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    SMOC1 SPARC related modular calcium binding 1 [ Homo sapiens (human) ]

    Gene ID: 64093, updated on 17-Jun-2024

    Summary

    Official Symbol
    SMOC1provided by HGNC
    Official Full Name
    SPARC related modular calcium binding 1provided by HGNC
    Primary source
    HGNC:HGNC:20318
    See related
    Ensembl:ENSG00000198732 MIM:608488; AllianceGenome:HGNC:20318
    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
    OAS
    Summary
    This gene encodes a multi-domain secreted protein that may have a critical role in ocular and limb development. Mutations in this gene are associated with microphthalmia and limb anomalies. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]
    Expression
    Biased expression in brain (RPKM 47.3), testis (RPKM 23.8) and 6 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SMOC1 in Genome Data Viewer
    Location:
    14q24.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (69879416..70032366)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (64087047..64239860)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (70346133..70499083)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA11 Neighboring gene uncharacterized LOC100506358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:70309156-70309730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:70309731-70310303 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5883 Neighboring gene ribosomal protein L7a pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:70419797-70420298 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:70445787-70446286 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:70454077-70454578 Neighboring gene small nucleolar RNA, C/D box 169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8650 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:70477330-70478529 Neighboring gene Sharpr-MPRA regulatory region 14883 Neighboring gene Sharpr-MPRA regulatory region 1041 Neighboring gene MPRA-validated peak2186 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:70527273-70528472 Neighboring gene Sharpr-MPRA regulatory region 1623 Neighboring gene solute carrier family 8 member A3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5885 Neighboring gene ADAM metallopeptidase domain 20 pseudogene Neighboring gene uncharacterized LOC107984686 Neighboring gene MPRA-validated peak2187 silencer

    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
    Microphthalmia with limb anomalies
    MedGen: C0599973 OMIM: 206920 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Genetic association suggests that SMOC1 mediates between prenatal sex hormones and digit ratio.
    EBI GWAS Catalog
    Genome-wide association study of ancestry-specific TB risk in the South African Coloured population.
    EBI GWAS Catalog
    Multistage genome-wide association meta-analyses identified two new loci for bone mineral density.
    EBI GWAS Catalog
    Seventy-five genetic loci influencing the human red blood cell.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Microarray analysis indicates HIV-1 Tat-induced upregulation of SPARC related modular calcium binding 1 (SMOC1) in primary human brain microvascular endothelial cells PubMed
    Vif vif HIV-1 Vif upregulates the expression of SPARC related modular calcium binding 1 (SMOC1) in Vif-expression T cells PubMed

    Go to the HIV-1, Human Interaction Database

    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 IEA
    Inferred from Electronic Annotation
    more info
     
    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 
    Process Evidence Code Pubs
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in eye development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in limb development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of osteoblast differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in basement membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    SPARC-related modular calcium-binding protein 1
    Names
    secreted modular calcium-binding protein 1

    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_028217.1 RefSeqGene

      Range
      5020..157970
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001034852.3NP_001030024.1  SPARC-related modular calcium-binding protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001030024.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AJ249900, AK098441, BC011548, BQ183777, DA805236
      Consensus CDS
      CCDS32110.1
      UniProtKB/Swiss-Prot
      Q9H4F8
      Related
      ENSP00000355110.4, ENST00000361956.8
      Conserved Domains (4) summary
      cd00104
      Location:4787
      KAZAL_FS; Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the ...
      pfam00086
      Location:95158
      Thyroglobulin_1; Thyroglobulin type-1 repeat
      pfam16597
      Location:159217
      Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain
      cd16240
      Location:315429
      EFh_SPARC_SMOC1; EF-hand, extracellular calcium-binding (EC) motif, found in secreted modular calcium-binding protein 1 (SMOC-1)
    2. NM_001425244.1NP_001412173.1  SPARC-related modular calcium-binding protein 1 isoform 3 precursor

      Status: REVIEWED

      Source sequence(s)
      AL135747, AL157789
    3. NM_001425245.1NP_001412174.1  SPARC-related modular calcium-binding protein 1 isoform 4 precursor

      Status: REVIEWED

      Source sequence(s)
      AL135747, AL157789
    4. NM_022137.6NP_071420.1  SPARC-related modular calcium-binding protein 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_071420.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site at the 3' terminal exon compared to variant 1. This results in an isoform (2) that is 1 aa shorter than isoform 1.
      Source sequence(s)
      AJ249900, AK098441, AK289988, BC008608, BC011548, BQ183777, DA805236
      Consensus CDS
      CCDS9798.1
      UniProtKB/Swiss-Prot
      A8K1S3, B2R7P5, Q96F78, Q9H4F8
      Related
      ENSP00000370680.4, ENST00000381280.4
      Conserved Domains (4) summary
      cd00104
      Location:4787
      KAZAL_FS; Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the ...
      pfam00086
      Location:95158
      Thyroglobulin_1; Thyroglobulin type-1 repeat
      pfam16597
      Location:159217
      Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain
      cd16240
      Location:315429
      EFh_SPARC_SMOC1; EF-hand, extracellular calcium-binding (EC) motif, found in secreted modular calcium-binding protein 1 (SMOC-1)

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      69879416..70032366
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005267995.2XP_005268052.1  SPARC-related modular calcium-binding protein 1 isoform X1

      Conserved Domains (5) summary
      cd00104
      Location:4787
      KAZAL_FS; Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the ...
      cd00191
      Location:237303
      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:375436
      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 ...
      pfam00086
      Location:95158
      Thyroglobulin_1; Thyroglobulin type-1 repeat
      pfam16597
      Location:159228
      Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain
    2. XM_005267996.2XP_005268053.1  SPARC-related modular calcium-binding protein 1 isoform X2

      Conserved Domains (5) summary
      cd00104
      Location:4787
      KAZAL_FS; Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the ...
      cd00191
      Location:237303
      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:375436
      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 ...
      pfam00086
      Location:95158
      Thyroglobulin_1; Thyroglobulin type-1 repeat
      pfam16597
      Location:159228
      Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      64087047..64239860
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376573.1XP_054232548.1  SPARC-related modular calcium-binding protein 1 isoform X1

    2. XM_054376574.1XP_054232549.1  SPARC-related modular calcium-binding protein 1 isoform X2