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EFEMP1 EGF containing fibulin extracellular matrix protein 1 [ Homo sapiens (human) ]

Gene ID: 2202, updated on 6-Jan-2019

Summary

Official Symbol
EFEMP1provided by HGNC
Official Full Name
EGF containing fibulin extracellular matrix protein 1provided by HGNC
Primary source
HGNC:HGNC:3218
See related
Ensembl:ENSG00000115380 MIM:601548
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DHRD; DRAD; FBNL; MLVT; MTLV; S1-5; FBLN3; FIBL-3
Summary
This gene encodes a member of the fibulin family of extracellular matrix glycoproteins. Like all members of this family, the encoded protein contains tandemly repeated epidermal growth factor-like repeats followed by a C-terminus fibulin-type domain. This gene is upregulated in malignant gliomas and may play a role in the aggressive nature of these tumors. Mutations in this gene are associated with Doyne honeycomb retinal dystrophy. Alternatively spliced transcript variants that encode the same protein have been described.[provided by RefSeq, Nov 2009]
Expression
Broad expression in placenta (RPKM 172.1), lung (RPKM 80.6) and 21 other tissues See more
Orthologs

Genomic context

See EFEMP1 in Genome Data Viewer
Location:
2p16.1
Exon count:
12
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (55865962..55924163, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (56093097..56151298, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene polyribonucleotide nucleotidyltransferase 1 Neighboring gene uncharacterized LOC107985811 Neighboring gene uncharacterized LOC112268416 Neighboring gene uncharacterized LOC105374690 Neighboring gene RNA, 7SK small nuclear pseudogene 208 Neighboring gene MIR217 host gene Neighboring gene microRNA 217

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Doyne honeycomb retinal dystrophy
MedGen: C1832174 OMIM: 126600 GeneReviews: Not available
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NHGRI GWAS Catalog

Description
A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
NHGRI GWA Catalog
A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis.
NHGRI GWA Catalog
A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits.
NHGRI GWA Catalog
Genome-wide association analysis identifies 20 loci that influence adult height.
NHGRI GWA Catalog
Genome-wide association analysis identifies six new loci associated with forced vital capacity.
NHGRI GWA Catalog
Genome-wide association study of height and body mass index in Australian twin families.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
NHGRI GWA Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
NHGRI GWA Catalog
Identification of 15 loci influencing height in a Korean population.
NHGRI GWA Catalog
Many sequence variants affecting diversity of adult human height.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog
Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 is identified to have a physical interaction with EGF containing fibulin-like extracellular matrix protein 1 (EFEMP1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Elastic fibre formation, organism-specific biosystem (from REACTOME)
    Elastic fibre formation, organism-specific biosystemElastic fibres (EF) are a major structural constituent of dynamic connective tissues such as large arteries and lung parenchyma, where they provide essential properties of elastic recoil and resilien...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Molecules associated with elastic fibres, organism-specific biosystem (from REACTOME)
    Molecules associated with elastic fibres, organism-specific biosystemProteins found associated with microfibrils include vitronectin (Dahlback et al. 1990), latent transforming growth factor beta-binding proteins (Kielty et al. 2002, Munger & Sheppard 2011), emilin (B...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ35535, MGC111353

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
epidermal growth factor receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
epidermal growth factor-activated receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
extracellular matrix structural constituent HDA PubMed 
growth factor activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
camera-type eye development IEP
Inferred from Expression Pattern
more info
PubMed 
embryonic eye morphogenesis IEP
Inferred from Expression Pattern
more info
PubMed 
epidermal growth factor receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of chondrocyte differentiation IDA
Inferred from Direct Assay
more info
PubMed 
peptidyl-tyrosine phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
post-embryonic eye morphogenesis IEP
Inferred from Expression Pattern
more info
PubMed 
regulation of signaling receptor activity IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
visual perception TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
EGF-containing fibulin-like extracellular matrix protein 1
Names
EGF containing fibulin like extracellular matrix protein 1
extracellular protein S1-5
fibulin-3

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_009098.1 RefSeqGene

    Range
    4635..62836
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001039348.3NP_001034437.1  EGF-containing fibulin-like extracellular matrix protein 1 precursor

    See identical proteins and their annotated locations for NP_001034437.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the longer transcript. Variants 2 and 3 encode the same protein.
    Source sequence(s)
    AC010895, AK290599, AK312639, U03877
    Consensus CDS
    CCDS1857.1
    UniProtKB/Swiss-Prot
    Q12805
    UniProtKB/TrEMBL
    A0A0S2Z4F1, B2R6M6
    Related
    ENSP00000347596.3, ENST00000355426.7
    Conserved Domains (4) summary
    smart00179
    Location:214244
    EGF_CA; Calcium-binding EGF-like domain
    pfam07645
    Location:173206
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:274297
    cEGF; Complement Clr-like EGF-like
    cl00057
    Location:292324
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  2. NM_001039349.2NP_001034438.1  EGF-containing fibulin-like extracellular matrix protein 1 precursor

    See identical proteins and their annotated locations for NP_001034438.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 2. Variants 2 and 3 encode the same protein.
    Source sequence(s)
    AC010895, BC014410, DA264704, U03877
    Consensus CDS
    CCDS1857.1
    UniProtKB/Swiss-Prot
    Q12805
    UniProtKB/TrEMBL
    A0A0S2Z4F1
    Related
    ENSP00000378058.2, ENST00000394555.6
    Conserved Domains (4) summary
    smart00179
    Location:214244
    EGF_CA; Calcium-binding EGF-like domain
    pfam07645
    Location:173206
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:274297
    cEGF; Complement Clr-like EGF-like
    cl00057
    Location:292324
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    55865962..55924163 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005264205.4XP_005264262.1  EGF-containing fibulin-like extracellular matrix protein 1 isoform X1

    Conserved Domains (3) summary
    smart00179
    Location:344383
    EGF_CA; Calcium-binding EGF-like domain
    pfam07645
    Location:303336
    EGF_CA; Calcium-binding EGF domain
    cl21504
    Location:174201
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
  2. XM_017003586.2XP_016859075.1  EGF-containing fibulin-like extracellular matrix protein 1 isoform X3

    UniProtKB/TrEMBL
    A0A0S2Z3V1
    Conserved Domains (2) summary
    smart00179
    Location:214253
    EGF_CA; Calcium-binding EGF-like domain
    pfam07645
    Location:173206
    EGF_CA; Calcium-binding EGF domain
  3. XM_024452755.1XP_024308523.1  EGF-containing fibulin-like extracellular matrix protein 1 isoform X2

    Conserved Domains (4) summary
    smart00179
    Location:214244
    EGF_CA; Calcium-binding EGF-like domain
    pfam07645
    Location:173206
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:274297
    cEGF; Complement Clr-like EGF-like
    cl00057
    Location:292324
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  4. XM_024452756.1XP_024308524.1  EGF-containing fibulin-like extracellular matrix protein 1 isoform X2

    Conserved Domains (4) summary
    smart00179
    Location:214244
    EGF_CA; Calcium-binding EGF-like domain
    pfam07645
    Location:173206
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:274297
    cEGF; Complement Clr-like EGF-like
    cl00057
    Location:292324
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  5. XM_024452757.1XP_024308525.1  EGF-containing fibulin-like extracellular matrix protein 1 isoform X3

    Conserved Domains (2) summary
    smart00179
    Location:214253
    EGF_CA; Calcium-binding EGF-like domain
    pfam07645
    Location:173206
    EGF_CA; Calcium-binding EGF domain

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_004105.3: Suppressed sequence

    Description
    NM_004105.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
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