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

Gene ID: 7812, updated on 10-Oct-2020

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
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
Expression
Ubiquitous expression in fat (RPKM 208.0), thyroid (RPKM 164.2) and 25 other tissues See more
Orthologs

Genomic context

See CSDE1 in Genome Data Viewer
Location:
1p13.2
Exon count:
21
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (114716916..114757984, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (115259534..115300671, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 432, pseudogene Neighboring gene NRAS proto-oncogene, GTPase Neighboring gene RNY1 pseudogene 13 Neighboring gene suppressor of IKBKE 1 Neighboring gene nuclear receptor subfamily 1 group H member 5, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Common genetic variants on 1p13.2 associate with risk of autism.
GeneReviews: Not available

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: SIKE1

Homology

Clone Names

  • FLJ26882, DKFZp779B0247, DKFZp779J1455

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
male gonad development TAS
Traceable Author Statement
more info
PubMed 
nuclear-transcribed mRNA catabolic process, no-go decay IMP
Inferred from Mutant Phenotype
more info
PubMed 
stress granule assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
CRD-mediated mRNA stability complex IDA
Inferred from Direct Assay
more info
PubMed 
Golgi apparatus IDA
Inferred from Direct Assay
more info
 
cytoplasmic stress granule IEA
Inferred from Electronic Annotation
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

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)

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_001007553.3NP_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
    O75534
    UniProtKB/TrEMBL
    A0A024R0E2
    Related
    ENSP00000351329.4, ENST00000358528.9
    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
  2. NM_001130523.3NP_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/Swiss-Prot
    O75534
    Related
    ENSP00000358543.1, ENST00000369530.5
    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
  3. NM_001242891.2NP_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/Swiss-Prot
    O75534
    Related
    ENSP00000481762.1, ENST00000610726.4
    Conserved Domains (4) summary
    smart00357
    Location:396459
    CSP; Cold shock protein domain
    pfam00313
    Location:232294
    CSD; 'Cold-shock' DNA-binding domain
    pfam12901
    Location:818833
    SUZ-C; SUZ-C motif
    cl25438
    Location:231404
    RNB; RNB domain
  4. NM_001242892.2NP_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
    O75534
    UniProtKB/TrEMBL
    A0A024R0E2
    Related
    ENSP00000432958.1, ENST00000534699.5
    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
  5. NM_001242893.2NP_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/Swiss-Prot
    O75534
    UniProtKB/TrEMBL
    A0A024R0K2
    Related
    ENSP00000261443.5, ENST00000261443.9
    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
  6. NM_007158.6NP_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/Swiss-Prot
    O75534
    UniProtKB/TrEMBL
    A0A024R0K2
    Related
    ENSP00000342408.6, ENST00000339438.10
    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

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    114716916..114757984 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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