CSDE1 cold shock domain containing E1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CSDE1provided by HGNC
Official Full Name: cold shock domain containing E1provided by HGNC
Primary source: HGNC:HGNC:29905
See related: Ensembl:ENSG00000009307 MIM:191510; AllianceGenome:HGNC:29905
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: UNR; D1S155E
Summary: Enables RNA stem-loop binding activity. Involved in IRES-dependent viral translational initiation; nuclear-transcribed mRNA catabolic process, no-go decay; and stress granule assembly. Located in Golgi apparatus; cytosol; and plasma membrane. Part of CRD-mediated mRNA stability complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in fat (RPKM 208.0), thyroid (RPKM 164.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p13.2

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (114716916..114757984, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (114728361..114769423, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (115259537..115300605, complement)

Chromosome 1 - NC_000001.11 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CSDE1 promotes miR-451 biogenesis.
Title: CSDE1 promotes miR-451 biogenesis.
Cold shock domain-containing protein E1 is a posttranscriptional regulator of the LDL receptor.
Title: Cold shock domain-containing protein E1 is a posttranscriptional regulator of the LDL receptor.
Reduced miR-371b-5p expression drives tumor progression via CSDE1/RAC1 regulation in triple-negative breast cancer.
Title: Reduced miR-371b-5p expression drives tumor progression via CSDE1/RAC1 regulation in triple-negative breast cancer.
Coordinated post-transcriptional control of oncogene-induced senescence by UNR/CSDE1.
Title: Coordinated post-transcriptional control of oncogene-induced senescence by UNR/CSDE1.
The CDT of Helicobacter hepaticus induces pro-survival autophagy and nucleoplasmic reticulum formation concentrating the RNA binding proteins UNR/CSDE1 and P62/SQSTM1.
Title: The CDT of Helicobacter hepaticus induces pro-survival autophagy and nucleoplasmic reticulum formation concentrating the RNA binding proteins UNR/CSDE1 and P62/SQSTM1.
Cold Shock Domain Containing E1 (CSDE1) Protein is Overexpressed and Can be Targeted to Inhibit Invasiveness in Pancreatic Cancer Cells.
Title: Cold Shock Domain Containing E1 (CSDE1) Protein is Overexpressed and Can be Targeted to Inhibit Invasiveness in Pancreatic Cancer Cells.
Oncolytic virotherapy induced CSDE1 neo-antigenesis restricts VSV replication but can be targeted by immunotherapy.
Title: Oncolytic virotherapy induced CSDE1 neo-antigenesis restricts VSV replication but can be targeted by immunotherapy.
The role of CSDE1 in translational reprogramming and human diseases.
Title: The role of CSDE1 in translational reprogramming and human diseases.
Our study defines a new autism-related syndrome and highlights the functional role of CSDE1 in synapse development and synaptic transmission.
Title: Disruptive variants of CSDE1 associate with autism and interfere with neuronal development and synaptic transmission.
Csde1 is involved in feed-back control in protein homeostasis and that it dampens stochastic changes in mRNA expression
Title: Csde1 binds transcripts involved in protein homeostasis and controls their expression in an erythroid cell line.

Submit: New GeneRIF Correction See all GeneRIFs (26)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Common genetic variants on 1p13.2 associate with risk of autism. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	Cellular biotinylated cold shock domain containing E1, RNA-binding (CSDE1) protein is incorporated into HIV-1 Gag virus-like particles	PubMed
nucleocapsid	gag	HIV-1 NC is identified to have a physical interaction with cold shock domain containing E1, RNA-binding (CSDE1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-11939 (e-PCR)
- UniSTS:83495

SHGC-32741 (e-PCR)
- UniSTS:67373

D1S2038E (e-PCR)
- UniSTS:151463

RH64700 (e-PCR)
- UniSTS:62961

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RISC complex binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	HDA more info	PubMed
enables RNA stem-loop binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in CRD-mediated mRNA stabilization	IDA Inferred from Direct Assay more info	PubMed
involved_in IRES-dependent viral translational initiation	IDA Inferred from Direct Assay more info	PubMed
involved_in male gonad development	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	IDA Inferred from Direct Assay more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, no-go decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cytoplasmic translation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of translational initiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in stress granule assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of CRD-mediated mRNA stability complex	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
located_in P-body	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic stress granule	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
part_of mCRD-mediated mRNA stability complex	IPI Inferred from Physical Interaction more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: cold shock domain-containing protein E1

Names: N-ras upstream gene protein; NRAS-related; cold shock domain containing E1, RNA binding; 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_001007553.3 → NP_001007554.1 cold shock domain-containing protein E1 isoform 1

See identical proteins and their annotated locations for NP_001007554.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence compared to variant 4. The resulting isoform (1) is shorter at the N-terminus compared to isoform 4. Variants 1 and 5 both encode isoform 1.

Source sequence(s)

AB020692, BP202324, BU681634

Consensus CDS

CCDS30812.1

UniProtKB/Swiss-Prot

A8K281, E9PGZ0, G5E9Q2, O75534, O94961, Q5TF04, Q5TF05, Q68DF1, Q68DI9, Q9Y2S4

UniProtKB/TrEMBL

Q9GZV0

Related

ENSP00000351329.4, ENST00000358528.9

Conserved Domains (3) summary

smart00357
Location:350 → 413

CSP; Cold shock protein domain

pfam00313
Location:186 → 248

CSD; 'Cold-shock' DNA-binding domain

pfam12901
Location:756 → 788

SUZ-C; SUZ-C motif
NM_001130523.3 → NP_001123995.1 cold shock domain-containing protein E1 isoform 3

See identical proteins and their annotated locations for NP_001123995.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 4. The resulting isoform (3) has the same N- and C-termini but lacks an internal segment compared to isoform 4.

Source sequence(s)

AB020692, BP202324, BU681634, CR749431

Consensus CDS

CCDS44197.1

UniProtKB/TrEMBL

Q9GZV0

Related

ENSP00000358543.1, ENST00000369530.5

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
NM_001242891.2 → NP_001229820.1 cold shock domain-containing protein E1 isoform 4

See identical proteins and their annotated locations for NP_001229820.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) represents the longest transcript and encodes the longest isoform (4).

Source sequence(s)

AB020692, BP202324, BU681634, CR749431

Consensus CDS

CCDS55626.1

UniProtKB/TrEMBL

Q9GZV0

Related

ENSP00000481762.1, ENST00000610726.5

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
NM_001242892.2 → NP_001229821.1 cold shock domain-containing protein E1 isoform 1

See identical proteins and their annotated locations for NP_001229821.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence compared to variant 4. The resulting isoform (1) is shorter at the N-terminus compared to isoform 4. Variants 1 and 5 both encode isoform 1.

Source sequence(s)

AB020692, AK290146, AL096773, BP202324, BU681634

Consensus CDS

CCDS30812.1

UniProtKB/Swiss-Prot

A8K281, E9PGZ0, G5E9Q2, O75534, O94961, Q5TF04, Q5TF05, Q68DF1, Q68DI9, Q9Y2S4

UniProtKB/TrEMBL

Q9GZV0

Related

ENSP00000432958.1, ENST00000534699.5

Conserved Domains (3) summary

smart00357
Location:350 → 413

CSP; Cold shock protein domain

pfam00313
Location:186 → 248

CSD; 'Cold-shock' DNA-binding domain

pfam12901
Location:756 → 788

SUZ-C; SUZ-C motif
NM_001242893.2 → NP_001229822.1 cold shock domain-containing protein E1 isoform 2

See identical proteins and their annotated locations for NP_001229822.1

Status: VALIDATED

Description

Transcript Variant: This variant (6) differs in the 5' UTR and lacks two alternate coding exons compared to variant 4. The resulting isoform (2) is shorter at the N-terminus and lacks an internal segment compared to isoform 4. Variants 2 and 6 both encode isoform 2.

Source sequence(s)

AB020692, AL096773, BC017662, BP202324, BU681634

Consensus CDS

CCDS30811.1

UniProtKB/TrEMBL

Q9GZV0

Related

ENSP00000261443.5, ENST00000261443.9

Conserved Domains (4) summary

smart00357
Location:319 → 382

CSP; Cold shock protein domain

pfam00313
Location:155 → 217

CSD; 'Cold-shock' DNA-binding domain

pfam12901
Location:725 → 757

SUZ-C; SUZ-C motif

cl09927
Location:26 → 90

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. Both domains ...
NM_007158.6 → NP_009089.4 cold shock domain-containing protein E1 isoform 2

See identical proteins and their annotated locations for NP_009089.4

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks two alternate coding exons compared to variant 4. The resulting isoform (2) is shorter at the N-terminus and lacks an internal segment compared to isoform 4. Variants 2 and 6 both encode isoform 2.

Source sequence(s)

AB020692, BC032446, BP202324, BU681634

Consensus CDS

CCDS30811.1

UniProtKB/TrEMBL

Q9GZV0

Related

ENSP00000342408.6, ENST00000339438.10

Conserved Domains (4) summary

smart00357
Location:319 → 382

CSP; Cold shock protein domain

pfam00313
Location:155 → 217

CSD; 'Cold-shock' DNA-binding domain

pfam12901
Location:725 → 757

SUZ-C; SUZ-C motif

cl09927
Location:26 → 90

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. Both domains ...