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    KDELR3 KDEL endoplasmic reticulum protein retention receptor 3 [ Homo sapiens (human) ]

    Gene ID: 11015, updated on 9-Dec-2024

    Summary

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    Official Symbol
    KDELR3provided by HGNC
    Official Full Name
    KDEL endoplasmic reticulum protein retention receptor 3provided by HGNC
    Primary source
    HGNC:HGNC:6306
    See related
    Ensembl:ENSG00000100196 MIM:619900; AllianceGenome:HGNC:6306
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ERD23; ERD2L3
    Summary
    This gene encodes a member of the KDEL endoplasmic reticulum protein retention receptor family. Retention of resident soluble proteins in the lumen of the endoplasmic reticulum (ER) is achieved in both yeast and animal cells by their continual retrieval from the cis-Golgi, or a pre-Golgi compartment. Sorting of these proteins is dependent on a C-terminal tetrapeptide signal, usually lys-asp-glu-leu (KDEL) in animal cells, and his-asp-glu-leu (HDEL) in S. cerevisiae. This process is mediated by a receptor that recognizes, and binds the tetrapeptide-containing protein, and returns it to the ER. In yeast, the sorting receptor encoded by a single gene, ERD2, is a seven-transmembrane protein. Unlike yeast, several human homologs of the ERD2 gene, constituting the KDEL receptor gene family, have been described. KDELR3 was the third member of the family to be identified. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
    Expression
    Ubiquitous expression in stomach (RPKM 15.1), gall bladder (RPKM 11.6) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KDELR3 in Genome Data Viewer
    Location:
    22q13.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (38468096..38483447)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (38932363..38947716)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (38864101..38879452)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373029 Neighboring gene potassium inwardly rectifying channel subfamily J member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38839066-38839566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38847863-38848482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38848483-38849101 Neighboring gene uncharacterized LOC124905116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38857412-38857912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38859483-38859982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38861409-38861910 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13719 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13720 Neighboring gene DEAD-box helicase 17 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:38901381-38902272 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:38902273-38903164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:38908748-38909556 Neighboring gene CRISPRi-validated cis-regulatory element chr22.1887 Neighboring gene DNA meiotic recombinase 1 Neighboring gene MPRA-validated peak4491 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13723 Neighboring gene uncharacterized LOC105373031 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:38966777-38967287

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Melanoblast transcriptome analysis reveals pathways promoting melanoma metastasis. Marie KL, et al. Nat Commun, 2020 Jan 16. PMID 31949145, Free PMC Article
    2. The dynamic organisation of the secretory pathway. Pelham HR. Cell Struct Funct, 1996 Oct. PMID 9118249
    3. Cell-type-specific differences in KDEL receptor clustering in mammalian cells. Bauer A, et al. PLoS One, 2020. PMID 32645101, Free PMC Article
    4. A molecular specificity code for the three mammalian KDEL receptors. Raykhel I, et al. J Cell Biol, 2007 Dec 17. PMID 18086916, Free PMC Article
    5. Reevaluating human gene annotation: a second-generation analysis of chromosome 22. Collins JE, et al. Genome Res, 2003 Jan. PMID 12529303, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Cell-type-specific differences in KDEL receptor clustering in mammalian cells.
      Title: Cell-type-specific differences in KDEL receptor clustering in mammalian cells.
    Submit: New GeneRIF Correction

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ER retention sequence binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables KDEL sequence 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 protein retention in ER lumen IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    colocalizes_with COPI-coated vesicle membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in cis-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in transport vesicle TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    ER lumen protein-retaining receptor 3
    Names
    KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3
    KDEL receptor 3

    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)

    1. NM_006855.4 → NP_006846.1  ER lumen protein-retaining receptor 3 isoform a

      See identical proteins and their annotated locations for NP_006846.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AI753246, AL035081, Z97056
      Consensus CDS
      CCDS13972.1
      UniProtKB/Swiss-Prot
      A8K7T7, B8ZZ26, O43731, O95557, Q4V750, Q4V767, Q53FP4, Q53GK1
      Related
      ENSP00000216014.4, ENST00000216014.9
      Conserved Domains (1) summary
      pfam00810
      Location:29 → 169
      ER_lumen_recept; ER lumen protein retaining receptor

    2. NM_016657.3 → NP_057839.1  ER lumen protein-retaining receptor 3 isoform b

      See identical proteins and their annotated locations for NP_057839.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate 3' terminal exon, compared to variant 1. It encodes isoform b which is shorter and has a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      BC098131, BU621350, Z97056
      Consensus CDS
      CCDS46705.1
      UniProtKB/Swiss-Prot
      O43731
      Related
      ENSP00000386918.3, ENST00000409006.3
      Conserved Domains (1) summary
      pfam00810
      Location:29 → 169
      ER_lumen_recept; ER lumen protein retaining receptor

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      38468096..38483447
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      38932363..38947716
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O43731.1 GenPept UniProtKB/Swiss-Prot:O43731

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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