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    SPON1 spondin 1 [ Homo sapiens (human) ]

    Gene ID: 10418, updated on 9-Dec-2024

    Summary

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    Official Symbol
    SPON1provided by HGNC
    Official Full Name
    spondin 1provided by HGNC
    Primary source
    HGNC:HGNC:11252
    See related
    Ensembl:ENSG00000262655 MIM:604989; AllianceGenome:HGNC:11252
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    f-spondin; VSGP/F-spondin
    Summary
    Predicted to enable LBD domain binding activity and metal ion binding activity. Predicted to be an extracellular matrix structural constituent. Predicted to be involved in cell adhesion. Predicted to act upstream of or within negative regulation of amyloid-beta formation; positive regulation of amyloid precursor protein catabolic process; and positive regulation of protein processing. Located in collagen-containing extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in gall bladder (RPKM 73.6), urinary bladder (RPKM 33.9) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SPON1 in Genome Data Viewer
    Location:
    11p15.2
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (13962723..14268133)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (14055316..14360665)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (13984270..14289679)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:13944875-13946074 Neighboring gene RNA, 5S ribosomal pseudogene 331 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:13960135-13960636 Neighboring gene long intergenic non-protein coding RNA 2683 Neighboring gene uncharacterized LOC124902637 Neighboring gene NANOG hESC enhancer GRCh37_chr11:13987555-13988073 Neighboring gene NANOG hESC enhancer GRCh37_chr11:14043232-14043739 Neighboring gene NANOG hESC enhancer GRCh37_chr11:14165203-14165715 Neighboring gene RNA, 5S ribosomal pseudogene 332 Neighboring gene Sharpr-MPRA regulatory region 134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:14252080-14252666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:14280438-14280962 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:14280963-14281486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4471 Neighboring gene RAS related 2 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:14362237-14362911 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:14373862-14374748 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:14374749-14375635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3170 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3171 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3172 Neighboring gene NANOG hESC enhancer GRCh37_chr11:14385715-14386272 Neighboring gene Sharpr-MPRA regulatory region 2156 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:14428638-14429316 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:14443710-14444362 Neighboring gene 60S ribosomal protein L13a-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Effect of F-spondin on cementoblastic differentiation of human periodontal ligament cells. Kitagawa M, et al. Biochem Biophys Res Commun, 2006 Oct 27. PMID 16965763
    2. Increased SPON1 promotes pancreatic ductal adenocarcinoma progression by enhancing IL-6 trans-signalling. Huo Y, et al. Cell Prolif, 2022 May. PMID 35487760, Free PMC Article
    3. The crystal structure of the heparin-binding reelin-N domain of f-spondin. Tan K, et al. J Mol Biol, 2008 Sep 19. PMID 18602404, Free PMC Article
    4. Evaluation of relationship between SPON1 gene and genetic susceptibility of postmenopausal osteoporosis. Ma W, et al. Artif Cells Nanomed Biotechnol, 2020 Dec. PMID 32484721
    5. VSGP/F-spondin: a new ovarian cancer marker. Pyle-Chenault RA, et al. Tumour Biol, 2005 Sep-Oct. PMID 16103746

    See all (39) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SPON1 is an independent prognostic biomarker for ovarian cancer.
      Title: SPON1 is an independent prognostic biomarker for ovarian cancer.
    2. Increased SPON1 promotes pancreatic ductal adenocarcinoma progression by enhancing IL-6 trans-signalling.
      Title: Increased SPON1 promotes pancreatic ductal adenocarcinoma progression by enhancing IL-6 trans-signalling.
    3. Prognostic and Diagnostic Values of miR-506 and SPON 1 in Colorectal Cancer with Clinicopathological Considerations.
      Title: Prognostic and Diagnostic Values of miR-506 and SPON 1 in Colorectal Cancer with Clinicopathological Considerations.
    4. Evaluation of relationship between SPON1 gene and genetic susceptibility of postmenopausal osteoporosis.
      Title: Evaluation of relationship between SPON1 gene and genetic susceptibility of postmenopausal osteoporosis.
    5. SPON1 rs2618516 polymorphism moderated the effects of APOE on working memory in terms of both in behaviors and in the level of brain activations.
      Title: APOE influences working memory in non-demented elderly through an interaction with SPON1 rs2618516.
    6. gene expression experiment revealed that CYP2B6, SPON1, and GSG1L can be activated concomitantly through a constitutive androstane receptor (CAR) activation pathway
      Title: Genome-Wide Pharmacogenomic Study on Methadone Maintenance Treatment Identifies SNP rs17180299 and Multiple Haplotypes on CYP2B6, SPON1, and GSG1L Associated with Plasma Concentrations of Methadone R- and S-enantiomers in Heroin-Dependent Patients.
    7. SPON1 promotes metastatic progression through Fak and Src dependent pathway in human osteosarcoma.
      Title: Spondin 1 promotes metastatic progression through Fak and Src dependent pathway in human osteosarcoma.
    8. These data suggest that SPON1 may be associated with the differential rate of cognitive decline in Alzheimer disease.
      Title: Genome-wide association study of the rate of cognitive decline in Alzheimer's disease.
    9. High SPON1 expression is associated with high-grade gliomas.
      Title: Experimental validation of 5 in-silico predicted glioma biomarkers.
    10. Genome-wide scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity
      Title: Genome-wide scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    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

    EBI GWAS Catalog

    Description
    A genome-wide association study of inflammatory biomarker changes in response to fenofibrate treatment in the Genetics of Lipid Lowering Drug and Diet Network.
    EBI GWAS Catalog
    Genome-wide association study of ancestry-specific TB risk in the South African Coloured population.
    EBI GWAS Catalog
    Genome-wide association study of the rate of cognitive decline in Alzheimer's disease.
    EBI GWAS Catalog
    Genome-wide scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vif vif HIV-1 Vif downregulates the expression of spondin 1 (SPON1, extracellular matrix protein) in Vif-expression T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0762, MGC10724

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables LBD domain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables extracellular matrix structural constituent RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of amyloid-beta formation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of amyloid precursor protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of protein processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    colocalizes_with collagen-containing extracellular matrix HDA PubMed 
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
    		  
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular space HDA PubMed 

    General protein information

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    Preferred Names
    spondin-1
    Names
    spondin 1, (f-spondin) extracellular matrix protein
    spondin 1, extracellular matrix protein
    vascular smooth muscle cell growth-promoting factor

    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_006108.4 → NP_006099.2  spondin-1 precursor

      See identical proteins and their annotated locations for NP_006099.2

      Status: VALIDATED

      Source sequence(s)
      AB018305, AK291780, BQ026865
      Consensus CDS
      CCDS73262.1
      UniProtKB/Swiss-Prot
      A8K6W5, O94862, Q8NCD7, Q8WUR5, Q9HCB6
      Related
      ENSP00000460236.1, ENST00000576479.4
      Conserved Domains (4) summary
      cd08544
      Location:43 → 182
      Reeler; the N-terminal domain of reelin, F-spondin, and a variety of other proteins
      pfam00090
      Location:562 → 610
      TSP_1; Thrombospondin type 1 domain
      pfam06468
      Location:205 → 392
      Spond_N; Spondin_N
      pfam19028
      Location:669 → 720
      TSP1_spondin; Spondin-like TSP1 domain

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      13962723..14268133
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      14055316..14360665
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HCB6.2 GenPept UniProtKB/Swiss-Prot:Q9HCB6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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