Human Gene EFEMP1 (ENST00000355426.8_7) from GENCODE V47lift37
  Description: EGF containing fibulin extracellular matrix protein 1, transcript variant 2 (from RefSeq NM_001039348.3)
Gencode Transcript: ENST00000355426.8_7
Gencode Gene: ENSG00000115380.20_13
Transcript (Including UTRs)
   Position: hg19 chr2:56,093,102-56,150,917 Size: 57,816 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr2:56,094,208-56,149,575 Size: 55,368 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:56,093,102-56,150,917)mRNA (may differ from genome)Protein (493 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: FBLN3_HUMAN
DESCRIPTION: RecName: Full=EGF-containing fibulin-like extracellular matrix protein 1; AltName: Full=Extracellular protein S1-5; AltName: Full=Fibrillin-like protein; AltName: Full=Fibulin-3; Short=FIBL-3; Flags: Precursor;
FUNCTION: Binds EGFR, the EGF receptor, inducing EGFR autophosphorylation and the activation of downstream signaling pathways. May play a role in cell adhesion and migration. May function as a negative regulator of chondrocyte differentiation. In the olfactory epithelium, it may regulate glial cell migration, differentiation and the ability of glial cells to support neuronal neurite outgrowth.
SUBUNIT: Interacts with ECM1. Interacts with TIMP3.
INTERACTION: P10398:ARAF; NbExp=3; IntAct=EBI-536772, EBI-365961; P54259:ATN1; NbExp=3; IntAct=EBI-536772, EBI-945980;
SUBCELLULAR LOCATION: Secreted, extracellular space (By similarity). Secreted, extracellular space, extracellular matrix (By similarity). Note=Localizes to the lamina propria underneath the olfactory epithelium (By similarity).
TISSUE SPECIFICITY: In the eye, associated with photoreceptor outer and inner segment regions, the nerve fiber layer, outer nuclear layer and inner and outer plexiform layers of the retina.
DISEASE: Defects in EFEMP1 are a cause of Doyne honeycomb retinal dystrophy (DHRD) [MIM:126600]; also known as malattia leventinese (MLVT) (ML). DHRD is an autosomal dominant disease characterized by yellow-white deposits known as drusen that accumulate beneath the retinal pigment epithelium.
MISCELLANEOUS: Up-regulated in malignant gliomas. May increase glioma cell adhesiveness and invasive properties.
SIMILARITY: Belongs to the fibulin family.
SIMILARITY: Contains 6 EGF-like domains.
WEB RESOURCE: Name=Mutations of the EFEMP1 gene; Note=Retina International's Scientific Newsletter; URL="http://www.retina-international.org/files/sci-news/efempmut.htm";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/EFEMP1";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: EFEMP1
Diseases sorted by gene-association score: doyne honeycomb degeneration of retina* (1331), pleural cancer (11), retinal drusen (9), wolfram syndrome (7), macular degeneration, age-related, 1 (7), degeneration of macula and posterior pole (6), hereditary choroidal atrophy (5), partial central choroid dystrophy (5), fundus dystrophy (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • D015127 9,10-Dimethyl-1,2-benzanthracene
  • D010634 Phenobarbital
  • C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone
  • C573693 2-(4-((4-(6-methoxy-3-pyridinyl)-5-(4-(trifluoromethoxy)phenyl)-2-thiazolyl)methoxy)-2-methylphenoxy)acetic acid
  • C049584 2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine
  • C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone
  • C434003 3-(4-methylphenylsulfonyl)-2-propenenitrile
  • D015122 6-Mercaptopurine
  • D000082 Acetaminophen
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 467.91 RPKM in Artery - Aorta
Total median expression: 2621.19 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -40.80120-0.340 Picture PostScript Text
3' UTR -230.701106-0.209 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR026824 - Efemp1/Efemp2
IPR000742 - EG-like_dom
IPR001881 - EGF-like_Ca-bd
IPR013032 - EGF-like_CS
IPR000152 - EGF-type_Asp/Asn_hydroxyl_site
IPR018097 - EGF_Ca-bd_CS

Pfam Domains:
PF07645 - Calcium-binding EGF domain
PF12661 - Human growth factor-like EGF
PF12662 - Complement Clr-like EGF-like

SCOP Domains:
57196 - EGF/Laminin
57184 - Growth factor receptor domain

ModBase Predicted Comparative 3D Structure on Q12805
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005006 epidermal growth factor-activated receptor activity
GO:0005154 epidermal growth factor receptor binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0008083 growth factor activity

Biological Process:
GO:0006355 regulation of transcription, DNA-templated
GO:0007173 epidermal growth factor receptor signaling pathway
GO:0007601 visual perception
GO:0010469 regulation of receptor activity
GO:0018108 peptidyl-tyrosine phosphorylation
GO:0032331 negative regulation of chondrocyte differentiation
GO:0043010 camera-type eye development
GO:0048048 embryonic eye morphogenesis
GO:0048050 post-embryonic eye morphogenesis

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0031012 extracellular matrix
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  U03877 - Human extracellular protein (S1-5) mRNA, complete cds.
AK092854 - Homo sapiens cDNA FLJ35535 fis, clone SPLEN2002419, highly similar to EGF-containing fibulin-like extracellular matrix protein 1 precursor.
AX747769 - Sequence 1294 from Patent EP1308459.
BC014410 - Homo sapiens EGF-containing fibulin-like extracellular matrix protein 1, mRNA (cDNA clone MGC:19906 IMAGE:4549067), complete cds.
BC098561 - Homo sapiens EGF-containing fibulin-like extracellular matrix protein 1, mRNA (cDNA clone MGC:111353 IMAGE:30561133), complete cds.
AK301402 - Homo sapiens cDNA FLJ53670 complete cds, highly similar to EGF-containing fibulin-like extracellularmatrix protein 1 precursor.
AK293058 - Homo sapiens cDNA FLJ77823 complete cds, highly similar to Homo sapiens EGF-containing fibulin-like extracellular matrix protein 1, transcript variant 3, mRNA.
AK290599 - Homo sapiens cDNA FLJ77681 complete cds, highly similar to Homo sapiens EGF-containing fibulin-like extracellular matrix protein 1 (EFEMP1), transcript variant 1, mRNA.
AK301531 - Homo sapiens cDNA FLJ55670 complete cds, highly similar to EGF-containing fibulin-like extracellularmatrix protein 1 precursor.
AB209212 - Homo sapiens mRNA for EGF-containing fibulin-like extracellular matrix protein 1 isoform b variant protein.
DQ892514 - Synthetic construct clone IMAGE:100005144; FLH187049.01X; RZPDo839D0372D EGF-containing fibulin-like extracellular matrix protein 1 (EFEMP1) gene, encodes complete protein.
AK312639 - Homo sapiens cDNA, FLJ93024, highly similar to Homo sapiens EGF-containing fibulin-like extracellular matrix protein 1 (EFEMP1), transcript variant 1, mRNA.
KJ891147 - Synthetic construct Homo sapiens clone ccsbBroadEn_00541 EFEMP1 gene, encodes complete protein.
KR710444 - Synthetic construct Homo sapiens clone CCSBHm_00012683 EFEMP1 (EFEMP1) mRNA, encodes complete protein.
DQ895728 - Synthetic construct Homo sapiens clone IMAGE:100010188; FLH187045.01L; RZPDo839D0362D EGF-containing fibulin-like extracellular matrix protein 1 (EFEMP1) gene, encodes complete protein.
AB527786 - Synthetic construct DNA, clone: pF1KB5868, Homo sapiens EFEMP1 gene for EGF-containing fibulin-like extracellular matrix protein 1, without stop codon, in Flexi system.
KU178058 - Homo sapiens EGF containing fibulin-like extracellular matrix protein 1 isoform 1 (EFEMP1) mRNA, partial cds.
KU178059 - Homo sapiens EGF containing fibulin-like extracellular matrix protein 1 isoform 2 (EFEMP1) mRNA, partial cds, alternatively spliced.
JD296556 - Sequence 277580 from Patent EP1572962.
JD088717 - Sequence 69741 from Patent EP1572962.
JD313076 - Sequence 294100 from Patent EP1572962.
JD280216 - Sequence 261240 from Patent EP1572962.
JD165108 - Sequence 146132 from Patent EP1572962.
JD041792 - Sequence 22816 from Patent EP1572962.
JD376534 - Sequence 357558 from Patent EP1572962.
CU676981 - Synthetic construct Homo sapiens gateway clone IMAGE:100019659 5' read EFEMP1 mRNA.
JD061008 - Sequence 42032 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q12805 (Reactome details) participates in the following event(s):

R-HSA-1592387 Fibulin binds elastic fibres
R-HSA-2328048 Emilin is found in elastic fibres
R-HSA-2161282 Elastic fibres bind associated proteins
R-HSA-2129379 Molecules associated with elastic fibres
R-HSA-1566948 Elastic fibre formation
R-HSA-1474244 Extracellular matrix organization

-  Other Names for This Gene
  Alternate Gene Symbols: A8K3I4, B4DW75, D6W5D2, ENST00000355426.1, ENST00000355426.2, ENST00000355426.3, ENST00000355426.4, ENST00000355426.5, ENST00000355426.6, ENST00000355426.7, FBLN3, FBLN3_HUMAN, FBNL, NM_001039348, Q12805, Q541U7, uc317zbn.1, uc317zbn.2
UCSC ID: ENST00000355426.8_7
RefSeq Accession: NM_001039348.3
Protein: Q12805 (aka FBLN3_HUMAN or FBL3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.