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

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: human all
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Genomic context

Location:: 3 F2.2; 3 45.25 cM

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	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_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Epigenetic modification of CSDE1 locus dictates immune recognition of nascent tumorigenic cells.
Title: Epigenetic modification of CSDE1 locus dictates immune recognition of nascent tumorigenic cells.
Strap associates with Csde1 and affects expression of select Csde1-bound transcripts
Title: Strap associates with Csde1 and affects expression of select Csde1-bound transcripts.
These results have uncovered a crucial role of Csde1 in the proper control of both radial and tangential migration of precerebellar neurons.
Title: The control of precerebellar neuron migration by RNA-binding protein Csde1.
Post-transcriptional repression of Gata6 expression by Unr contributes to the stabilization of the embryonic stem cells pluripotent state.
Title: The RNA-binding protein Unr prevents mouse embryonic stem cells differentiation toward the primitive endoderm lineage.
Feedback control of mRNA translation is involved in regulating Unr expression.
Title: Regulation of Unr expression by 5'- and 3'-untranslated regions of its mRNA through modulation of stability and IRES mediated translation.
the PITSLRE IRES interacts with the Unr protein, which is more prominently expressed at the G2/M stage of the cell cycle
Title: Regulation of the cell-cycle-dependent internal ribosome entry site of the PITSLRE protein kinase: roles of Unr (upstream of N-ras) protein and phosphorylated translation initiation factor eIF-2alpha.

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Variation

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Alleles

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

Endonuclease-mediated (6)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RISC complex binding	IDA Inferred from Direct Assay more info	PubMed
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	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	ISO Inferred from Sequence Orthology 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	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 positive regulation of cytoplasmic translation	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
part_of mCRD-mediated mRNA stability complex	ISO Inferred from Sequence Orthology more info
located_in mitochondrial inner membrane	HDA more info	PubMed
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: 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)

NM_001161854.2 → NP_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

Q3TXH7, Q3U4S7, Q8JZN2

Related

ENSMUSP00000142983.2, ENSMUST00000198180.5

Conserved Domains (4) summary

smart00357
Location:319 → 382

CSP; Cold shock protein domain

TIGR00358
Location:154 → 327

3_prime_RNase; VacB and RNase II family 3'-5' exoribonucleases

pfam00313
Location:155 → 217

CSD; 'Cold-shock' DNA-binding domain

pfam12901
Location:741 → 757

SUZ-C; SUZ-C motif
NM_001310693.1 → NP_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, Q8R3R1

Related

ENSMUSP00000143050.2, ENSMUST00000199240.5

Conserved Domains (4) summary

smart00357
Location:220 → 283

CSP; Cold shock protein domain

pfam00313
Location:56 → 118

CSD; 'Cold-shock' DNA-binding domain

pfam12901
Location:642 → 658

SUZ-C; SUZ-C motif

cl09927
Location:391 → 451

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. ...
NM_144901.4 → NP_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

Q3TXH7, Q3U1S6, Q3U4S7

Related

ENSMUSP00000029446.9, ENSMUST00000029446.13

Conserved Domains (4) summary

smart00357
Location:350 → 413

CSP; Cold shock protein domain

TIGR00358
Location:185 → 358

3_prime_RNase; VacB and RNase II family 3'-5' exoribonucleases

pfam00313
Location:186 → 248

CSD; 'Cold-shock' DNA-binding domain

pfam12901
Location:772 → 788

SUZ-C; SUZ-C motif

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000069.7 Reference GRCm39 C57BL/6J

Range

102927347..102965502

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

Q3TXH7, Q3U4S7

Conserved Domains (4) summary

smart00357
Location:396 → 459

CSP; Cold shock protein domain

TIGR00358
Location:231 → 404

3_prime_RNase; VacB and RNase II family 3'-5' exoribonucleases

pfam00313
Location:232 → 294

CSD; 'Cold-shock' DNA-binding domain

pfam12901
Location:818 → 834

SUZ-C; SUZ-C motif
XM_006501398.3 → XP_006501461.1 cold shock domain-containing protein E1 isoform X2

UniProtKB/TrEMBL

Q3TXH7, Q3U4S7

Conserved Domains (4) summary

smart00357
Location:365 → 428

CSP; Cold shock protein domain

TIGR00358
Location:200 → 373

3_prime_RNase; VacB and RNase II family 3'-5' exoribonucleases

pfam00313
Location:201 → 263

CSD; 'Cold-shock' DNA-binding domain

pfam12901
Location:787 → 803

SUZ-C; SUZ-C motif