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    Csde1 cold shock domain containing E1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 117180, updated on 13-Apr-2024

    Summary

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    Official Symbol
    Csde1provided by RGD
    Official Full Name
    cold shock domain containing E1provided by RGD
    Primary source
    RGD:619726
    See related
    Ensembl:ENSRNOG00000061058 AllianceGenome:RGD:619726
    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
    Unr
    Summary
    Predicted to enable RNA stem-loop binding activity. Predicted to be involved in IRES-dependent viral translational initiation; nuclear-transcribed mRNA catabolic process, no-go decay; and stress granule assembly. Predicted to be located in Golgi apparatus; cytosol; and plasma membrane. Predicted to be part of CRD-mediated mRNA stability complex. Orthologous to human CSDE1 (cold shock domain containing E1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Muscle (RPKM 2777.5), Heart (RPKM 1612.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Csde1 in Genome Data Viewer
    Location:
    2q34
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (193234546..193271301)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (190546015..190582787)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (205525194..205552987)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene suppressor of IKBKE 1 Neighboring gene LYR motif containing 7, pseudogene 1 Neighboring gene NRAS proto-oncogene, GTPase Neighboring gene adenosine monophosphate deaminase 1

    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. In vitro evidence that upstream of N-ras participates in the regulation of parathyroid hormone messenger ribonucleic acid stability. Dinur M, et al. Mol Endocrinol, 2006 Jul. PMID 16469771
    2. Characterization of unr; a gene closely linked to N-ras. Jeffers M, et al. Nucleic Acids Res, 1990 Aug 25. PMID 2204029, Free PMC Article
    3. UNR, a new partner of poly(A)-binding protein, plays a key role in translationally coupled mRNA turnover mediated by the c-fos major coding-region determinant. Chang TC, et al. Genes Dev, 2004 Aug 15. PMID 15314026, Free PMC Article
    4. JUNB-FBXO21-ERK axis promotes cartilage degeneration in osteoarthritis by inhibiting autophagy. Lin Z, et al. Aging Cell, 2021 Feb. PMID 33450132, Free PMC Article
    5. FMRP recruitment of β-catenin to the translation pre-initiation complex represses translation. Ehyai S, et al. EMBO Rep, 2018 Dec. PMID 30361391, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Unr, together with the other proteins in the RNA binding complex, determines PTH mRNA stability.
      Title: In vitro evidence that upstream of N-ras participates in the regulation of parathyroid hormone messenger ribonucleic acid stability.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RISC complex binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RISC complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA stem-loop binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA stem-loop binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in CRD-mediated mRNA stabilization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in CRD-mediated mRNA stabilization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in IRES-dependent viral translational initiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in IRES-dependent viral translational initiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, no-go decay IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, no-go decay ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of cytoplasmic translation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of cytoplasmic translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in stress granule assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in stress granule assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in stress granule assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of CRD-mediated mRNA stability complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of CRD-mediated mRNA stability complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in P-body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasmic stress granule IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of mCRD-mediated mRNA stability complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of mCRD-mediated mRNA stability complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    cold shock domain-containing protein E1
    Names
    cold shock domain containing E1, RNA binding
    cold shock domain containing E1, RNA binding-like
    upstream of NRAS

    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_001415020.1 → NP_001401949.1  cold shock domain-containing protein E1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000002
      Related
      ENSRNOP00000088817.1, ENSRNOT00000098635.1

    2. NM_054006.3 → NP_446458.1  cold shock domain-containing protein E1 isoform 1

      See identical proteins and their annotated locations for NP_446458.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000002
      UniProtKB/Swiss-Prot
      P18395
      UniProtKB/TrEMBL
      A6K3K0
      Conserved Domains (3) summary
      smart00357
      Location:350 → 413
      CSP; Cold shock protein domain
      pfam00313
      Location:187 → 248
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:756 → 788
      SUZ-C; SUZ-C motif

    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_086020.1 Reference GRCr8

      Range
      193234546..193271301
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063281178.1 → XP_063137248.1  cold shock domain-containing protein E1 isoform X3

      UniProtKB/Swiss-Prot
      P18395

    2. XM_063281179.1 → XP_063137249.1  cold shock domain-containing protein E1 isoform X4

    3. XM_063281176.1 → XP_063137246.1  cold shock domain-containing protein E1 isoform X1

      UniProtKB/TrEMBL
      A0A8L2R0L1

    4. XM_063281177.1 → XP_063137247.1  cold shock domain-containing protein E1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6B200

    5. XM_039101591.2 → XP_038957519.1  cold shock domain-containing protein E1 isoform X3

      UniProtKB/Swiss-Prot
      P18395
      UniProtKB/TrEMBL
      A6K3K0
      Conserved Domains (3) summary
      smart00357
      Location:350 → 413
      CSP; Cold shock protein domain
      pfam00313
      Location:187 → 248
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:756 → 788
      SUZ-C; SUZ-C motif

    6. XM_063281180.1 → XP_063137250.1  cold shock domain-containing protein E1 isoform X4

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P18395.1 GenPept UniProtKB/Swiss-Prot:P18395

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