx-beta domain

    2. XM_011250055.4 → XP_011248357.1  FRAS1-related extracellular matrix protein 1 isoform X1

      See identical proteins and their annotated locations for XP_011248357.1

      UniProtKB/TrEMBL
      A2ADN1
      Conserved Domains (3) summary
      smart00034
      Location:2046 → 2168
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:1489 → 1596
      Cadherin_3; Cadherin-like
      cl02522
      Location:1746 → 1828
      Calx-beta; Calx-beta domain

    3. XM_006538015.2 → XP_006538078.1  FRAS1-related extracellular matrix protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006538078.1

      UniProtKB/TrEMBL
      A2ADN1
      Conserved Domains (3) summary
      smart00034
      Location:2046 → 2168
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:1489 → 1596
      Cadherin_3; Cadherin-like
      cl02522
      Location:1746 → 1828
      Calx-beta; Calx-beta domain

    4. XM_006538014.4 → XP_006538077.1  FRAS1-related extracellular matrix protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006538077.1

      UniProtKB/TrEMBL
      A2ADN1
      Conserved Domains (3) summary
      smart00034
      Location:2046 → 2168
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:1489 → 1596
      Cadherin_3; Cadherin-like
      cl02522
      Location:1746 → 1828
      Calx-beta; Calx-beta domain

    5. XM_030253616.1 → XP_030109476.1  FRAS1-related extracellular matrix protein 1 isoform X2

      Conserved Domains (3) summary
      smart00034
      Location:1741 → 1863
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:1184 → 1291
      Cadherin_3; Cadherin-like
      cl02522
      Location:1441 → 1523
      Calx-beta; Calx-beta domain

    6. XM_006538018.2 → XP_006538081.1  FRAS1-related extracellular matrix protein 1 isoform X3

      Conserved Domains (3) summary
      smart00034
      Location:1368 → 1490
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:811 → 918
      Cadherin_3; Cadherin-like
      cl02522
      Location:1068 → 1150
      Calx-beta; Calx-beta domain

    7. XM_036164191.1 → XP_036020084.1  FRAS1-related extracellular matrix protein 1 isoform X4

      Conserved Domains (3) summary
      smart00034
      Location:582 → 704
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:25 → 132
      Cadherin_3; Cadherin-like
      cl02522
      Location:282 → 364
      Calx-beta; Calx-beta domain

    8. XM_036164192.1 → XP_036020085.1  FRAS1-related extracellular matrix protein 1 isoform X4

      Conserved Domains (3) summary
      smart00034
      Location:582 → 704
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:25 → 132
      Cadherin_3; Cadherin-like
      cl02522
      Location:282 → 364
      Calx-beta; Calx-beta domain

    RNA

    1. XR_390326.4 RNA Sequence

    2. XR_001784157.2 RNA Sequence

    3. XR_003954973.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q684R7.1 GenPept UniProtKB/Swiss-Prot:Q684R7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools