Format

Send to:

Choose Destination

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

Gene ID: 64093, updated on 7-Jun-2020

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
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

Genomic context

See SMOC1 in Genome Data Viewer
Location:
14q24.2
Exon count:
12
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (69879388..70032366)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (70346105..70499083)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 10266 Neighboring gene solute carrier family 10 member 1 Neighboring gene uncharacterized LOC100506358 Neighboring gene ribosomal protein L7a pseudogene 6 Neighboring gene small nucleolar RNA, C/D box 169 Neighboring gene Sharpr-MPRA regulatory region 14883 Neighboring gene solute carrier family 8 member A3 Neighboring gene ADAM metallopeptidase domain 20 pseudogene Neighboring gene uncharacterized LOC107984686

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 Compare labs

NHGRI GWAS Catalog

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cell differentiation IEA
Inferred from Electronic Annotation
more info
 
eye development IMP
Inferred from Mutant Phenotype
more info
PubMed 
limb development IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of osteoblast differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
basement membrane IEA
Inferred from Electronic Annotation
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)

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
    ENSP00000355110.3, ENST00000361956.7
    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_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
    Q9H4F8
    UniProtKB/TrEMBL
    A0A024R6E0
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

    Range
    69879388..70032366
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005267995.1XP_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_005267996.1XP_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
Support Center