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    Sspo SCO-spondin [ Rattus norvegicus (Norway rat) ]

    Gene ID: 474348, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Sspoprovided by RGD
    Official Full Name
    SCO-spondinprovided by RGD
    Primary source
    RGD:1549716
    See related
    EnsemblRapid:ENSRNOG00000025848 AllianceGenome:RGD:1549716
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Scospondin
    Summary
    Predicted to be involved in cell adhesion. Predicted to be located in cytoplasm. Predicted to be active in extracellular matrix and extracellular space. Orthologous to human SSPOP (SCO-spondin, pseudogene). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 20.1), Thymus (RPKM 2.4) and 3 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See Sspo in Genome Data Viewer
    Location:
    4q24
    Exon count:
    104
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (78725829..78781330)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (77394915..77450526)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (78076695..78133676)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134486766 Neighboring gene transfer RNA cysteine (anticodon GCA) 28 Neighboring gene KRAB-A domain containing 1 Neighboring gene zinc finger protein 467 Neighboring gene uncharacterized LOC120102263 Neighboring gene zinc finger protein 862 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Effects of SCO-spondin thrombospondin type 1 repeats (TSR) in comparison to Reissner's fiber material on the differentiation of the B104 neuroblastoma cell line. El-Bitar F, et al. Cell Tissue Res, 2001 Jun. PMID 11456412
    2. Transcription of SCO-spondin in the subcommissural organ: evidence for down-regulation mediated by serotonin. Richter HG, et al. Brain Res Mol Brain Res, 2004 Oct 22. PMID 15469891
    3. Alpha1beta1-integrin is an essential signal for neurite outgrowth induced by thrombospondin type 1 repeats of SCO-spondin. Bamdad M, et al. Cell Tissue Res, 2004 Jan. PMID 14564503
    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. Molecular study of the genus Astraeus. Phosri C, et al. Mycol Res, 2007 Mar. PMID 17360168

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    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
    		  

    General protein information

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    Preferred Names
    SCO-spondin
    Names
    subcommissural organ 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_001007016.1 → NP_001007017.1  SCO-spondin precursor

      See identical proteins and their annotated locations for NP_001007017.1

      Status: PROVISIONAL

      Source sequence(s)
      AJ629845
      UniProtKB/Swiss-Prot
      Q700K0
      Related
      ENSRNOP00000037189.2, ENSRNOT00000035906.5
      Conserved Domains (13) summary
      smart00192
      Location:1497 → 1528
      LDLa; Low-density lipoprotein receptor domain class A
      smart00209
      Location:2543 → 2595
      TSP1; Thrombospondin type 1 repeats
      smart00215
      Location:2932 → 2979
      VWC_out; von Willebrand factor (vWF) type C domain
      smart00216
      Location:556 → 716
      VWD; von Willebrand factor (vWF) type D domain
      smart00231
      Location:2070 → 2226
      FA58C; Coagulation factor 5/8 C-terminal domain, discoidin domain
      cd00057
      Location:2111 → 2225
      FA58C; Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
      cd00112
      Location:1421 → 1455
      LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...
      pfam00057
      Location:1568 → 1604
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00090
      Location:2819 → 2867
      TSP_1; Thrombospondin type 1 domain
      pfam00094
      Location:1019 → 1168
      VWD; von Willebrand factor type D domain
      pfam01826
      Location:1280 → 1336
      TIL; Trypsin Inhibitor like cysteine rich domain
      pfam08742
      Location:1206 → 1276
      C8; C8 domain
      cl17735
      Location:4980 → 5035
      VWC; von Willebrand factor type C domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      78725829..78781330
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063286438.1 → XP_063142508.1  SCO-spondin isoform X1

      UniProtKB/Swiss-Prot
      Q700K0
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q700K0.1 GenPept UniProtKB/Swiss-Prot:Q700K0

    Gene LinkOut

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

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