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    Csdc2 cold shock domain containing C2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 266600, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Csdc2provided by RGD
    Official Full Name
    cold shock domain containing C2provided by RGD
    Primary source
    RGD:628780
    See related
    Ensembl:ENSRNOG00000005332 AllianceGenome:RGD:628780
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Pippin
    Summary
    Enables RNA binding activity. Predicted to be involved in regulation of mRNA stability. Located in nucleus. Orthologous to human CSDC2 (cold shock domain containing C2). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Brain (RPKM 92.8), Adrenal (RPKM 67.9) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Csdc2 in Genome Data Viewer
    Location:
    7q34
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (115332134..115346599)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (113451998..113466464)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (123168811..123183336)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene RNA polymerase III subunit H Neighboring gene small nucleolar RNA SNORA44 Neighboring gene nucleoporin 160 like 1 Neighboring gene phosphomannomutase 1 Neighboring gene uncharacterized LOC134479945 Neighboring gene NADH:ubiquinone oxidoreductase subunit B11B

    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. CSDC2, a cold shock domain RNA-binding protein in decidualization. Vallejo G, et al. J Cell Physiol, 2018 Jan. PMID 30078185
    2. Thyroid hormones induce sumoylation of the cold shock domain-containing protein PIPPin in developing rat brain and in cultured neurons. Bono E, et al. Endocrinology, 2007 Jan. PMID 17053029
    3. RNA-binding ability of PIPPin requires the entire protein. Raimondi L, et al. J Cell Mol Med, 2003 Jan-Mar. PMID 12767259, Free PMC Article
    4. Specific neurons of brain cortex and cerebellum are PIPPin positive. Nastasi T, et al. Neuroreport, 2000 Jul 14. PMID 10923677
    5. PIPPin is a brain-specific protein that contains a cold-shock domain and binds specifically to H1 degrees and H3.3 mRNAs. Nastasi T, et al. J Biol Chem, 1999 Aug 20. PMID 10446180

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Uterine suppression of CSDC2 through intrauterine-injected-specific small interfering RNA (siRNA) led to abnormal decidualization in early pregnancy, with more extended antimesometrial area and with poor M development if compared with control siRNA-injected animals. These results suggest that CSDC2 could be a regulator during decidua development.
      Title: CSDC2, a cold shock domain RNA-binding protein in decidualization.
    2. Data show that only recombinant proteins that contain all the putative PIPPin domains show RNA-binding ability.
      Title: RNA-binding ability of PIPPin requires the entire protein.
    3. significant difference among euthyroid and hypothyroid newborn rats concerns sumoylation of nuclear PIPPin, which is abolished by hypothyroidism
      Title: Thyroid hormones induce sumoylation of the cold shock domain-containing protein PIPPin in developing rat brain and in cultured neurons.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables mRNA 3'-UTR binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of mRNA stability IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    cold shock domain-containing protein C2
    Names
    RNA-binding protein pippin
    cold shock domain containing C2, RNA binding

    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_001170542.1 → NP_001164013.1  cold shock domain-containing protein C2

      See identical proteins and their annotated locations for NP_001164013.1

      Status: VALIDATED

      Source sequence(s)
      CK844327, CO401519, CO405729, DY318921, X89962
      UniProtKB/Swiss-Prot
      Q63430
      UniProtKB/TrEMBL
      A6HT33
      Related
      ENSRNOP00000007091.5, ENSRNOT00000007091.7
      Conserved Domains (1) summary
      cd04458
      Location:71 → 135
      CSP_CDS; Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. ...

    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_086025.1 Reference GRCr8

      Range
      115332134..115346599
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039078503.2 → XP_038934431.1  cold shock domain-containing protein C2 isoform X2

      Conserved Domains (1) summary
      PTZ00449
      Location:28 → 126
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

    2. XM_063263068.1 → XP_063119138.1  cold shock domain-containing protein C2 isoform X3

    3. XM_039078504.2 → XP_038934432.1  cold shock domain-containing protein C2 isoform X4

      Conserved Domains (1) summary
      PRK14950
      Location:28 → 75
      PRK14950; DNA polymerase III subunits gamma and tau; Provisional

    4. XM_063263067.1 → XP_063119137.1  cold shock domain-containing protein C2 isoform X1

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q63430.3 GenPept UniProtKB/Swiss-Prot:Q63430

    Gene LinkOut

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