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Aliases for ECM1 Gene

Aliases for ECM1 Gene

  • Extracellular Matrix Protein 1 2 3 3 5
  • Secretory Component P85 3 4
  • Testicular Tissue Protein Li 61 3
  • URBWD 3

External Ids for ECM1 Gene

Previous GeneCards Identifiers for ECM1 Gene

  • GC01P148322
  • GC01P146227
  • GC01P147255
  • GC01P147697
  • GC01P147293
  • GC01P148747
  • GC01P150480
  • GC01P121858

Summaries for ECM1 Gene

Entrez Gene Summary for ECM1 Gene

  • This gene encodes a soluble protein that is involved in endochondral bone formation, angiogenesis, and tumor biology. It also interacts with a variety of extracellular and structural proteins, contributing to the maintenance of skin integrity and homeostasis. Mutations in this gene are associated with lipoid proteinosis disorder (also known as hyalinosis cutis et mucosae or Urbach-Wiethe disease) that is characterized by generalized thickening of skin, mucosae and certain viscera. Alternatively spliced transcript variants encoding distinct isoforms have been described for this gene. [provided by RefSeq, Feb 2011]

GeneCards Summary for ECM1 Gene

ECM1 (Extracellular Matrix Protein 1) is a Protein Coding gene. Diseases associated with ECM1 include Lipoid Proteinosis Of Urbach And Wiethe and Lichen Sclerosus. Among its related pathways are ERK Signaling and Integrin Pathway. Gene Ontology (GO) annotations related to this gene include enzyme binding and protein C-terminus binding.

UniProtKB/Swiss-Prot for ECM1 Gene

  • Involved in endochondral bone formation as negative regulator of bone mineralization. Stimulates the proliferation of endothelial cells and promotes angiogenesis. Inhibits MMP9 proteolytic activity.

Gene Wiki entry for ECM1 Gene

Additional gene information for ECM1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ECM1 Gene

Genomics for ECM1 Gene

GeneHancer (GH) Regulatory Elements for ECM1 Gene

Promoters and enhancers for ECM1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J150507 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 659.6 +0.5 459 2.3 HDGF HDAC1 PTBP1 NFXL1 POLR2B GLIS2 E2F8 ZNF366 SMARCC2 ZFP91 ECM1 PRPF3 PI4KB MRPS21 ADAMTSL4 RPRD2 SETDB1 ZNF687 GABPB2 POGZ
GH01J150506 Enhancer 0.9 ENCODE 650.7 -1.1 -1087 0.5 ATF1 ARNT FEZF1 TCF12 E2F8 RXRA ZNF592 SMARCA4 ZNF184 GLIS1 ECM1 C1orf56 PIP5K1A MIR6878 TARS2
GH01J150362 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 9.2 -143.2 -143204 5.2 CLOCK FEZF1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC ZC3H11A RPRD2 SETDB1 PRPF3 SF3B4 PI4KB ZNF687 UBE2D3P3 PIP5K1A ARNT HIST2H2AB
GH01J150486 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 9.3 -20.4 -20371 1.7 CLOCK ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 TARS2 SETDB1 PIP5K1A PRPF3 SF3B4 PI4KB GABPB2 ZNF687 UBE2D3P3 ARNT
GH01J150476 Enhancer 0.9 Ensembl ENCODE 21.6 -30.3 -30325 2.2 HDAC1 MEIS2 LEF1 FOXA2 ZNF133 FEZF1 ZBTB7B ZFHX2 MTA3 CTBP1 ECM1 MRPS21 ADAMTSL4 LOC100289061 ADAMTSL4-AS1 PIP5K1A APH1A C1orf54 PI4KB GABPB2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ECM1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ECM1 gene promoter:
  • YY1
  • c-Myb
  • PPAR-alpha
  • CREB
  • ISGF-3
  • AP-1
  • NF-1/L
  • NF-1
  • NF-E2 p45
  • NF-E2

Genomic Locations for ECM1 Gene

Genomic Locations for ECM1 Gene
5,779 bases
Plus strand
5,779 bases
Plus strand

Genomic View for ECM1 Gene

Genes around ECM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ECM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ECM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ECM1 Gene

Proteins for ECM1 Gene

  • Protein details for ECM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Extracellular matrix protein 1
    Protein Accession:
    Secondary Accessions:
    • A8K8S0
    • B4DW49
    • B4DY60
    • O43266
    • Q5T5G4
    • Q5T5G5
    • Q5T5G6
    • Q8IZ60

    Protein attributes for ECM1 Gene

    540 amino acids
    Molecular mass:
    60674 Da
    Quaternary structure:
    • Interacts (via C-terminus) with HSPG2 (via C-terminus). Interacts with EFEMP1/FBLN3 and LAMB3. Interacts with MMP9.

    Alternative splice isoforms for ECM1 Gene


neXtProt entry for ECM1 Gene

Post-translational modifications for ECM1 Gene

  • Glycosylation at isoforms=2, 4530, Asn444, Thr391, isoforms=4354, isoforms=2, 3, 4119, and Tyr43
  • Modification sites at PhosphoSitePlus

Other Protein References for ECM1 Gene

No data available for DME Specific Peptides for ECM1 Gene

Domains & Families for ECM1 Gene

Gene Families for ECM1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted secreted proteins

Protein Domains for ECM1 Gene

Suggested Antigen Peptide Sequences for ECM1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ECM1: view

No data available for UniProtKB/Swiss-Prot for ECM1 Gene

Function for ECM1 Gene

Molecular function for ECM1 Gene

UniProtKB/Swiss-Prot Function:
Involved in endochondral bone formation as negative regulator of bone mineralization. Stimulates the proliferation of endothelial cells and promotes angiogenesis. Inhibits MMP9 proteolytic activity.
GENATLAS Biochemistry:
extracellular matrix protein 1,with two alternative spliced isoform,1.8kb,expressed in heart,placenta,1.4kb,in tonsils and keratinocytes

Phenotypes From GWAS Catalog for ECM1 Gene

Gene Ontology (GO) - Molecular Function for ECM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002020 protease binding IPI 16512877
GO:0004871 obsolete signal transducer activity HMP --
GO:0005134 interleukin-2 receptor binding IEA --
GO:0005515 protein binding IPI 19275936
GO:0008022 protein C-terminus binding IPI 12604605
genes like me logo Genes that share ontologies with ECM1: view
genes like me logo Genes that share phenotypes with ECM1: view

Human Phenotype Ontology for ECM1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for ECM1 Gene

MGI Knock Outs for ECM1:
  • Ecm1 Ecm1<tm1b(EUCOMM)Hmgu>
  • Ecm1 Ecm1<tm1Bsun>

Animal Model Products

miRNA for ECM1 Gene

miRTarBase miRNAs that target ECM1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for ECM1 Gene

Localization for ECM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ECM1 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ECM1 gene
Compartment Confidence
extracellular 5
nucleus 2
cytosol 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ECM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IEA --
GO:0031012 extracellular matrix IDA 20870722
GO:0031089 platelet dense granule lumen TAS --
GO:0070062 extracellular exosome HDA 19199708
genes like me logo Genes that share ontologies with ECM1: view

Pathways & Interactions for ECM1 Gene

genes like me logo Genes that share pathways with ECM1: view

Gene Ontology (GO) - Biological Process for ECM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001503 ossification IEA --
GO:0001525 angiogenesis IEA --
GO:0001938 positive regulation of endothelial cell proliferation IDA 11292659
GO:0001960 negative regulation of cytokine-mediated signaling pathway IEA --
GO:0002576 platelet degranulation TAS --
genes like me logo Genes that share ontologies with ECM1: view

No data available for SIGNOR curated interactions for ECM1 Gene

Drugs & Compounds for ECM1 Gene

No Compound Related Data Available

Transcripts for ECM1 Gene

mRNA/cDNA for ECM1 Gene

Unigene Clusters for ECM1 Gene

Extracellular matrix protein 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ECM1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b · 7c ^ 8a · 8b · 8c ^ 9a · 9b ^ 10 ^ 11 ^ 12
SP1: - - -
SP2: - - - - -
SP3: -
SP4: - -
SP5: - -
SP6: -
SP8: - - - - - -
SP9: -

Relevant External Links for ECM1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ECM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ECM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for ECM1 Gene

This gene is overexpressed in Esophagus - Mucosa (x23.9), Cervix - Ectocervix (x5.9), and Vagina (x5.0).

Protein differential expression in normal tissues from HIPED for ECM1 Gene

This gene is overexpressed in Cervix (17.5), Plasma (11.8), Serum (9.6), Urine (7.0), and Synovial fluid (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ECM1 Gene

NURSA nuclear receptor signaling pathways regulating expression of ECM1 Gene:


SOURCE GeneReport for Unigene cluster for ECM1 Gene:


mRNA Expression by UniProt/SwissProt for ECM1 Gene:

Tissue specificity: Expressed in breast cancer tissues. Little or no expression observed in normal breast tissues. Expressed in skin; wide expression is observed throughout the dermis with minimal expression in the epidermis.

Evidence on tissue expression from TISSUES for ECM1 Gene

  • Skin(4.8)
  • Liver(4.4)
  • Bone marrow(4.1)
  • Nervous system(3.6)
  • Thyroid gland(2.6)

Phenotype-based relationships between genes and organs from Gene ORGANizer for ECM1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • eye
  • face
  • head
  • larynx
  • lip
  • mouth
  • neck
  • scalp
  • tongue
  • vocal cord
  • digit
  • foot
  • lower limb
  • nail
  • toe
  • blood
  • hair
  • skin
  • sweat gland
  • white blood cell
genes like me logo Genes that share expression patterns with ECM1: view

No data available for Protein tissue co-expression partners for ECM1 Gene

Orthologs for ECM1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ECM1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ECM1 34 33
  • 99.51 (n)
(Canis familiaris)
Mammalia ECM1 34 33
  • 85.16 (n)
(Bos Taurus)
Mammalia ECM1 34 33
  • 84.28 (n)
(Rattus norvegicus)
Mammalia Ecm1 33
  • 79.72 (n)
(Mus musculus)
Mammalia Ecm1 16 34 33
  • 79.22 (n)
(Monodelphis domestica)
Mammalia ECM1 34
  • 53 (a)
(Anolis carolinensis)
Reptilia ECM1 34
  • 47 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ecm1 33
  • 51.62 (n)
(Danio rerio)
Actinopterygii ECM1 (2 of 2) 34
  • 34 (a)
ecm1b 34
  • 26 (a)
Species where no ortholog for ECM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for ECM1 Gene

Gene Tree for ECM1 (if available)
Gene Tree for ECM1 (if available)
Evolutionary constrained regions (ECRs) for ECM1: view image

Paralogs for ECM1 Gene Pseudogenes for ECM1 Gene

genes like me logo Genes that share paralogs with ECM1: view

No data available for Paralogs for ECM1 Gene

Variants for ECM1 Gene

Sequence variations from dbSNP and Humsavar for ECM1 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs121909114 pathogenic, Lipid proteinosis 150,511,784(+) C/T coding_sequence_variant, intron_variant, stop_gained
rs121909115 pathogenic, Lipid proteinosis 150,509,696(+) C/T coding_sequence_variant, stop_gained
rs121909116 pathogenic, Lipid proteinosis, Lipoid proteinosis (LiP) [MIM:247100] 150,510,989(+) T/A coding_sequence_variant, missense_variant
rs746217361 pathogenic, Lipid proteinosis 150,511,475(+) C/A/T coding_sequence_variant, intron_variant, stop_gained, synonymous_variant
rs869025563 pathogenic, Lipid proteinosis 150,511,574(+) C/T coding_sequence_variant, intron_variant, stop_gained

Structural Variations from Database of Genomic Variants (DGV) for ECM1 Gene

Variant ID Type Subtype PubMed ID
nsv1006838 CNV gain 25217958

Variation tolerance for ECM1 Gene

Residual Variation Intolerance Score: 66.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.47; 85.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ECM1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ECM1 Gene

Disorders for ECM1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for ECM1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
lipoid proteinosis of urbach and wiethe
  • lipoid proteinosis
lichen sclerosus
  • lichen sclerosus et atrophicus
benign mesenchymoma
  • mesenchymoma, benign
epidermodysplasia verruciformis
  • ev
doyne honeycomb retinal dystrophy
  • dhrd
- elite association - COSMIC cancer census association via MalaCards
Search ECM1 in MalaCards View complete list of genes associated with diseases


  • Lipoid proteinosis (LiP) [MIM:247100]: Rare autosomal recessive disorder characterized by generalized thickening of skin, mucosae and certain viscera. Classical features include beaded eyelid papules and laryngeal infiltration leading to hoarseness. Histologically, there is widespread deposition of hyaline material and disruption/reduplication of basement membrane. {ECO:0000269 PubMed:11929856, ECO:0000269 PubMed:12603844}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for ECM1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with ECM1: view

No data available for Genatlas for ECM1 Gene

Publications for ECM1 Gene

  1. The human extracellular matrix gene 1 (ECM1): genomic structure, cDNA cloning, expression pattern, and chromosomal localization. (PMID: 9367673) Smits P … Merregaert J (Genomics 1997) 2 3 4 22 58
  2. Characterization of the human extracellular matrix protein 1 gene on chromosome 1q21. (PMID: 9501329) Johnson MR … Francomano CA (Matrix biology : journal of the International Society for Matrix Biology 1997) 2 3 4 22 58
  3. Genetic analysis in a Dutch study sample identifies more ulcerative colitis susceptibility loci and shows their additive role in disease risk. (PMID: 19861958) Festen EA … Weersma RK (The American journal of gastroenterology 2010) 3 22 44 58
  4. ECM1 interacts with fibulin-3 and the beta 3 chain of laminin 332 through its serum albumin subdomain-like 2 domain. (PMID: 19275936) Sercu S … Merregaert J (Matrix biology : journal of the International Society for Matrix Biology 2009) 3 4 22 58
  5. Extracellular matrix protein 1 inhibits the activity of matrix metalloproteinase 9 through high-affinity protein/protein interactions. (PMID: 16512877) Fujimoto N … Uitto J (Experimental dermatology 2006) 3 4 22 58

Products for ECM1 Gene

Sources for ECM1 Gene

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