ECM2 encodes extracellular matrix protein 2, so named because it shares extensive similarity with known extracelluar matrix proteins. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2010] See more...

Aliases for ECM2 Gene

Aliases for ECM2 Gene

  • Extracellular Matrix Protein 2 2 3 4 5
  • Matrix Glycoprotein SC1/ECM2 2 3 4
  • Extracellular Matrix Protein 2, Female Organ And Adipocyte Specific 2 3
  • ECM2 5

External Ids for ECM2 Gene

Previous GeneCards Identifiers for ECM2 Gene

  • GC09M086084
  • GC09M086985
  • GC09M088556
  • GC09M090599
  • GC09M090597
  • GC09M092335
  • GC09M094297
  • GC09M095257
  • GC09M064935

Summaries for ECM2 Gene

Entrez Gene Summary for ECM2 Gene

  • ECM2 encodes extracellular matrix protein 2, so named because it shares extensive similarity with known extracelluar matrix proteins. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2010]

GeneCards Summary for ECM2 Gene

ECM2 (Extracellular Matrix Protein 2) is a Protein Coding gene. Diseases associated with ECM2 include Fraser Syndrome 1. Among its related pathways are Integrin Pathway and ERK Signaling. Gene Ontology (GO) annotations related to this gene include heparin binding and collagen binding. An important paralog of this gene is KERA.

UniProtKB/Swiss-Prot Summary for ECM2 Gene

Gene Wiki entry for ECM2 Gene

Additional gene information for ECM2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ECM2 Gene

Genomics for ECM2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ECM2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J092533 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +0.9 879 4.3 SP1 PKNOX1 CEBPB FOXA2 ASH2L YY1 JUND GATA3 SPI1 MAFK ECM2 CENPP ASPN OMD OGN IPPK BICD2 piR-55705-056
GH09J092759 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 5.1 -226.4 -226352 6.8 SP1 CREB1 CTCF HNRNPL PRDM10 ZNF629 REST SIX5 IKZF1 ZNF692 BICD2 lnc-CENPP-18 PHF2 CENPP ZNF484 LINC00475 IPPK ECM2 RF00017-7713
GH09J092668 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 4.6 -133.3 -133337 3.8 SP1 CREB1 GATAD2A TEAD4 ZNF629 SIX5 IKZF1 KDM1A POLR2A NFRKB IPPK LOC107987095 lnc-CENPP-1 CENPP NOL8 PHF2 ECM2 piR-48554
GH09J092715 Enhancer 1 Ensembl ENCODE dbSUPER 10 -179.6 -179646 2.9 CTCF ZNF143 ZIC2 REST RAD21 TRIM22 RUNX3 SMC3 EBF1 ZNF654 CENPP ECM2 piR-37501 piR-38423-072 BICD2 IPPK
GH09J092423 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 4.6 +111.0 111034 4.6 YY1 POLR2A OMD CENPP NOL8 OGN ECM2 lnc-ECM2-2 ASPN
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ECM2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ECM2

Top Transcription factor binding sites by QIAGEN in the ECM2 gene promoter:
  • AML1a
  • E2F
  • E2F-1
  • HSF1 (long)
  • HSF1short
  • ISGF-3
  • Nkx2-5
  • S8
  • TBP
  • TFIID

Genomic Locations for ECM2 Gene

Genomic Locations for ECM2 Gene
chr9:92,493,547-92,536,841
(GRCh38/hg38)
Size:
43,295 bases
Orientation:
Minus strand
chr9:95,255,829-95,298,937
(GRCh37/hg19)
Size:
43,109 bases
Orientation:
Minus strand

Genomic View for ECM2 Gene

Genes around ECM2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ECM2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ECM2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ECM2 Gene

Proteins for ECM2 Gene

  • Protein details for ECM2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O94769-ECM2_HUMAN
    Recommended name:
    Extracellular matrix protein 2
    Protein Accession:
    O94769
    Secondary Accessions:
    • B2R730
    • E2PU11
    • Q5T9F2
    • Q7Z3D0

    Protein attributes for ECM2 Gene

    Size:
    699 amino acids
    Molecular mass:
    79789 Da
    Quaternary structure:
    • Interacts with numerous extracellular matrix proteins (By similarity). Interacts with MSL1 and RASSF1 (By similarity).
    SequenceCaution:
    • Sequence=CAD97940.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for ECM2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ECM2 Gene

Post-translational modifications for ECM2 Gene

  • Glycosylation at Asn378, Asn449, and Asn506
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

No data available for DME Specific Peptides for ECM2 Gene

Domains & Families for ECM2 Gene

Gene Families for ECM2 Gene

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

Protein Domains for ECM2 Gene

InterPro:
Blocks:
  • von Willebrand factor, type C
ProtoNet:

Suggested Antigen Peptide Sequences for ECM2 Gene

GenScript: Design optimal peptide antigens:
  • Matrix glycoprotein SC1/ECM2 (ECM2_HUMAN)
  • ECM2 protein (Q3KR19_HUMAN)
  • ECM2 protein (Q6PID0_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O94769

UniProtKB/Swiss-Prot:

ECM2_HUMAN :
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class I subfamily.
Family:
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class I subfamily.
genes like me logo Genes that share domains with ECM2: view

Function for ECM2 Gene

Molecular function for ECM2 Gene

UniProtKB/Swiss-Prot Function:
Promotes matrix assembly and cell adhesiveness.
GENATLAS Biochemistry:
extracellular matrix 2,predominantly expressed in adipose tissue,mammary gland,ovary and uterus

Phenotypes From GWAS Catalog for ECM2 Gene

Gene Ontology (GO) - Molecular Function for ECM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005178 integrin binding TAS 9790758
GO:0005515 protein binding IEA --
GO:0005518 collagen binding IEA --
GO:0008201 heparin binding IBA 21873635
GO:0070052 collagen V binding IBA 21873635
genes like me logo Genes that share ontologies with ECM2: view
genes like me logo Genes that share phenotypes with ECM2: view

Animal Model Products

  • Taconic Biosciences Mouse Models for ECM2

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ECM2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ECM2 Gene

Localization for ECM2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ECM2 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
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 ECM2 gene
Compartment Confidence
extracellular 4
plasma membrane 1
cytoskeleton 1
mitochondrion 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for ECM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005614 interstitial matrix IEA --
GO:0031012 extracellular matrix TAS,IBA 21873635
genes like me logo Genes that share ontologies with ECM2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ECM2 Gene

Pathways & Interactions for ECM2 Gene

PathCards logo

SuperPathways for ECM2 Gene

SuperPathway Contained pathways
1 Integrin Pathway
.67
.67
.56
.56
.50
.38
2 ERK Signaling
.61
.61
.58
.51
.49
3 Phospholipase-C Pathway
.56
.56
genes like me logo Genes that share pathways with ECM2: view

Pathways by source for ECM2 Gene

13 Qiagen pathways for ECM2 Gene
  • ERK Signaling
  • FAK1 Signaling
  • GnRH Signaling
  • ILK Signaling
  • Inhibition of Angiogenesis by TSP1

Gene Ontology (GO) - Biological Process for ECM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007160 cell-matrix adhesion TAS 9790758
GO:0010811 positive regulation of cell-substrate adhesion IBA 21873635
GO:0030198 extracellular matrix organization IBA 21873635
genes like me logo Genes that share ontologies with ECM2: view

No data available for SIGNOR curated interactions for ECM2 Gene

Drugs & Compounds for ECM2 Gene

No Compound Related Data Available

Transcripts for ECM2 Gene

mRNA/cDNA for ECM2 Gene

3 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ECM2

Alternative Splicing Database (ASD) splice patterns (SP) for ECM2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b · 10c ^ 11a · 11b · 11c · 11d ^ 12
SP1: - - - -
SP2: - - -
SP3: - - -
SP4:
SP5: -
SP6:
SP7:

Relevant External Links for ECM2 Gene

GeneLoc Exon Structure for
ECM2

Expression for ECM2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ECM2 Gene

mRNA differential expression in normal tissues according to GTEx for ECM2 Gene

This gene is overexpressed in Artery - Coronary (x5.4), Artery - Tibial (x4.9), and Artery - Aorta (x4.8).

Protein differential expression in normal tissues from HIPED for ECM2 Gene

This gene is overexpressed in Ovary (21.3), Breast (18.4), Heart (12.9), and Adipocyte (10.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ECM2 Gene



Protein tissue co-expression partners for ECM2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ECM2

SOURCE GeneReport for Unigene cluster for ECM2 Gene:

Hs.117060

mRNA Expression by UniProt/SwissProt for ECM2 Gene:

O94769-ECM2_HUMAN
Tissue specificity: Expressed predominantly in adipose tissue as well as female-specific organs such as mammary gland, ovary, and uterus.

Evidence on tissue expression from TISSUES for ECM2 Gene

  • Eye(4.2)
  • Heart(2.2)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with ECM2: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for ECM2 Gene

Orthologs for ECM2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ECM2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia ECM2 30 31
  • 99.14 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia ECM2 30 31
  • 85.33 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia ECM2 30 31
  • 82.06 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia LOC100910978 30
  • 82.02 (n)
Mouse
(Mus musculus)
Mammalia Ecm2 30 17 31
  • 81.05 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia ECM2 31
  • 68 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia ECM2 31
  • 44 (a)
OneToOne
Chicken
(Gallus gallus)
Aves ECM2 30 31
  • 65.98 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia ECM2 31
  • 55 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii ecm2 30 31
  • 56.5 (n)
OneToOne
Species where no ortholog for ECM2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for ECM2 Gene

ENSEMBL:
Gene Tree for ECM2 (if available)
TreeFam:
Gene Tree for ECM2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ECM2: view image

Paralogs for ECM2 Gene

Paralogs for ECM2 Gene

(7) SIMAP similar genes for ECM2 Gene using alignment to 5 proteins:

  • ECM2_HUMAN
  • Q3KR19_HUMAN
  • Q5T9F3_HUMAN
  • Q5T9F4_HUMAN
  • Q6PID0_HUMAN

Pseudogenes.org Pseudogenes for ECM2 Gene

genes like me logo Genes that share paralogs with ECM2: view

Variants for ECM2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ECM2 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs10120210 - p.Gln56Pro
rs34758505 - p.Arg204Gln
rs35496743 - p.Thr109Ser

Additional dbSNP identifiers (rs#s) for ECM2 Gene

Structural Variations from Database of Genomic Variants (DGV) for ECM2 Gene

Variant ID Type Subtype PubMed ID
esv1019101 CNV insertion 17803354
esv3621081 CNV loss 21293372
esv3891693 CNV gain 25118596
nsv1047337 CNV loss 25217958
nsv1049599 CNV loss 25217958
nsv1052846 CNV loss 25217958
nsv1115209 CNV deletion 24896259
nsv527206 CNV loss 19592680

Variation tolerance for ECM2 Gene

Residual Variation Intolerance Score: 73.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.88; 48.53% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ECM2 Gene

Human Gene Mutation Database (HGMD)
ECM2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ECM2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ECM2 Gene

Disorders for ECM2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for ECM2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
fraser syndrome 1
  • frasrs1
- elite association - COSMIC cancer census association via MalaCards
Search ECM2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for ECM2

genes like me logo Genes that share disorders with ECM2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ECM2 Gene

Publications for ECM2 Gene

  1. Identification of a novel gene (ECM2) encoding a putative extracellular matrix protein expressed predominantly in adipose and female-specific tissues and its chromosomal localization to 9q22.3. (PMID: 9790758) Nishiu J … Nakamura Y (Genomics 1998) 2 3 4 23
  2. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 3 4
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  4. Matrix glycoprotein SC1/ECM2 augments B lymphopoiesis. (PMID: 9345023) Oritani K … Kincade PW (Blood 1997) 3 23
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3

Products for ECM2 Gene

Sources for ECM2 Gene