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

Gene ID: 329872, updated on 2-Nov-2024

Summary

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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, Nov 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
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data 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

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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

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Associated conditions

Description Tests
head blebs
GeneReviews: Not available

Variation

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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

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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

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Preferred Names
FRAS1-related extracellular matrix protein 1

NCBI Reference Sequences (RefSeq)

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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

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