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

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; AllianceGenome:HGNC:3153
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: mouse all
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Genomic context

Location:: 1q21.2

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (150508109..150513789)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (149632949..149638627)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (150480585..150486265)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ECM1 promotes migration and invasion in endometriosis.
Title: ECM1 promotes migration and invasion in endometriosis.
TET2-mediated ECM1 hypomethylation promotes the neovascularization in active proliferative diabetic retinopathy.
Title: TET2-mediated ECM1 hypomethylation promotes the neovascularization in active proliferative diabetic retinopathy.
Downregulation of extracellular matrix protein 1 effectively ameliorates osteoarthritis progression in vivo.
Title: Downregulation of extracellular matrix protein 1 effectively ameliorates osteoarthritis progression in vivo.
Lipoid proteinosis: Novel ECM1 pathogenic variants and intrafamilial variability in four unrelated Arab families.
Title: Lipoid proteinosis: Novel ECM1 pathogenic variants and intrafamilial variability in four unrelated Arab families.
Associations between Extracellular Matrix Protein 1 Gene Polymorphism and Progression of Liver Disease.
Title: Associations between Extracellular Matrix Protein 1 Gene Polymorphism and Progression of Liver Disease.
4D-quantitative proteomics signature of asthenozoospermia and identification of extracellular matrix protein 1 as a novel biomarker for sperm motility.
Title: 4D-quantitative proteomics signature of asthenozoospermia and identification of extracellular matrix protein 1 as a novel biomarker for sperm motility.
Hoarse voice in children as the presenting feature of ECM1-related lipoid proteinosis.
Title: Hoarse voice in children as the presenting feature of ECM1-related lipoid proteinosis.
HLA-A2.1-restricted ECM1-derived epitope LA through DC cross-activation priming CD8(+) T and NK cells: a novel therapeutic tumour vaccine.
Title: HLA-A2.1-restricted ECM1-derived epitope LA through DC cross-activation priming CD8(+) T and NK cells: a novel therapeutic tumour vaccine.
Extracellular matrix protein-1 secretory isoform promotes ovarian cancer through increasing alternative mRNA splicing and stemness.
Title: Extracellular matrix protein-1 secretory isoform promotes ovarian cancer through increasing alternative mRNA splicing and stemness.
Gene silencing of extracellular matrix protein 1 (ECM1) results in phenotypic alterations of dermal fibroblasts reminiscent of clinical features of lichen sclerosus.
Title: Gene silencing of extracellular matrix protein 1 (ECM1) results in phenotypic alterations of dermal fibroblasts reminiscent of clinical features of lichen sclerosus.

Submit: New GeneRIF Correction See all GeneRIFs (70)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Lipid proteinosis MedGen: C0023795 OMIM: 247100 GeneReviews: Lipoid Proteinosis	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables interleukin-2 receptor binding	IEA Inferred from Electronic Annotation more info
enables protease binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in angiogenesis	IEA Inferred from Electronic Annotation more info
involved_in biomineral tissue development	IEA Inferred from Electronic Annotation more info
involved_in chondrocyte development	IEA Inferred from Electronic Annotation more info
involved_in endochondral bone growth	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of bone mineralization	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cytokine-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of peptidase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in ossification	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of angiogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of canonical NF-kappaB signal transduction	HMP more info	PubMed
involved_in positive regulation of endothelial cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of T cell migration	IEA Inferred from Electronic Annotation more info
involved_in regulation of bone mineralization	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of type 2 immune response	IEA Inferred from Electronic Annotation more info
involved_in signal transduction	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in collagen-containing extracellular matrix	HDA more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in collagen-containing extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular matrix	NAS Non-traceable Author Statement more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in platelet dense granule lumen	TAS Traceable Author Statement more info

General protein information

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Preferred Names: extracellular matrix protein 1

Names: secretory component p85; testicular tissue protein Li 61

NCBI Reference Sequences (RefSeq)

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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

NG_012062.1 RefSeqGene

Range

5099..10779

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001202858.2 → NP_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:5 → 567

ECM1; Extracellular matrix protein 1 (ECM1)
NM_004425.4 → NP_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

A8K8S0, B4DW49, B4DY60, O43266, Q16610, Q5T5G4, Q5T5G5, Q5T5G6, Q8IZ60

UniProtKB/TrEMBL

A0A140VJI7

Related

ENSP00000358043.4, ENST00000369047.9

Conserved Domains (1) summary

pfam05782
Location:5 → 540

ECM1; Extracellular matrix protein 1 (ECM1)
NM_022664.3 → NP_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:5 → 415

ECM1; Extracellular matrix protein 1 (ECM1)