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    Csde1 cold shock domain containing E1, RNA binding [ Mus musculus (house mouse) ]

    Gene ID: 229663, updated on 10-Feb-2019

    Summary

    Official Symbol
    Csde1provided by MGI
    Official Full Name
    cold shock domain containing E1, RNA bindingprovided by MGI
    Primary source
    MGI:MGI:92356
    See related
    Ensembl:ENSMUSG00000068823
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    unr; D3Jfr1; AA960392; BC016898; mKIAA0885
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 33.8), bladder adult (RPKM 26.6) and 25 other tissues See more
    Orthologs

    Genomic context

    See Csde1 in Genome Data Viewer
    Location:
    3 F2.2; 3 45.25 cM
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 3 NC_000069.6 (103020431..103058186)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (102824469..102862112)

    Chromosome 3 - NC_000069.6Genomic Context describing neighboring genes Neighboring gene nuclear receptor subfamily 1, group H, member 5 Neighboring gene suppressor of IKBKE 1 Neighboring gene neuroblastoma ras oncogene Neighboring gene adenosine monophosphate deaminase 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (2) 

    Pathways from BioSystems

    • mRNA processing, organism-specific biosystem (from WikiPathways)
      mRNA processing, organism-specific biosystemAdapted from Reactome, see: [http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1675.1 REACT 1675.1] This process describes the conversion of precursor messenger RNA into mature messenge...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC19174

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    nuclear-transcribed mRNA catabolic process, no-go decay ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    CRD-mediated mRNA stability complex ISO
    Inferred from Sequence Orthology
    more info
     
    Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
     
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    mitochondrial inner membrane HDA PubMed 
    plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    cold shock domain-containing protein E1
    Names
    NRAS-related
    upstream of NRAS

    NCBI Reference Sequences (RefSeq)

    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_001161854.2NP_001155326.1  cold shock domain-containing protein E1 isoform 2

      See identical proteins and their annotated locations for NP_001155326.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the coding region compared to variant 1. The resulting protein (isoform 2) is shorter and has the same N- and C-termini compared to isoform 1.
      Source sequence(s)
      AA178550, AC163297, AK151970
      Consensus CDS
      CCDS79990.1
      UniProtKB/TrEMBL
      Q8JZN2
      Related
      ENSMUSP00000142983.1, ENSMUST00000198180.4
      Conserved Domains (4) summary
      smart00357
      Location:319382
      CSP; Cold shock protein domain
      pfam00313
      Location:155217
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:741757
      SUZ-C; SUZ-C motif
      cl09927
      Location:490550
      S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
    2. NM_001310693.1NP_001297622.1  cold shock domain-containing protein E1 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start site compared to variant 1. The encoded isoform (3) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AA178550, AC163297, AK151970, AK168556, CJ077513
      Consensus CDS
      CCDS79991.1
      UniProtKB/TrEMBL
      A0A0G2JF72, Q8JZN2
      Related
      ENSMUSP00000143050.1, ENSMUST00000199240.4
      Conserved Domains (4) summary
      smart00357
      Location:220283
      CSP; Cold shock protein domain
      pfam00313
      Location:56118
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:642658
      SUZ-C; SUZ-C motif
      cl09927
      Location:391451
      S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
    3. NM_144901.4NP_659150.1  cold shock domain-containing protein E1 isoform 1

      See identical proteins and their annotated locations for NP_659150.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA178550, AC163297, AK151970, BC062097
      Consensus CDS
      CCDS38569.1
      UniProtKB/Swiss-Prot
      Q91W50
      UniProtKB/TrEMBL
      Q3U1S6, Q8JZN2
      Related
      ENSMUSP00000029446.8, ENSMUST00000029446.12
      Conserved Domains (4) summary
      smart00357
      Location:350413
      CSP; Cold shock protein domain
      pfam00313
      Location:186248
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:772788
      SUZ-C; SUZ-C motif
      cl09927
      Location:521581
      S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000069.6 Reference GRCm38.p4 C57BL/6J

      Range
      103020431..103058186
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006501397.1XP_006501460.1  cold shock domain-containing protein E1 isoform X1

      Conserved Domains (3) summary
      smart00357
      Location:396459
      CSP; Cold shock protein domain
      pfam00313
      Location:232294
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:818834
      SUZ-C; SUZ-C motif
    2. XM_006501398.1XP_006501461.1  cold shock domain-containing protein E1 isoform X2

      Conserved Domains (4) summary
      smart00357
      Location:365428
      CSP; Cold shock protein domain
      pfam00313
      Location:201263
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:787803
      SUZ-C; SUZ-C motif
      cl09927
      Location:536596
      S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
    3. XM_017319550.1XP_017175039.1  cold shock domain-containing protein E1 isoform X3

      UniProtKB/Swiss-Prot
      Q91W50
      UniProtKB/TrEMBL
      Q3U1S6
      Conserved Domains (4) summary
      smart00357
      Location:350413
      CSP; Cold shock protein domain
      pfam00313
      Location:186248
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:772788
      SUZ-C; SUZ-C motif
      cl09927
      Location:521581
      S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
    4. XM_006501399.2XP_006501462.1  cold shock domain-containing protein E1 isoform X4

      See identical proteins and their annotated locations for XP_006501462.1

      UniProtKB/TrEMBL
      Q8JZN2
      Related
      ENSMUSP00000143028.1, ENSMUST00000199571.4
      Conserved Domains (4) summary
      smart00357
      Location:319382
      CSP; Cold shock protein domain
      pfam00313
      Location:155217
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:741757
      SUZ-C; SUZ-C motif
      cl09927
      Location:490550
      S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
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