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    SSPOP SCO-spondin, pseudogene [ Homo sapiens (human) ]

    Gene ID: 23145, updated on 14-Nov-2024

    Summary

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    Official Symbol
    SSPOPprovided by HGNC
    Official Full Name
    SCO-spondin, pseudogeneprovided by HGNC
    Primary source
    HGNC:HGNC:21998
    See related
    Ensembl:ENSG00000197558 MIM:617356; AllianceGenome:HGNC:21998
    Gene type
    pseudo
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SSPO
    Summary
    Predicted to enable peptidase inhibitor activity. Predicted to be involved in cell adhesion. Predicted to be located in cytoplasm. Predicted to be part of plasma membrane protein complex. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Nov 2024]
    Annotation information
    Annotation category: suggests misassembly
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    all
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    Genomic context

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    See SSPOP in Genome Data Viewer
    Location:
    7q36.1
    Exon count:
    103
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (149776042..149833965)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (150957942..151015873)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (149473131..149531054)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149412332-149412964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149417350-149418244 Neighboring gene KRAB-A domain containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149432150-149433066 Neighboring gene uncharacterized LOC124901771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149438995-149439524 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:149463303-149463978 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18765 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18766 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18767 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18768 Neighboring gene zinc finger protein 467 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:149479128-149479704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:149480282-149480858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149480859-149481434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149482621-149483120 Neighboring gene Sharpr-MPRA regulatory region 4172 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:149484857-149485446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149487626-149488414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149496913-149497414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149497415-149497914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18769 Neighboring gene zinc finger protein 862 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:149552405-149552958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:149552959-149553510 Neighboring gene ATP6V0E2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:149570857-149571825 Neighboring gene ATPase H+ transporting V0 subunit e2

    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. SCO-spondin: a new member of the thrombospondin family secreted by the subcommissural organ is a candidate in the modulation of neuronal aggregation. Gobron S, et al. J Cell Sci, 1996 May. PMID 8743952
    2. Subcommissural organ/Reissner's fiber complex: characterization of SCO-spondin, a glycoprotein with potent activity on neurite outgrowth. Gobron S, et al. Glia, 2000 Nov. PMID 11008217
    3. Placental expression of SCO-spondin during mouse and human development. Gonçalves-Mendes N, et al. Gene Expr Patterns, 2004 May. PMID 15053980
    4. Mouse SCO-spondin, a gene of the thrombospondin type 1 repeat (TSR) superfamily expressed in the brain. Gonçalves-Mendes N, et al. Gene, 2003 Jul 17. PMID 12909363
    5. The thrombospondin type 1 repeat (TSR) and neuronal differentiation: roles of SCO-spondin oligopeptides on neuronal cell types and cell lines. Meiniel A, et al. Int Rev Cytol, 2003. PMID 14692680

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    3. demonstrated SCO-spondin expression at relevant steps of gestation in the placenta
      Title: Placental expression of SCO-spondin during mouse and human development.
    Submit: New GeneRIF Correction

    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

    Variation

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    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

    Other Names

    • SCO protein, thrombospondin domain containing
    • SCO-spondin
    • SCO-spondin homolog (Bos taurus)
    • subcommissural organ spondin

    Clone Names

    • FLJ36112, FLJ45737, KIAA2036

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables peptidase inhibitor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular space TAS
    Traceable Author Statement
    more info
    		 PubMed 

    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.

    RNA

    1. NR_163594.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC004877, KF459635, KF459640, KF495712
      Related
      ENST00000378016.5

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      149776042..149833965
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      150957942..151015873
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_198455.2: Suppressed sequence

      Description
      NM_198455.2: This RefSeq record was removed by NCBI staff. Contact [email protected] for further information.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2VEC9.2 GenPept UniProtKB/Swiss-Prot:A2VEC9

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials