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

    Gene ID: 117180, updated on 9-Dec-2024

    Summary

    Official Symbol
    Csde1provided by RGD
    Official Full Name
    cold shock domain containing E1provided by RGD
    Primary source
    RGD:619726
    See related
    EnsemblRapid: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 RISC complex binding activity; RNA stem-loop binding activity; and lncRNA binding activity. Predicted to be involved in IRES-dependent viral translational initiation; regulation of gene expression; 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 and mCRD-mediated mRNA stability complex. Orthologous to human CSDE1 (cold shock domain containing E1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Muscle (RPKM 2777.5), Heart (RPKM 1612.9) and 9 other tissues See more
    Orthologs
    NEW
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    Genomic context

    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

    Expression

    • 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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 binding IEA
    Inferred from Electronic Annotation
    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 lncRNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables lncRNA binding ISO
    Inferred from Sequence Orthology
    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 positive regulation of 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 cytoplasm 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

    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)

    NEW Try the new Transcript table

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

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000002
      UniProtKB/TrEMBL
      A6K3K1
    2. NM_054006.3NP_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:350413
      CSP; Cold shock protein domain
      pfam00313
      Location:187248
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:756788
      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_063281178.1XP_063137248.1  cold shock domain-containing protein E1 isoform X3

      UniProtKB/Swiss-Prot
      P18395
      UniProtKB/TrEMBL
      A6K3K0
    2. XM_063281179.1XP_063137249.1  cold shock domain-containing protein E1 isoform X4

      UniProtKB/TrEMBL
      A6K3K1
    3. XM_063281176.1XP_063137246.1  cold shock domain-containing protein E1 isoform X1

      UniProtKB/TrEMBL
      A0A8L2R0L1, A6K3K0
      Related
      ENSRNOP00000095101.2, ENSRNOT00000104644.2
    4. XM_063281177.1XP_063137247.1  cold shock domain-containing protein E1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6B200, A6K3K1
    5. XM_039101591.2XP_038957519.1  cold shock domain-containing protein E1 isoform X3

      UniProtKB/Swiss-Prot
      P18395
      UniProtKB/TrEMBL
      A6K3K0
      Related
      ENSRNOP00000069264.3, ENSRNOT00000091210.3
      Conserved Domains (3) summary
      smart00357
      Location:350413
      CSP; Cold shock protein domain
      pfam00313
      Location:187248
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:756788
      SUZ-C; SUZ-C motif
    6. XM_063281180.1XP_063137250.1  cold shock domain-containing protein E1 isoform X4

      UniProtKB/TrEMBL
      A6K3K1
      Related
      ENSRNOP00000088817.2, ENSRNOT00000098635.2