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    SMOC2 SPARC related modular calcium binding 2 [ Homo sapiens (human) ]

    Gene ID: 64094, updated on 20-May-2024

    Summary

    Official Symbol
    SMOC2provided by HGNC
    Official Full Name
    SPARC related modular calcium binding 2provided by HGNC
    Primary source
    HGNC:HGNC:20323
    See related
    Ensembl:ENSG00000112562 MIM:607223; AllianceGenome:HGNC:20323
    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
    DTDP1; SMAP2; MST117; MSTP117; MSTP140; bA37D8.1; bA270C4A.1; dJ421D16.1
    Summary
    This gene encodes a member of the SPARC family (secreted protein acidic and rich in cysteine/osteonectin/BM-40), which are highly expressed during embryogenesis and wound healing. The gene product is a matricellular protein which promotes matrix assembly and can stimulate endothelial cell proliferation and migration, as well as angiogenic activity. Associated with pulmonary function, this secretory gene product contains a Kazal domain, two thymoglobulin type-1 domains, and two EF-hand calcium-binding domains. The encoded protein may serve as a target for controlling angiogenesis in tumor growth and myocardial ischemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
    Expression
    Broad expression in endometrium (RPKM 68.7), gall bladder (RPKM 54.9) and 18 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    6q27
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (168441184..168667992)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (169784308..170014051)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (168841864..169068672)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378140 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:168811985-168813184 Neighboring gene uncharacterized LOC105378141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168855369-168855870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168857582-168858555 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:168870327-168871526 Neighboring gene uncharacterized LOC124901466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168897617-168898335 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:168929287-168929424 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:168941003-168941930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169007268-169007804 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91285 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91305 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:169059822-169060322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169067581-169068082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169068083-169068582 Neighboring gene uncharacterized LOC124901467 Neighboring gene uncharacterized LOC124901468

    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?

    Phenotypes

    Associated conditions

    Description Tests
    Dentin dysplasia type I
    MedGen: C0399379 OMIM: 125400 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study of generalized vitiligo in an isolated European founder population identifies SMOC2, in close proximity to IDDM8.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding ISA
    Inferred from Sequence Alignment
    more info
    PubMed 
    enables extracellular matrix binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables heparin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in basement membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cell periphery IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    SPARC-related modular calcium-binding protein 2
    Names
    SMAP-2
    SMOC-2
    secreted modular calcium-binding protein 2
    smooth muscle associated protein 2
    thyroglobulin type-1 repeat containing protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_032781.1 RefSeqGene

      Range
      5034..231842
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001166412.2NP_001159884.1  SPARC-related modular calcium-binding protein 2 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001159884.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AI032288, BC028420
      Consensus CDS
      CCDS55076.1
      UniProtKB/Swiss-Prot
      B3KPS7, Q4G169, Q5TAT7, Q5TAT8, Q86VV9, Q96SF3, Q9H1L3, Q9H1L4, Q9H3U0, Q9H3U7, Q9H4F7, Q9HCV2
      Related
      ENSP00000348630.3, ENST00000356284.7
      Conserved Domains (4) summary
      smart00280
      Location:3984
      KAZAL; Kazal type serine protease inhibitors
      cd00191
      Location:215281
      TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
      pfam16597
      Location:154212
      Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain
      cl08302
      Location:352410
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    2. NM_022138.3NP_071421.1  SPARC-related modular calcium-binding protein 2 isoform 1 precursor

      See identical proteins and their annotated locations for NP_071421.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB014737, AI032288, AL136099, BC028420
      Consensus CDS
      CCDS5307.1
      UniProtKB/Swiss-Prot
      Q9H3U7
      Related
      ENSP00000346537.5, ENST00000354536.9
      Conserved Domains (4) summary
      smart00280
      Location:3984
      KAZAL; Kazal type serine protease inhibitors
      cd00191
      Location:226292
      TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
      pfam16597
      Location:154223
      Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain
      cl08302
      Location:363421
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      168441184..168667992
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011536066.2XP_011534368.1  SPARC-related modular calcium-binding protein 2 isoform X2

      See identical proteins and their annotated locations for XP_011534368.1

      Conserved Domains (4) summary
      smart00280
      Location:3984
      KAZAL; Kazal type serine protease inhibitors
      cd00191
      Location:215281
      TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
      pfam16597
      Location:154212
      Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain
      cl08302
      Location:352410
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    2. XM_011536065.2XP_011534367.1  SPARC-related modular calcium-binding protein 2 isoform X1

      Conserved Domains (4) summary
      smart00280
      Location:3984
      KAZAL; Kazal type serine protease inhibitors
      cd00191
      Location:226292
      TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
      cd00252
      Location:363424
      SPARC_EC; SPARC_EC; extracellular Ca2+ binding domain (containing 2 EF-hand motifs) of SPARC and related proteins (QR1, SC1/hevin, testican and tsc-36/FRP). SPARC (BM-40) is a multifunctional glycoprotein, a matricellular protein, that functions to regulate ...
      pfam16597
      Location:154223
      Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      169784308..170014051
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356216.1XP_054212191.1  SPARC-related modular calcium-binding protein 2 isoform X2

    2. XM_054356215.1XP_054212190.1  SPARC-related modular calcium-binding protein 2 isoform X1