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

    Gene ID: 229663, updated on 23-Jun-2021

    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
    u; unr; D3Jfr; 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
    NEW
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    Genomic context

    See Csde1 in Genome Data Viewer
    Location:
    3 F2.2; 3 45.25 cM
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (102927347..102965502)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (103020431..103058186)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (102824469..102862112)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene nuclear receptor subfamily 1, group H, member 5 Neighboring gene predicted gene, 22826 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 Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Pathways from PubChem

    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
    enables RNA 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 IRES-dependent viral translational initiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in nuclear-transcribed mRNA catabolic process, no-go decay ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in stress granule assembly ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    part_of CRD-mediated mRNA stability complex ISO
    Inferred from Sequence Orthology
    more info
     
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in mitochondrial inner membrane HDA PubMed 
    located_in 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)

    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_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
      ENSMUSP00000142983.2, ENSMUST00000198180.5
      Conserved Domains (4) summary
      smart00357
      Location:319382
      CSP; Cold shock protein domain
      TIGR00358
      Location:154327
      3_prime_RNase; VacB and RNase II family 3'-5' exoribonucleases
      pfam00313
      Location:155217
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:741757
      SUZ-C; SUZ-C motif
    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
      ENSMUSP00000143050.2, ENSMUST00000199240.5
      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
      ENSMUSP00000029446.9, ENSMUST00000029446.13
      Conserved Domains (4) summary
      smart00357
      Location:350413
      CSP; Cold shock protein domain
      TIGR00358
      Location:185358
      3_prime_RNase; VacB and RNase II family 3'-5' exoribonucleases
      pfam00313
      Location:186248
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:772788
      SUZ-C; SUZ-C motif

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000069.7 Reference GRCm39 C57BL/6J

      Range
      102927347..102965502
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006501397.2XP_006501460.1  cold shock domain-containing protein E1 isoform X1

      Conserved Domains (4) summary
      smart00357
      Location:396459
      CSP; Cold shock protein domain
      TIGR00358
      Location:231404
      3_prime_RNase; VacB and RNase II family 3'-5' exoribonucleases
      pfam00313
      Location:232294
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:818834
      SUZ-C; SUZ-C motif
    2. XM_006501398.3XP_006501461.1  cold shock domain-containing protein E1 isoform X2

      Conserved Domains (4) summary
      smart00357
      Location:365428
      CSP; Cold shock protein domain
      TIGR00358
      Location:200373
      3_prime_RNase; VacB and RNase II family 3'-5' exoribonucleases
      pfam00313
      Location:201263
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:787803
      SUZ-C; SUZ-C motif
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