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ECM1 extracellular matrix protein 1 [ Homo sapiens (human) ]

Gene ID: 1893, updated on 18-Aug-2020

Summary

Official Symbol
ECM1provided by HGNC
Official Full Name
extracellular matrix protein 1provided by HGNC
Primary source
HGNC:HGNC:3153
See related
Ensembl:ENSG00000143369 MIM:602201
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
URBWD
Summary
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]
Expression
Biased expression in esophagus (RPKM 332.0), gall bladder (RPKM 47.3) and 3 other tissues See more
Orthologs

Genomic context

See ECM1 in Genome Data Viewer
Location:
1q21.2
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (150508109..150513789)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (150480487..150486265)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene regulation of nuclear pre-mRNA domain containing 2 Neighboring gene threonyl-tRNA synthetase 2, mitochondrial Neighboring gene microRNA 6878 Neighboring gene focally amplified long non-coding RNA in epithelial cancer Neighboring gene CRISPRi-validated cis-regulatory element chr1.8461

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 Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat Treatment with cannabinoids inhibits HIV-1 Tat-enhanced attachment of U937 cells to collagen IV, laminin, or ECM1 proteins, which is linked to the cannabinoid receptor type 2 and the modulation of beta1-integrin and actin distribution PubMed
tat HIV-1 Tat enhances adhesion of human U937 monocyte-like cells to proteins of the extracellular matrix, such as collagen IV, laminin, and ECM1 PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
extracellular matrix structural constituent RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
interleukin-2 receptor binding IEA
Inferred from Electronic Annotation
more info
 
laminin binding IPI
Inferred from Physical Interaction
more info
PubMed 
protease binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein C-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
angiogenesis IEA
Inferred from Electronic Annotation
more info
 
biomineral tissue development IEA
Inferred from Electronic Annotation
more info
 
chondrocyte development IEA
Inferred from Electronic Annotation
more info
 
endochondral bone growth IEA
Inferred from Electronic Annotation
more info
 
inflammatory response IEA
Inferred from Electronic Annotation
more info
 
negative regulation of bone mineralization IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cytokine-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
negative regulation of peptidase activity IDA
Inferred from Direct Assay
more info
PubMed 
ossification IEA
Inferred from Electronic Annotation
more info
 
platelet degranulation TAS
Traceable Author Statement
more info
 
positive regulation of I-kappaB kinase/NF-kappaB signaling HMP PubMed 
positive regulation of angiogenesis IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of endothelial cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of T cell migration IEA
Inferred from Electronic Annotation
more info
 
regulation of bone mineralization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
regulation of type 2 immune response IEA
Inferred from Electronic Annotation
more info
 
signal transduction IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
collagen-containing extracellular matrix HDA PubMed 
collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen-containing extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA PubMed 
extracellular matrix NAS
Non-traceable Author Statement
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
platelet dense granule lumen TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
extracellular matrix protein 1
Names
secretory component p85
testicular tissue protein Li 61

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_012062.1 RefSeqGene

    Range
    5099..10779
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001202858.2NP_001189787.1  extracellular matrix protein 1 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001189787.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses alternate in-frame donor and acceptor splice sites at 2 adjacent exons compared to variant 1, resulting in a longer isoform (3) compared to isoform 1.
    Source sequence(s)
    AK097046, CA413352, DA963826
    Consensus CDS
    CCDS55632.1
    UniProtKB/Swiss-Prot
    Q16610
    Related
    ENSP00000358045.4, ENST00000369049.8
    Conserved Domains (1) summary
    pfam05782
    Location:5567
    ECM1; Extracellular matrix protein 1 (ECM1)
  2. NM_004425.4NP_004416.2  extracellular matrix protein 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_004416.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript, and encodes isoform 1.
    Source sequence(s)
    AL356356, CA413352, DA963826, U68186
    Consensus CDS
    CCDS953.1
    UniProtKB/Swiss-Prot
    Q16610
    UniProtKB/TrEMBL
    A0A140VJI7
    Related
    ENSP00000358043.4, ENST00000369047.9
    Conserved Domains (1) summary
    pfam05782
    Location:5540
    ECM1; Extracellular matrix protein 1 (ECM1)
  3. NM_022664.3NP_073155.2  extracellular matrix protein 1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_073155.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame coding exon compared to variant 1, resulting in a shorter isoform (2) missing an internal protein segment compared to isoform 1.
    Source sequence(s)
    AK097046, AL356356, CA413352, DA963826, U68187
    Consensus CDS
    CCDS954.1
    UniProtKB/Swiss-Prot
    Q16610
    Related
    ENSP00000271630.6, ENST00000346569.6
    Conserved Domains (1) summary
    pfam05782
    Location:5415
    ECM1; Extracellular matrix protein 1 (ECM1)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    150508109..150513789
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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