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

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 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. Predicted to be located in Golgi apparatus; cytosol; and plasma membrane. Predicted to be part of CRD-mediated mRNA stability complex. Orthologous to human CSDE1 (cold shock domain containing E1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Muscle (RPKM 2777.5), Heart (RPKM 1612.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

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_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Unr, together with the other proteins in the RNA binding complex, determines PTH mRNA stability.
Title: In vitro evidence that upstream of N-ras participates in the regulation of parathyroid hormone messenger ribonucleic acid stability.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BE101892 (e-PCR)
- UniSTS:243760

AU049819 (e-PCR)
- UniSTS:146265

AA960392 (e-PCR)
- UniSTS:159162

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

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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)

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

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002
NM_054006.3 → NP_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:350 → 413

CSP; Cold shock protein domain

pfam00313
Location:187 → 248

CSD; 'Cold-shock' DNA-binding domain

pfam12901
Location:756 → 788

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

NC_086020.1 Reference GRCr8

Range

193234546..193271301

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063281178.1 → XP_063137248.1 cold shock domain-containing protein E1 isoform X3

UniProtKB/Swiss-Prot

P18395
XM_063281179.1 → XP_063137249.1 cold shock domain-containing protein E1 isoform X4
XM_063281176.1 → XP_063137246.1 cold shock domain-containing protein E1 isoform X1

UniProtKB/TrEMBL

A0A8L2R0L1

Related

ENSRNOP00000095101.2, ENSRNOT00000104644.2
XM_063281177.1 → XP_063137247.1 cold shock domain-containing protein E1 isoform X2

UniProtKB/TrEMBL

A0A8I6B200
XM_039101591.2 → XP_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:350 → 413

CSP; Cold shock protein domain

pfam00313
Location:187 → 248

CSD; 'Cold-shock' DNA-binding domain

pfam12901
Location:756 → 788

SUZ-C; SUZ-C motif
XM_063281180.1 → XP_063137250.1 cold shock domain-containing protein E1 isoform X4

Related

ENSRNOP00000088817.2, ENSRNOT00000098635.2