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

Gene ID: 229663, updated on 12-Feb-2023

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 AllianceGenome:MGI:92356
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; mKIAA0885
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. Located in mitochondrial inner membrane. Is expressed in heart; limb; lung; small intestine; and testis. Orthologous to human CSDE1 (cold shock domain containing E1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 33.8), bladder adult (RPKM 26.6) and 25 other tissues See more
Orthologs
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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)

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)
  • Targeted (3)  1 citation
  • Endonuclease-mediated (4) 

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
 
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
 
part_of mCRD-mediated mRNA stability complex 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)

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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_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