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

Gene ID: 329872, updated on 5-Mar-2024

Summary

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; central nervous system; eye; genitourinary system; 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, Apr 2022]
Expression
Broad expression in limb E14.5 (RPKM 2.7), CNS E11.5 (RPKM 2.1) and 19 other tissues See more
Orthologs
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Genomic context

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
head blebs
GeneReviews: Not available

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

General gene information

Markers

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
 
acts_upstream_of_or_within cell adhesion IEA
Inferred from Electronic Annotation
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
 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
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

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_001198811.2NP_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, E9Q5Z7
    Related
    ENSMUSP00000102849.2, ENSMUST00000107230.9
    Conserved Domains (3) summary
    smart00034
    Location:20462168
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:14891596
    Cadherin_3; Cadherin-like
    cl02522
    Location:17461828
    Calx-beta; Calx-beta domain
  2. NM_177863.5NP_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
    UniProtKB/TrEMBL
    E9Q5Z7
    Related
    ENSMUSP00000071627.6, ENSMUST00000071708.12
    Conserved Domains (3) summary
    smart00034
    Location:20652187
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:364508
    Cadherin_3; Cadherin-like
    cl02522
    Location:17651847
    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_006538013.5XP_006538076.1  FRAS1-related extracellular matrix protein 1 isoform X1

    See identical proteins and their annotated locations for XP_006538076.1

    UniProtKB/TrEMBL
    A2ADN1, E9Q5Z7
    Conserved Domains (3) summary
    smart00034
    Location:20462168
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:14891596
    Cadherin_3; Cadherin-like
    cl02522
    Location:17461828
    Calx-beta; Calx-beta domain
  2. XM_011250055.4XP_011248357.1  FRAS1-related extracellular matrix protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011248357.1

    UniProtKB/TrEMBL
    A2ADN1, E9Q5Z7
    Conserved Domains (3) summary
    smart00034
    Location:20462168
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:14891596
    Cadherin_3; Cadherin-like
    cl02522
    Location:17461828
    Calx-beta; Calx-beta domain
  3. XM_006538015.2XP_006538078.1  FRAS1-related extracellular matrix protein 1 isoform X1

    See identical proteins and their annotated locations for XP_006538078.1

    UniProtKB/TrEMBL
    A2ADN1, E9Q5Z7
    Conserved Domains (3) summary
    smart00034
    Location:20462168
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:14891596
    Cadherin_3; Cadherin-like
    cl02522
    Location:17461828
    Calx-beta; Calx-beta domain
  4. XM_006538014.4XP_006538077.1  FRAS1-related extracellular matrix protein 1 isoform X1

    See identical proteins and their annotated locations for XP_006538077.1

    UniProtKB/TrEMBL
    A2ADN1, E9Q5Z7
    Conserved Domains (3) summary
    smart00034
    Location:20462168
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:14891596
    Cadherin_3; Cadherin-like
    cl02522
    Location:17461828
    Calx-beta; Calx-beta domain
  5. XM_030253616.1XP_030109476.1  FRAS1-related extracellular matrix protein 1 isoform X2

    UniProtKB/TrEMBL
    E9Q5Z7
    Conserved Domains (3) summary
    smart00034
    Location:17411863
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:11841291
    Cadherin_3; Cadherin-like
    cl02522
    Location:14411523
    Calx-beta; Calx-beta domain
  6. XM_006538018.2XP_006538081.1  FRAS1-related extracellular matrix protein 1 isoform X3

    Conserved Domains (3) summary
    smart00034
    Location:13681490
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:811918
    Cadherin_3; Cadherin-like
    cl02522
    Location:10681150
    Calx-beta; Calx-beta domain
  7. XM_036164191.1XP_036020084.1  FRAS1-related extracellular matrix protein 1 isoform X4

    Conserved Domains (3) summary
    smart00034
    Location:582704
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:25132
    Cadherin_3; Cadherin-like
    cl02522
    Location:282364
    Calx-beta; Calx-beta domain
  8. XM_036164192.1XP_036020085.1  FRAS1-related extracellular matrix protein 1 isoform X4

    Conserved Domains (3) summary
    smart00034
    Location:582704
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    pfam16184
    Location:25132
    Cadherin_3; Cadherin-like
    cl02522
    Location:282364
    Calx-beta; Calx-beta domain

RNA

  1. XR_390326.4 RNA Sequence

  2. XR_001784157.2 RNA Sequence

  3. XR_003954973.1 RNA Sequence