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

    Gene ID: 7812, updated on 3-Nov-2024

    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 RISC complex binding activity; RNA stem-loop binding activity; and lncRNA binding activity. Involved in IRES-dependent viral translational initiation; regulation of gene expression; and stress granule assembly. Located in Golgi apparatus; cytosol; and plasma membrane. Part of CRD-mediated mRNA stability complex and mCRD-mediated mRNA stability complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in fat (RPKM 208.0), thyroid (RPKM 164.2) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See CSDE1 in Genome Data Viewer
    Location:
    1p13.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (114716916..114757984, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (114728361..114769423, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (115259537..115300605, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak381 silencer Neighboring gene RNA, 7SL, cytoplasmic 432, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1549 Neighboring gene NRAS proto-oncogene, GTPase Neighboring gene RNY1 pseudogene 13 Neighboring gene MPRA-validated peak382 silencer Neighboring gene MPRA-validated peak383 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:115300157-115301150 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:115322492-115323058 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:115323059-115323624 Neighboring gene suppressor of IKBKE 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:115332573-115333482 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:115333483-115334390 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:115337845-115338062 Neighboring gene nuclear receptor subfamily 1 group H member 5, pseudogene Neighboring gene MPRA-validated peak384 silencer

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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?

    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

    Clone Names

    • FLJ26882, DKFZp779B0247, DKFZp779J1455

    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 PubMed 
    enables RNA stem-loop binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables lncRNA binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables mRNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    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

    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)

    NEW Try the new Transcript table

    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
      A8K281, E9PGZ0, G5E9Q2, O75534, O94961, Q5TF04, Q5TF05, Q68DF1, Q68DI9, Q9Y2S4
      UniProtKB/TrEMBL
      Q9GZV0
      Related
      ENSP00000351329.4, ENST00000358528.9
      Conserved Domains (3) summary
      smart00357
      Location:350413
      CSP; Cold shock protein domain
      pfam00313
      Location:186248
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:756788
      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/TrEMBL
      Q9GZV0
      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/TrEMBL
      Q9GZV0
      Related
      ENSP00000481762.1, ENST00000610726.5
      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
    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
      A8K281, E9PGZ0, G5E9Q2, O75534, O94961, Q5TF04, Q5TF05, Q68DF1, Q68DI9, Q9Y2S4
      UniProtKB/TrEMBL
      Q9GZV0
      Related
      ENSP00000432958.1, ENST00000534699.5
      Conserved Domains (3) summary
      smart00357
      Location:350413
      CSP; Cold shock protein domain
      pfam00313
      Location:186248
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:756788
      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/TrEMBL
      Q9GZV0
      Related
      ENSP00000261443.5, ENST00000261443.9
      Conserved Domains (4) summary
      smart00357
      Location:319382
      CSP; Cold shock protein domain
      pfam00313
      Location:155217
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:725757
      SUZ-C; SUZ-C motif
      cl09927
      Location:2690
      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 ...
    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/TrEMBL
      Q9GZV0
      Related
      ENSP00000342408.6, ENST00000339438.10
      Conserved Domains (4) summary
      smart00357
      Location:319382
      CSP; Cold shock protein domain
      pfam00313
      Location:155217
      CSD; 'Cold-shock' DNA-binding domain
      pfam12901
      Location:725757
      SUZ-C; SUZ-C motif
      cl09927
      Location:2690
      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 ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      114728361..114769423 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)