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

Gene ID: 266600, updated on 2-Nov-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
EnsemblRapid: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. Predicted to be located in nucleus. Predicted to be active in cytoplasm. Orthologous to human CSDC2 (cold shock domain containing C2). [provided by Alliance of Genome Resources, Nov 2024]
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 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, ENSRNOT00000007091.8
    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

    Related
    ENSRNOP00000102835.1, ENSRNOT00000161236.1
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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