Human Gene ECM1 (ENST00000369047.9_6) from GENCODE V47lift37
  Description: extracellular matrix protein 1, transcript variant 1 (from RefSeq NM_004425.4)
Gencode Transcript: ENST00000369047.9_6
Gencode Gene: ENSG00000143369.15_8
Transcript (Including UTRs)
   Position: hg19 chr1:150,480,585-150,486,265 Size: 5,681 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr1:150,480,686-150,485,943 Size: 5,258 Coding Exon Count: 10 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:150,480,585-150,486,265)mRNA (may differ from genome)Protein (540 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ECM1_HUMAN
DESCRIPTION: RecName: Full=Extracellular matrix protein 1; AltName: Full=Secretory component p85; Flags: Precursor;
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.
SUBUNIT: Interacts (via C-terminus) with HSPG2 (via C-terminus). Interacts with EFEMP1/FBLN3 and LAMB3. Interacts with MMP9.
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix.
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.
DISEASE: Defects in ECM1 are the cause of lipoid proteinosis (LiP) [MIM:247100]; also known as lipoid proteinosis of Urbach and Wiethe or hyalinosis cutis et mucosae. LiP is a 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.

-  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: ECM1
Diseases sorted by gene-association score: urbach-wiethe disease* (1702), lichen sclerosus (29), benign mesenchymoma (12), epidermodysplasia verruciformis (9), doyne honeycomb degeneration of retina (7), alveolar soft-part sarcoma (6), breast cancer (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           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: 440.85 RPKM in Esophagus - Mucosa
Total median expression: 969.58 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 -30.10101-0.298 Picture PostScript Text
3' UTR -101.70322-0.316 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
IPR008605 - ECM1

Pfam Domains:
PF05782 - Extracellular matrix protein 1 (ECM1)

SCOP Domains:
48552 - Serum albumin-like

ModBase Predicted Comparative 3D Structure on Q16610
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    
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 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0002020 protease binding
GO:0005134 interleukin-2 receptor binding
GO:0005515 protein binding
GO:0008022 protein C-terminus binding
GO:0019899 enzyme binding
GO:0043236 laminin binding

Biological Process:
GO:0001503 ossification
GO:0001525 angiogenesis
GO:0001938 positive regulation of endothelial cell proliferation
GO:0001960 negative regulation of cytokine-mediated signaling pathway
GO:0002576 platelet degranulation
GO:0002828 regulation of type 2 immune response
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006954 inflammatory response
GO:0007165 signal transduction
GO:0010466 negative regulation of peptidase activity
GO:0030500 regulation of bone mineralization
GO:0030502 negative regulation of bone mineralization
GO:0031214 biomineral tissue development
GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0045766 positive regulation of angiogenesis
GO:2000404 regulation of T cell migration

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0031012 extracellular matrix
GO:0031089 platelet dense granule lumen
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  HM005374 - Homo sapiens clone HTL-T-61 testicular tissue protein Li 61 mRNA, complete cds.
AK097205 - Homo sapiens cDNA FLJ39886 fis, clone SPLEN2016421, highly similar to EXTRACELLULAR MATRIX PROTEIN 1 PRECURSOR.
AK097046 - Homo sapiens cDNA FLJ39727 fis, clone SMINT2015326, highly similar to EXTRACELLULAR MATRIX PROTEIN 1 PRECURSOR.
BC023505 - Homo sapiens extracellular matrix protein 1, mRNA (cDNA clone MGC:3614 IMAGE:3614195), complete cds.
DQ112074 - Homo sapiens ECM1 short variant mRNA, complete cds, alternatively spliced.
DQ010946 - Homo sapiens ECM1 short variant (ECM1) mRNA, complete cds, alternatively spliced.
U68186 - Human extracellular matrix protein 1 mRNA, complete cds.
U68187 - Human extracellular matrix protein 1 mRNA, alternative splice variant, complete cds.
AK292435 - Homo sapiens cDNA FLJ76946 complete cds, highly similar to Homo sapiens extracellular matrix protein 1 (ECM1), transcript variant 1, mRNA.
AK301369 - Homo sapiens cDNA FLJ53669 complete cds, highly similar to Extracellular matrix protein 1 precursor.
AK316390 - Homo sapiens cDNA, FLJ79289 complete cds, highly similar to Extracellular matrix protein 1 precursor.
AK302279 - Homo sapiens cDNA FLJ54569 complete cds, highly similar to Extracellular matrix protein 1 precursor.
U65932 - Human extracellular matrix protein 1 (ECM1) mRNA, complete cds.
DQ893011 - Synthetic construct clone IMAGE:100005641; FLH191654.01X; RZPDo839F0777D extracellular matrix protein 1 (ECM1) gene, encodes complete protein.
DQ896257 - Synthetic construct Homo sapiens clone IMAGE:100010717; FLH191650.01L; RZPDo839F0767D extracellular matrix protein 1 (ECM1) gene, encodes complete protein.
JD116272 - Sequence 97296 from Patent EP1572962.
JD123255 - Sequence 104279 from Patent EP1572962.

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

Protein Q16610 (Reactome details) participates in the following event(s):

R-HSA-481009 Exocytosis of platelet dense granule content
R-HSA-114608 Platelet degranulation
R-HSA-76005 Response to elevated platelet cytosolic Ca2+
R-HSA-76002 Platelet activation, signaling and aggregation
R-HSA-109582 Hemostasis

-  Other Names for This Gene
  Alternate Gene Symbols: A8K8S0, B4DW49, B4DY60, ECM1_HUMAN, ENST00000369047.1, ENST00000369047.2, ENST00000369047.3, ENST00000369047.4, ENST00000369047.5, ENST00000369047.6, ENST00000369047.7, ENST00000369047.8, NM_004425, O43266, Q16610, Q5T5G4, Q5T5G5, Q5T5G6, Q8IZ60, uc318hhe.1, uc318hhe.2
UCSC ID: ENST00000369047.9_6
RefSeq Accession: NM_004425.4
Protein: Q16610 (aka ECM1_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene ECM1:
lipoid-p (Lipoid Proteinosis)

-  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.