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ECM2 extracellular matrix protein 2 [ Homo sapiens (human) ]

Gene ID: 1842, updated on 3-Apr-2024

Summary

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Official Symbol
ECM2provided by HGNC
Official Full Name
extracellular matrix protein 2provided by HGNC
Primary source
HGNC:HGNC:3154
See related
Ensembl:ENSG00000106823 MIM:603479; AllianceGenome:HGNC:3154
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
Summary
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]
Expression
Broad expression in fat (RPKM 50.1), ovary (RPKM 21.0) and 14 other tissues See more
Orthologs
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Genomic context

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Location:
9q22.31
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (92493547..92559106, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (104660046..104703254, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (95255829..95298272, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene centromere protein P Neighboring gene osteomodulin Neighboring gene asporin Neighboring gene Sharpr-MPRA regulatory region 3268 Neighboring gene microRNA 4670 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:95320296-95321495 Neighboring gene uncharacterized LOC100128361 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:95383063-95383333 Neighboring gene inositol-pentakisphosphate 2-kinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28596 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28597 Neighboring gene uncharacterized LOC107987095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28598 Neighboring gene Sharpr-MPRA regulatory region 2132 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109781

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  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. Nishiu J, et al. Genomics, 1998 Sep 15. PMID 9790758
  2. Matrix glycoprotein SC1/ECM2 augments B lymphopoiesis. Oritani K, et al. Blood, 1997 Nov 1. PMID 9345023
  3. DNA sequence and analysis of human chromosome 9. Humphray SJ, et al. Nature, 2004 May 27. PMID 15164053, Free PMC Article
  4. Impaired plasma membrane localization of ubiquitin ligase complex underlies 3-M syndrome development. Wang P, et al. J Clin Invest, 2019 Jul 25. PMID 31343991, Free PMC Article
  5. The LIFEdb database in 2006. Mehrle A, et al. Nucleic Acids Res, 2006 Jan 1. PMID 16381901, Free PMC Article

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC126355, MGC126356

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables collagen V binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables heparin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables integrin binding TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell-matrix adhesion TAS
Traceable Author Statement
more info
 PubMed 
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cell-substrate adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
located_in interstitial matrix IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
extracellular matrix protein 2
Names
extracellular matrix protein 2, female organ and adipocyte specific
matrix glycoprotein SC1/ECM2

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.

mRNA and Protein(s)

  1. NM_001197295.2 → NP_001184224.1  extracellular matrix protein 2 isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AB011792, BM972177, BX537976, DC300418
    UniProtKB/TrEMBL
    B4DK93
    Conserved Domains (4) summary
    COG4886
    Location:469 → 651
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:299 → 322
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00093
    Location:103 → 157
    VWC; von Willebrand factor type C domain
    cl26018
    Location:298 → 550
    NEL; C-terminal novel E3 ligase, LRR-interacting

  2. NM_001197296.2 → NP_001184225.1  extracellular matrix protein 2 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice junction at the 5' end of an exon and differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) lacks an internal segment and has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AB011792, BX537976, DC300418
    Consensus CDS
    CCDS56578.1
    UniProtKB/TrEMBL
    B4DK93
    Related
    ENSP00000393971.2, ENST00000444490.6
    Conserved Domains (5) summary
    cd00116
    Location:296 → 525
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00031
    Location:588 → 610
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:299 → 322
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00093
    Location:103 → 157
    VWC; von Willebrand factor type C domain
    pfam13855
    Location:321 → 383
    LRR_8; Leucine rich repeat

  3. NM_001393.4 → NP_001384.1  extracellular matrix protein 2 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001384.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB011792, BM972177, DC300418
    Consensus CDS
    CCDS6698.1
    UniProtKB/Swiss-Prot
    B2R730, E2PU11, O94769, Q5T9F2, Q7Z3D0
    UniProtKB/TrEMBL
    B4DK93
    Related
    ENSP00000344758.5, ENST00000344604.10
    Conserved Domains (5) summary
    PRK15370
    Location:320 → 572
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    COG4886
    Location:491 → 673
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:321 → 344
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00093
    Location:103 → 157
    VWC; von Willebrand factor type C domain
    pfam14828
    Location:116 → 210
    Amnionless

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    92493547..92559106 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047422899.1 → XP_047278855.1  extracellular matrix protein 2 isoform X1

    UniProtKB/Swiss-Prot
    B2R730, E2PU11, O94769, Q5T9F2, Q7Z3D0

  2. XM_024447436.2 → XP_024303204.1  extracellular matrix protein 2 isoform X1

    UniProtKB/Swiss-Prot
    B2R730, E2PU11, O94769, Q5T9F2, Q7Z3D0
    UniProtKB/TrEMBL
    B4DK93
    Conserved Domains (5) summary
    PRK15370
    Location:320 → 572
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    COG4886
    Location:491 → 673
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:321 → 344
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00093
    Location:103 → 157
    VWC; von Willebrand factor type C domain
    pfam14828
    Location:116 → 210
    Amnionless

  3. XM_024447435.2 → XP_024303203.1  extracellular matrix protein 2 isoform X1

    UniProtKB/Swiss-Prot
    B2R730, E2PU11, O94769, Q5T9F2, Q7Z3D0
    UniProtKB/TrEMBL
    B4DK93
    Conserved Domains (5) summary
    PRK15370
    Location:320 → 572
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    COG4886
    Location:491 → 673
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:321 → 344
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00093
    Location:103 → 157
    VWC; von Willebrand factor type C domain
    pfam14828
    Location:116 → 210
    Amnionless

  4. XM_017014376.3 → XP_016869865.1  extracellular matrix protein 2 isoform X2

RNA

  1. XR_007061259.1 RNA Sequence

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791788.1 Reference GRCh38.p14 PATCHES

    Range
    328274..371451 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333086.1 → XP_054189061.1  extracellular matrix protein 2 isoform X1

    UniProtKB/Swiss-Prot
    B2R730, E2PU11, O94769, Q5T9F2, Q7Z3D0

  2. XM_054333085.1 → XP_054189060.1  extracellular matrix protein 2 isoform X1

    UniProtKB/Swiss-Prot
    B2R730, E2PU11, O94769, Q5T9F2, Q7Z3D0

  3. XM_054333087.1 → XP_054189062.1  extracellular matrix protein 2 isoform X2

RNA

  1. XR_008485819.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    104660046..104703254 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362232.1 → XP_054218207.1  extracellular matrix protein 2 isoform X1

  2. XM_054362231.1 → XP_054218206.1  extracellular matrix protein 2 isoform X1

  3. XM_054362233.1 → XP_054218208.1  extracellular matrix protein 2 isoform X2

RNA

  1. XR_008487958.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O94769.1 GenPept UniProtKB/Swiss-Prot:O94769

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