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SPON1 spondin 1 [ Homo sapiens (human) ]

Gene ID: 10418, updated on 2-Nov-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, Nov 2024]
Expression
Broad expression in gall bladder (RPKM 73.6), urinary bladder (RPKM 33.9) and 16 other tissues See more
Orthologs
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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 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)

Genotypes

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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