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

    Gene ID: 1842, updated on 10-Dec-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
    mouse all
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    Genomic context

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    See ECM2 in Genome Data Viewer
    Location:
    9q22.31
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (92493547..92559106, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (104660046..104703254, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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)

    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_2024_08

    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
      UniProtKB/TrEMBL
      B4DK93

    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
      UniProtKB/TrEMBL
      B4DK93

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

      UniProtKB/Swiss-Prot
      B2R730, E2PU11, O94769, Q5T9F2, Q7Z3D0
      UniProtKB/TrEMBL
      B4DK93

    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

      UniProtKB/TrEMBL
      B4DK93

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

      UniProtKB/TrEMBL
      B4DK93

    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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