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    SPON2 spondin 2 [ Homo sapiens (human) ]

    Gene ID: 10417, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SPON2provided by HGNC
    Official Full Name
    spondin 2provided by HGNC
    Primary source
    HGNC:HGNC:11253
    See related
    Ensembl:ENSG00000159674 MIM:605918; AllianceGenome:HGNC:11253
    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
    DIL1; DIL-1; MINDIN; M-SPONDIN
    Summary
    Predicted to enable antigen binding activity; lipopolysaccharide binding activity; and metal ion binding activity. Predicted to be involved in cell adhesion. Predicted to act upstream of or within several processes, including defense response to other organism; opsonization; and positive regulation of cytokine production. Located in extracellular exosome. Biomarker of meningioma. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in prostate (RPKM 48.4), endometrium (RPKM 37.2) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SPON2 in Genome Data Viewer
    Location:
    4p16.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (1166932..1208844, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (1165604..1208039, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (1160720..1202632, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene nascent polypeptide-associated complex subunit alpha, muscle-specific form-like Neighboring gene uncharacterized LOC105374344 Neighboring gene small nucleolar RNA SNORA48 Neighboring gene transmembrane p24 trafficking protein 11, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15122 Neighboring gene hornerin-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1143546-1144046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1144047-1144547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21143 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:1160925-1161208 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1165551-1166266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1166267-1166984 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21145 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1172226-1172726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1188097-1188808 Neighboring gene uncharacterized LOC100130872 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:1190349-1191548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1193431-1193980 Neighboring gene uncharacterized LOC124900164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21148 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15123 Neighboring gene CTBP1 antisense RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21149 Neighboring gene C-terminal binding protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1227715-1228270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1233764-1234264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15125 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21151 Neighboring gene CTBP1 divergent transcript

    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. In situ assessment of Mindin as a biomarker of podocyte lesions in diabetic nephropathy. Martins ALMDS, et al. PLoS One, 2023. PMID 37130106, Free PMC Article
    2. SPON2 Promotes M1-like Macrophage Recruitment and Inhibits Hepatocellular Carcinoma Metastasis by Distinct Integrin-Rho GTPase-Hippo Pathways. Zhang YL, et al. Cancer Res, 2018 May 1. PMID 29440144
    3. Elevated spondin-2 expression correlates with progression and prognosis in gastric cancer. Jin C, et al. Oncotarget, 2017 Feb 7. PMID 28060752, Free PMC Article
    4. Comprehensive analysis of the oncogenic and immunological role of SPON2 in human tumors. Tang J, et al. Medicine (Baltimore), 2023 Sep 15. PMID 37713832, Free PMC Article
    5. Upregulation of Spondin-2 protein expression correlates with poor prognosis in hepatocellular carcinoma. Feng Y, et al. J Int Med Res, 2019 Feb. PMID 30318967, Free PMC Article

    See all (46) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Comprehensive analysis of the oncogenic and immunological role of SPON2 in human tumors.
      Title: Comprehensive analysis of the oncogenic and immunological role of SPON2 in human tumors.
    2. In situ assessment of Mindin as a biomarker of podocyte lesions in diabetic nephropathy.
      Title: In situ assessment of Mindin as a biomarker of podocyte lesions in diabetic nephropathy.
    3. SPON2 promotes the bone metastasis of lung adenocarcinoma via activation of the NF-kappaB signaling pathway.
      Title: SPON2 promotes the bone metastasis of lung adenocarcinoma via activation of the NF-κB signaling pathway.
    4. Prostate cancer cellderived spondin 2 boosts osteogenic factor levels in osteoblasts via the PI3K/AKT/mTOR pathway.
      Title: Prostate cancer cell‑derived spondin 2 boosts osteogenic factor levels in osteoblasts via the PI3K/AKT/mTOR pathway.
    5. Tumor cell-derived SPON2 promotes M2-polarized tumor-associated macrophage infiltration and cancer progression by activating PYK2 in CRC.
      Title: Tumor cell-derived SPON2 promotes M2-polarized tumor-associated macrophage infiltration and cancer progression by activating PYK2 in CRC.
    6. The clinical significance of spondin 2 eccentric expression in peripheral blood mononuclear cells in bronchial asthma.
      Title: The clinical significance of spondin 2 eccentric expression in peripheral blood mononuclear cells in bronchial asthma.
    7. Cancer-associated Fibroblast-derived Spondin-2 Promotes Motility of Gastric Cancer Cells.
      Title: Cancer-associated Fibroblast-derived Spondin-2 Promotes Motility of Gastric Cancer Cells.
    8. Overexpression of Spondin-2 Is Associated with Recurrence-Free Survival in Patients with Localized Clear Cell Renal Cell Carcinoma.
      Title: Overexpression of Spondin-2 Is Associated with Recurrence-Free Survival in Patients with Localized Clear Cell Renal Cell Carcinoma.
    9. Spondin 2 promotes the proliferation, migration and invasion of gastric cancer cells.
      Title: Spondin 2 promotes the proliferation, migration and invasion of gastric cancer cells.
    10. PIK3AP1 and SPON2 Genes Are Differentially Methylated in Patients With Periodic Fever, Aphthous Stomatitis, Pharyngitis, and Adenitis (PFAPA) Syndrome.
      Title: PIK3AP1 and SPON2 Genes Are Differentially Methylated in Patients With Periodic Fever, Aphthous Stomatitis, Pharyngitis, and Adenitis (PFAPA) Syndrome.
    Submit: New GeneRIF Correction See all GeneRIFs (25)

    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
    Sequence variants in the RNF212 gene associate with genome-wide recombination rate.
    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ16313, FLJ22401, FLJ34460, DKFZp686G21139

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables antigen binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables lipopolysaccharide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 cellular response to lipopolysaccharide IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in defense response to fungus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in defense response to virus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in induction of bacterial agglutination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mast cell mediated immunity IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in opsonization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of interleukin-6 production IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of macrophage cytokine production IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of tumor necrosis factor production IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    spondin-2
    Names
    differentially expressed in cancerous and non-cancerous lung cells 1
    spondin 2, extracellular matrix protein

    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_001128325.3 → NP_001121797.2  spondin-2 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 all encode the same protein.
      Source sequence(s)
      AC092535
      UniProtKB/Swiss-Prot
      D3DVN9, Q4W5N4, Q9BUD6, Q9ULW1
      Related
      ENSP00000394832.1, ENST00000431380.5
      Conserved Domains (2) summary
      pfam06468
      Location:41 → 228
      Spond_N; Spondin_N
      pfam19028
      Location:278 → 330
      TSP1_spondin; Spondin-like TSP1 domain

    2. NM_001199021.2 → NP_001185950.2  spondin-2 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. It also represents a read-through transcript because it shares its first exon with that of the upstream, non-coding gene (GeneID:100130872). Variants 1, 2 and 3 all encode the same protein.
      Source sequence(s)
      AC092535
      UniProtKB/Swiss-Prot
      D3DVN9, Q4W5N4, Q9BUD6, Q9ULW1
      Related
      ENSP00000483599.1, ENST00000617421.4
      Conserved Domains (2) summary
      pfam06468
      Location:41 → 228
      Spond_N; Spondin_N
      pfam19028
      Location:278 → 330
      TSP1_spondin; Spondin-like TSP1 domain

    3. NM_012445.4 → NP_036577.2  spondin-2 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the same protein as variants 2 and 3.
      Source sequence(s)
      AC092535
      UniProtKB/Swiss-Prot
      D3DVN9, Q4W5N4, Q9BUD6, Q9ULW1
      Related
      ENSP00000290902.5, ENST00000290902.10
      Conserved Domains (2) summary
      pfam06468
      Location:41 → 228
      Spond_N; Spondin_N
      pfam19028
      Location:278 → 330
      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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      1166932..1208844 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      1165604..1208039 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BUD6.4 GenPept UniProtKB/Swiss-Prot:Q9BUD6

    Gene LinkOut

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

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