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    SPON1 spondin 1 [ Homo sapiens (human) ]

    Gene ID: 10418, updated on 2-Nov-2024

    Summary

    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
    NEW
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    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    HIV-1 interactions

    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

    General gene information

    Clone Names

    • KIAA0762, MGC10724

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables LBD domain binding  
    enables extracellular matrix structural constituent PubMed 
    enables metal ion binding  
    enables protein binding PubMed 

    General protein information

    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)

    NEW Try the new Transcript table

    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_006108.4NP_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:43182
      Reeler; the N-terminal domain of reelin, F-spondin, and a variety of other proteins
      pfam00090
      Location:562610
      TSP_1; Thrombospondin type 1 domain
      pfam06468
      Location:205392
      Spond_N; Spondin_N
      pfam19028
      Location:669720
      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)
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