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

Gene ID: 23145, updated on 5-Mar-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 several processes, including cell adhesion; negative regulation of catalytic activity; and regulation of peptidase activity. Predicted to be located in cytoplasm. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
Annotation information
Annotation category: suggests misassembly
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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Location:
7q36.1
Exon count:
103
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (149776042..149833965)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (150957942..151015873)
105.20220307 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. Placental expression of SCO-spondin during mouse and human development. Gonçalves-Mendes N, et al. Gene Expr Patterns, 2004 May. PMID 15053980
  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. 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
  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 (19) 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)

Genotypes

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 
part_of plasma membrane protein complex IEA
Inferred from Electronic Annotation
more info
  

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_2023_10

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 info@ncbi.nlm.nih.gov 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
Miscellaneous