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    Smoc1 SPARC related modular calcium binding 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 314280, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Smoc1provided by RGD
    Official Full Name
    SPARC related modular calcium binding 1provided by RGD
    Primary source
    RGD:1303126
    See related
    EnsemblRapid:ENSRNOG00000005998 AllianceGenome:RGD:1303126
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable extracellular matrix binding activity and heparin binding activity. Predicted to be involved in several processes, including extracellular matrix organization; limb development; and regulation of osteoblast differentiation. Predicted to act upstream of or within positive regulation of cell-substrate adhesion. Predicted to be active in basement membrane and extracellular space. Human ortholog(s) of this gene implicated in microphthalmia with limb anomalies. Orthologous to human SMOC1 (SPARC related modular calcium binding 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 178.0), Liver (RPKM 170.3) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Smoc1 in Genome Data Viewer
    Location:
    6q24
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (106432592..106593956)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (100701330..100897441)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (104718403..104879611)

    Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene solute carrier family 10 member 1 Neighboring gene phospholipase A2 group IB like 1 Neighboring gene uncharacterized LOC120103570 Neighboring gene uncharacterized LOC120103571 Neighboring gene uncharacterized LOC134479222 Neighboring gene solute carrier family 8 member A3 Neighboring gene cytochrome c oxidase assembly factor COX16 Neighboring gene a disintegrin and metallopeptidase domain 4-like 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Secretome analysis of human BMSCs and identification of SMOC1 as an important ECM protein in osteoblast differentiation. Choi YA, et al. J Proteome Res, 2010 Jun 4. PMID 20359165
    2. Nitric oxide inhibits glomerular TGF-beta signaling via SMOC-1. Dreieicher E, et al. J Am Soc Nephrol, 2009 Sep. PMID 19578009, Free PMC Article
    3. Characterization of SMOC-1, a novel modular calcium-binding protein in basement membranes. Vannahme C, et al. J Biol Chem, 2002 Oct 11. PMID 12130637
    4. Reduced CircSMOC1 Level Promotes Metabolic Reprogramming via PTBP1 (Polypyrimidine Tract-Binding Protein) and miR-329-3p in Pulmonary Arterial Hypertension Rats. Lu GF, et al. Hypertension, 2022 Nov. PMID 35997022
    5. SMOC1 is essential for ocular and limb development in humans and mice. Okada I, et al. Am J Hum Genet, 2011 Jan 7. PMID 21194678, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Reduced CircSMOC1 Level Promotes Metabolic Reprogramming via PTBP1 (Polypyrimidine Tract-Binding Protein) and miR-329-3p in Pulmonary Arterial Hypertension Rats.
      Title: Reduced CircSMOC1 Level Promotes Metabolic Reprogramming via PTBP1 (Polypyrimidine Tract-Binding Protein) and miR-329-3p in Pulmonary Arterial Hypertension Rats.
    2. NO attenuates SMOC-1 expression in acute glomerular inflammation, thereby limiting TGF-beta-mediated profibrotic signaling
      Title: Nitric oxide inhibits glomerular TGF-beta signaling via SMOC-1.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    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 extracellular matrix binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables heparin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within extracellular matrix organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in eye development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in limb development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of cell-substrate adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of osteoblast differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in basement membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in basement membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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

    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_001002835.2 → NP_001002835.1  SPARC-related modular calcium-binding protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001002835.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000006
      UniProtKB/TrEMBL
      A6JDL6, F1LSF2, Q6IE50
      Conserved Domains (5) summary
      smart00280
      Location:42 → 86
      KAZAL; Kazal type serine protease inhibitors
      cd00191
      Location:225 → 291
      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:363 → 424
      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:94 → 157
      Thyroglobulin_1; Thyroglobulin type-1 repeat
      pfam16597
      Location:158 → 216
      Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain

    2. NM_001412316.1 → NP_001399245.1  SPARC-related modular calcium-binding protein 1 isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000006
      UniProtKB/TrEMBL
      A0A8I6A4M6, A6JDL6
      Related
      ENSRNOP00000086850.1, ENSRNOT00000114143.2

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086024.1 Reference GRCr8

      Range
      106432592..106593956
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063261932.1 → XP_063118002.1  SPARC-related modular calcium-binding protein 1 isoform X3

    2. XM_006240284.5 → XP_006240346.1  SPARC-related modular calcium-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZYF0, A6JDL6
      Conserved Domains (5) summary
      smart00280
      Location:42 → 86
      KAZAL; Kazal type serine protease inhibitors
      cd00191
      Location:236 → 302
      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:374 → 435
      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:94 → 157
      Thyroglobulin_1; Thyroglobulin type-1 repeat
      pfam16597
      Location:158 → 227
      Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain

    3. XM_006240285.5 → XP_006240347.1  SPARC-related modular calcium-binding protein 1 isoform X2

      UniProtKB/TrEMBL
      A6JDL6
      Conserved Domains (5) summary
      smart00280
      Location:42 → 86
      KAZAL; Kazal type serine protease inhibitors
      cd00191
      Location:236 → 302
      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:374 → 435
      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:94 → 157
      Thyroglobulin_1; Thyroglobulin type-1 repeat
      pfam16597
      Location:158 → 227
      Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain

    4. XM_063261933.1 → XP_063118003.1  SPARC-related modular calcium-binding protein 1 isoform X4

    Nucleotide Protein Strain
    Heading Accession and Version

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