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SPON2 spondin 2 [ Homo sapiens (human) ]

Gene ID: 10417, updated on 27-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
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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
  • 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 Variation Viewer (GRCh37.p13)

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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