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

Gene ID: 11015, updated on 5-Mar-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
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Genomic context

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Location:
22q13.1
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (38468096..38483447)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (38932363..38947716)
105.20220307 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. Cell-type-specific differences in KDEL receptor clustering in mammalian cells. Bauer A, et al. PLoS One, 2020. PMID 32645101, Free PMC Article
  3. The dynamic organisation of the secretory pathway. Pelham HR. Cell Struct Funct, 1996 Oct. PMID 9118249
  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 (20) 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)

Genotypes

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 
Process Evidence Code Pubs
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
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_2023_10

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

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