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SPP1 secreted phosphoprotein 1 [ Homo sapiens (human) ]

Gene ID: 6696, updated on 2-Nov-2024

Summary

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Official Symbol
SPP1provided by HGNC
Official Full Name
secreted phosphoprotein 1provided by HGNC
Primary source
HGNC:HGNC:11255
See related
Ensembl:ENSG00000118785 MIM:166490; AllianceGenome:HGNC:11255
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
OPN; BNSP; BSPI; ETA-1
Summary
The protein encoded by this gene is involved in the attachment of osteoclasts to the mineralized bone matrix. The encoded protein is secreted and binds hydroxyapatite with high affinity. The osteoclast vitronectin receptor is found in the cell membrane and may be involved in the binding to this protein. This protein is also a cytokine that upregulates expression of interferon-gamma and interleukin-12. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
Expression
Biased expression in placenta (RPKM 1043.5), gall bladder (RPKM 1025.4) and 3 other tissues See more
Orthologs
mouse all
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Genomic context

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See SPP1 in Genome Data Viewer
Location:
4q22.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (87975714..87983411)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (91302203..91309899)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (88896866..88904563)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:88813182-88814381 Neighboring gene heat shock protein 90 alpha family class B member 3, pseudogene Neighboring gene Sharpr-MPRA regulatory region 543 Neighboring gene Sharpr-MPRA regulatory region 601 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:88842859-88843386 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:88843387-88843913 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:88856983-88857804 Neighboring gene uncharacterized LOC124900730 Neighboring gene SPP1 5' regulatory region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15559 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15560 Neighboring gene RNA, U1 small nuclear 36, pseudogene Neighboring gene polycystin 2, transient receptor potential cation channel Neighboring gene Sharpr-MPRA regulatory region 5607

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Dynamics of osteopontin levels and correlation with parasitemia in acute malaria in Uganda and Sweden.
    Title: Dynamics of osteopontin levels and correlation with parasitemia in acute malaria in Uganda and Sweden.
  2. The resistance to anoikis, mediated by Spp1, and the evasion of immune surveillance facilitate the invasion and metastasis of hepatocellular carcinoma.
    Title: The resistance to anoikis, mediated by Spp1, and the evasion of immune surveillance facilitate the invasion and metastasis of hepatocellular carcinoma.
  3. Expression of Osteopontin and Gremlin 1 Proteins in Cardiomyocytes in Ischemic Heart Failure.
    Title: Expression of Osteopontin and Gremlin 1 Proteins in Cardiomyocytes in Ischemic Heart Failure.
  4. Osteopontin deficiency promotes cartilaginous endplate degeneration by enhancing the NF-kappaB signaling to recruit macrophages and activate the NLRP3 inflammasome.
    Title: Osteopontin deficiency promotes cartilaginous endplate degeneration by enhancing the NF-κB signaling to recruit macrophages and activate the NLRP3 inflammasome.
  5. Osteopontin deletion attenuates cyst growth but exacerbates fibrosis in mice with cystic kidney disease.
    Title: Osteopontin deletion attenuates cyst growth but exacerbates fibrosis in mice with cystic kidney disease.
  6. NOX4 and its association with myeloperoxidase and osteopontin in regulating endochondral ossification.
    Title: NOX4 and its association with myeloperoxidase and osteopontin in regulating endochondral ossification.
  7. Relationships between Interleukin 18 -607 C/A and -137 G/C, Osteopontin -9250 C/T Genetic Polymorphisms and Systemic Inflammatory Response Syndrome in Coronary Artery Bypass Graft Surgery.
    Title: Relationships between Interleukin 18 -607 C/A and -137 G/C, Osteopontin -9250 C/T Genetic Polymorphisms and Systemic Inflammatory Response Syndrome in Coronary Artery Bypass Graft Surgery.
  8. LINC01133 promotes pancreatic ductal adenocarcinoma epithelial-mesenchymal transition mediated by SPP1 through binding to Arp3.
    Title: LINC01133 promotes pancreatic ductal adenocarcinoma epithelial-mesenchymal transition mediated by SPP1 through binding to Arp3.
  9. Single-cell transcriptome sequencing reveals SPP1-CD44-mediated macrophage-tumor cell interactions drive chemoresistance in TNBC.
    Title: Single-cell transcriptome sequencing reveals SPP1-CD44-mediated macrophage-tumor cell interactions drive chemoresistance in TNBC.
  10. Osteopontin/SPP1: a potential mediator between immune cells and vascular calcification.
    Title: Osteopontin/SPP1: a potential mediator between immune cells and vascular calcification.
Submit: New GeneRIF Correction See all GeneRIFs (1097)

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
GWAS of dental caries patterns in the permanent dentition.
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)

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

  • MGC110940

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cytokine activity IEA
Inferred from Electronic Annotation
more info
  
enables extracellular matrix binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables integrin binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables small molecule binding EXP
Inferred from Experiment
more info
 PubMed 
Process Evidence Code Pubs
involved_in androgen catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in biomineral tissue development IEA
Inferred from Electronic Annotation
more info
  
involved_in cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell adhesion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to testosterone stimulus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in decidualization TAS
Traceable Author Statement
more info
 PubMed 
involved_in embryo implantation TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of collateral sprouting of intact axon in response to injury IEA
Inferred from Electronic Annotation
more info
  
involved_in osteoblast differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of bone resorption IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of estradiol secretion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to 2,3,7,8-tetrachlorodibenzodioxine IEA
Inferred from Electronic Annotation
more info
  
involved_in response to macrophage colony-stimulating factor IEA
Inferred from Electronic Annotation
more info
  
involved_in response to steroid hormone IEA
Inferred from Electronic Annotation
more info
  
involved_in response to vitamin D IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
located_in cell projection IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
  
located_in extracellular space HDA PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular space IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
osteopontin
Names
SPP1/CALPHA1 fusion
early T-lymphocyte activation 1
lnc-PKD2-2-3
nephropontin
osteopontin/immunoglobulin alpha 1 heavy chain constant region fusion protein
secreted phosphoprotein 1 (osteopontin, bone sialoprotein I, early T-lymphocyte activation 1)
urinary stone protein
uropontin

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.

Genomic

  1. NG_030362.1 RefSeqGene

    Range
    5065..12762
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000582.3 → NP_000573.1  osteopontin isoform OPN-b precursor

    See identical proteins and their annotated locations for NP_000573.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 5. The resulting isoform (OPN-b, as described in PubMed: 7837791) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform e.
    Source sequence(s)
    AF052124, BX648003
    Consensus CDS
    CCDS3626.1
    UniProtKB/TrEMBL
    A6XMV6
    Related
    ENSP00000237623.7, ENST00000237623.11
    Conserved Domains (1) summary
    pfam00865
    Location:21 → 300
    Osteopontin; Osteopontin

  2. NM_001040058.2 → NP_001035147.1  osteopontin isoform OPN-a precursor

    See identical proteins and their annotated locations for NP_001035147.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence compared to variant 5. The resulting isoform (OPN-a, as described in PubMed: 7837791) has a shorter and distinct N-terminus compared to isoform e.
    Source sequence(s)
    AA665210, BC017387, CB117856
    Consensus CDS
    CCDS43250.1
    UniProtKB/Swiss-Prot
    B2RDA1, P10451, Q15681, Q15682, Q15683, Q4W597, Q567T5, Q8NBK2, Q96IZ1
    UniProtKB/TrEMBL
    A6XMV6
    Related
    ENSP00000378517.3, ENST00000395080.8
    Conserved Domains (1) summary
    pfam00865
    Location:21 → 314
    Osteopontin

  3. NM_001040060.2 → NP_001035149.1  osteopontin isoform OPN-c precursor

    See identical proteins and their annotated locations for NP_001035149.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 5. The resulting isoform (OPN-c, as described in PubMed: 7837791) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform e.
    Source sequence(s)
    AA665210, AC131944, BC093033
    Consensus CDS
    CCDS34027.1
    UniProtKB/TrEMBL
    C4B6Q2
    Related
    ENSP00000354042.4, ENST00000360804.4
    Conserved Domains (1) summary
    pfam00865
    Location:21 → 287
    Osteopontin; Osteopontin

  4. NM_001251829.2 → NP_001238758.1  osteopontin isoform 4 precursor

    See identical proteins and their annotated locations for NP_001238758.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and lacks two alternate in-frame exons compared to variant 5. The resulting isoform (4) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform e.
    Source sequence(s)
    AB209987, AC131944, CB117856, JF412667
    Consensus CDS
    CCDS93558.1
    UniProtKB/TrEMBL
    C4B6Q2, D6R9C5, Q3LGB0
    Related
    ENSP00000422973.2, ENST00000508233.6
    Conserved Domains (1) summary
    pfam00865
    Location:26 → 273
    Osteopontin; Osteopontin

  5. NM_001251830.2 → NP_001238759.1  osteopontin isoform 5

    See identical proteins and their annotated locations for NP_001238759.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) represents the longest transcript and encodes the longest isoform (5).
    Source sequence(s)
    AC131944, AK295491, CB117856, JF412667
    UniProtKB/TrEMBL
    A6XMV6, B7Z351
    Related
    ENST00000509659.5
    Conserved Domains (1) summary
    pfam00865
    Location:43 → 327
    Osteopontin; Osteopontin

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
    87975714..87983411
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    91302203..91309899
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P10451.1 GenPept UniProtKB/Swiss-Prot:P10451

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