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    SBSPON somatomedin B and thrombospondin type 1 domain containing [ Homo sapiens (human) ]

    Gene ID: 157869, updated on 26-Nov-2024

    Summary

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    Official Symbol
    SBSPONprovided by HGNC
    Official Full Name
    somatomedin B and thrombospondin type 1 domain containingprovided by HGNC
    Primary source
    HGNC:HGNC:30362
    See related
    Ensembl:ENSG00000164764 MIM:621005; AllianceGenome:HGNC:30362
    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
    RPESP; C8orf84
    Summary
    Predicted to be an extracellular matrix structural constituent. Located in collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in urinary bladder (RPKM 8.0), prostate (RPKM 7.0) and 19 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SBSPON in Genome Data Viewer
    Location:
    8q21.11
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (73064543..73093172, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (73493598..73522530, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (73976778..74005407, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene potassium voltage-gated channel subfamily B member 2 Neighboring gene uncharacterized LOC101926908 Neighboring gene uncharacterized LOC124901963 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:73792913-73793504 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:73793505-73794095 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:73794231-73795430 Neighboring gene NANOG hESC enhancer GRCh37_chr8:73837632-73838133 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:73909312-73909923 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:73912784-73913328 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:73913329-73913871 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:73913872-73914415 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:73914416-73914958 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:73916046-73916588 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:73916589-73917131 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19285 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19286 Neighboring gene RNA, U6 small nuclear 285, pseudogene Neighboring gene telomeric repeat binding factor 1 Neighboring gene uncharacterized LOC107986891 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:74085815-74086316 Neighboring gene Sharpr-MPRA regulatory region 10056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:74096970-74097470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:74097471-74097971 Neighboring gene heat shock protein 90 alpha family class B member 1 pseudogene

    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. Genetic variants near PDGFRA are associated with corneal curvature in Australians. Mishra A, et al. Invest Ophthalmol Vis Sci, 2012 Oct 11. PMID 22969067, Free PMC Article
    2. A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. Kenny EE, et al. PLoS Genet, 2012. PMID 22412388, Free PMC Article
    3. Expressed sequence tag analysis of human RPE/choroid for the NEIBank Project: over 6000 non-redundant transcripts, novel genes and splice variants. Wistow G, et al. Mol Vis, 2002 Jun 15. PMID 12107410
    4. Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver. Naba A, et al. BMC Cancer, 2014 Jul 18. PMID 25037231, Free PMC Article
    5. Glycoproteomics Reveals Decorin Peptides With Anti-Myostatin Activity in Human Atrial Fibrillation. Barallobre-Barreiro J, et al. Circulation, 2016 Sep 13. PMID 27559042, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
    EBI GWAS Catalog
    Genetic variants near PDGFRA are associated with corneal curvature in Australians.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    Component Evidence Code Pubs
    colocalizes_with collagen-containing extracellular matrix HDA PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    somatomedin-B and thrombospondin type-1 domain-containing protein
    Names
    RPE-spondin

    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_153225.4 → NP_694957.3  somatomedin-B and thrombospondin type-1 domain-containing protein precursor

      See identical proteins and their annotated locations for NP_694957.3

      Status: VALIDATED

      Source sequence(s)
      AC022893, AI698180, BC042877
      Consensus CDS
      CCDS43747.2
      UniProtKB/Swiss-Prot
      A8KAA5, Q8IVN8, Q96J64
      Related
      ENSP00000297354.6, ENST00000297354.7

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      73064543..73093172 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047421408.1 → XP_047277364.1  somatomedin-B and thrombospondin type-1 domain-containing protein isoform X1

    2. XM_017013145.2 → XP_016868634.1  somatomedin-B and thrombospondin type-1 domain-containing protein isoform X2

    3. XM_024447081.2 → XP_024302849.1  somatomedin-B and thrombospondin type-1 domain-containing protein isoform X3

    RNA

    1. XR_928762.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      73493598..73522530 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054359862.1 → XP_054215837.1  somatomedin-B and thrombospondin type-1 domain-containing protein isoform X1

    2. XM_054359863.1 → XP_054215838.1  somatomedin-B and thrombospondin type-1 domain-containing protein isoform X2

    3. XM_054359864.1 → XP_054215839.1  somatomedin-B and thrombospondin type-1 domain-containing protein isoform X3

    RNA

    1. XR_008487816.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IVN8.2 GenPept UniProtKB/Swiss-Prot:Q8IVN8

    Gene LinkOut

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