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    DERL3 derlin 3 [ Homo sapiens (human) ]

    Gene ID: 91319, updated on 11-Apr-2024

    Summary

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    Official Symbol
    DERL3provided by HGNC
    Official Full Name
    derlin 3provided by HGNC
    Primary source
    HGNC:HGNC:14236
    See related
    Ensembl:ENSG00000099958 MIM:610305; AllianceGenome:HGNC:14236
    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
    IZP6; LLN2; C22orf14; derlin-3
    Summary
    The protein encoded by this gene belongs to the derlin family, and resides in the endoplasmic reticulum (ER). Proteins that are unfolded or misfolded in the ER must be refolded or degraded to maintain the homeostasis of the ER. This protein appears to be involved in the degradation of misfolded glycoproteins in the ER. Several alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Oct 2008]
    Expression
    Broad expression in stomach (RPKM 12.2), duodenum (RPKM 11.1) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    22q11.23
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (23834503..23839006, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (24281689..24286190, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (24176690..24181193, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24122834-24123832 Neighboring gene matrix metallopeptidase 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24134505-24135005 Neighboring gene SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24145605-24146105 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24158117-24158618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24158619-24159120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24166870-24167403 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24167404-24167938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24168707-24169427 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:24181116-24181418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24184397-24184954 Neighboring gene skeletal muscle cis-regulatory module in DERL3 and SLC2A11 intergenic region Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:24189965-24190722 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24190723-24191478 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24191479-24192234 Neighboring gene solute carrier family 2 member 11 Neighboring gene RNA, 7SL, cytoplasmic 268, pseudogene Neighboring gene Sharpr-MPRA regulatory region 10281 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:24236245-24237052 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24237053-24237860 Neighboring gene MIF antisense RNA 1 Neighboring gene macrophage migration inhibitory factor

    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. Up-regulated DERL3 in fibroblast-like synoviocytes exacerbates inflammation of rheumatoid arthritis. Geng M, et al. Clin Immunol, 2020 Nov. PMID 32866644
    2. DERL3 functions as a tumor suppressor in gastric cancer. Li Y, et al. Comput Biol Chem, 2020 Feb. PMID 31862624
    3. Overexpression of Derlin 3 is associated with malignant phenotype of breast cancer cells. Shibata M, et al. Oncol Rep, 2017 Sep. PMID 28713959
    4. Repression of DERL3 via DNA methylation by Epstein-Barr virus latent membrane protein 1 in nasopharyngeal carcinoma. Kondo S, et al. Biochim Biophys Acta Mol Basis Dis, 2023 Feb. PMID 36372158
    5. A DERL3-associated defect in the degradation of SLC2A1 mediates the Warburg effect. Lopez-Serra P, et al. Nat Commun, 2014 Apr 3. PMID 24699711, Free PMC Article

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Repression of DERL3 via DNA methylation by Epstein-Barr virus latent membrane protein 1 in nasopharyngeal carcinoma.
      Title: Repression of DERL3 via DNA methylation by Epstein-Barr virus latent membrane protein 1 in nasopharyngeal carcinoma.
    2. Up-regulated DERL3 in fibroblast-like synoviocytes exacerbates inflammation of rheumatoid arthritis.
      Title: Up-regulated DERL3 in fibroblast-like synoviocytes exacerbates inflammation of rheumatoid arthritis.
    3. DERL3 is both a tumor suppressor of and a methylation biomarker for gastric cancer.
      Title: DERL3 functions as a tumor suppressor in gastric cancer.
    4. DERL3 promotes malignant phenotype in BC cells.
      Title: Overexpression of Derlin 3 is associated with malignant phenotype of breast cancer cells.
    5. SLC2A1 overexpression mediated by DERL3 epigenetic loss contributes to the Warburg effect.
      Title: A DERL3-associated defect in the degradation of SLC2A1 mediates the Warburg effect.
    6. Findings indicate that Derlin-3 provides the missing link between EDEM and p97 in the process of degrading misfolded glycoproteins.
      Title: Derlin-2 and Derlin-3 are regulated by the mammalian unfolded protein response and are required for ER-associated degradation.
    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

    EBI GWAS Catalog

    Description
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC71803

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-containing complex binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables signal recognition particle binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables signal recognition particle binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in ERAD pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ERAD pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ERAD pathway NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in ERAD pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in endoplasmic reticulum unfolded protein response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endoplasmic reticulum unfolded protein response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of retrograde protein transport, ER to cytosol IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein N-linked glycosylation via asparagine IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    derlin-3
    Names
    DERtrin 3
    Der1-like domain family, member 3
    degradation in endoplasmic reticulum protein 3
    der1-like protein 3

    NCBI Reference Sequences (RefSeq)

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    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_001002862.3 → NP_001002862.1  derlin-3 isoform 2

      See identical proteins and their annotated locations for NP_001002862.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is alternatively spliced at the 3' end compared to transcript variant 1, resulting in a slightly shorter isoform (2) with a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK092582, AL389876, AP000350, BC057830, CA313370
      Consensus CDS
      CCDS33615.1
      UniProtKB/Swiss-Prot
      F2Z3B6, Q6ICJ6, Q6PEX0, Q6ZUB5, Q96Q80
      Related
      ENSP00000315303.8, ENST00000318109.12
      Conserved Domains (1) summary
      pfam04511
      Location:13 → 202
      DER1; Der1-like family

    2. NM_001135751.2 → NP_001129223.1  derlin-3 isoform 1

      See identical proteins and their annotated locations for NP_001129223.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL389876, AW135031, BC057830, CA313370
      Consensus CDS
      CCDS46672.1
      UniProtKB/Swiss-Prot
      Q96Q80
      Related
      ENSP00000384744.3, ENST00000406855.7
      Conserved Domains (1) summary
      pfam04511
      Location:13 → 202
      DER1; Der1-like family

    3. NM_001363072.2 → NP_001350001.1  derlin-3 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) is alternatively spliced at the 3' end compared to transcript variant 1, resulting in a shorter isoform (4) with a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AP000350, CA313370
      Conserved Domains (1) summary
      pfam04511
      Location:13 → 202
      DER1; Der1-like family

    4. NM_198440.4 → NP_940842.2  derlin-3 isoform 3

      See identical proteins and their annotated locations for NP_940842.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains a long 3' terminal exon that is split into 2 exons in transcript variant 1. This results in early translation termination and a shorter isoform (3) compared to isoform 1.
      Source sequence(s)
      AK092582, AL389876, AP000350, BC057830, CA313370
      Consensus CDS
      CCDS42986.1
      UniProtKB/Swiss-Prot
      Q96Q80
      Related
      ENSP00000419399.1, ENST00000476077.1
      Conserved Domains (1) summary
      pfam04511
      Location:13 → 202
      DER1; Der1-like family

    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
      23834503..23839006 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441596.1 → XP_047297552.1  derlin-3 isoform X4

    2. XM_047441597.1 → XP_047297553.1  derlin-3 isoform X6

    3. XM_011530505.4 → XP_011528807.1  derlin-3 isoform X5

      See identical proteins and their annotated locations for XP_011528807.1

      Conserved Domains (1) summary
      pfam04511
      Location:13 → 201
      DER1; Der1-like family

    4. XM_047441595.1 → XP_047297551.1  derlin-3 isoform X3

    5. XM_017029078.3 → XP_016884567.2  derlin-3 isoform X1

    6. XM_047441594.1 → XP_047297550.1  derlin-3 isoform X2

      Related
      ENST00000290730.11

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187633.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      70865..75368 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329460.1 → XP_054185435.1  derlin-3 isoform X4

    2. XM_054329462.1 → XP_054185437.1  derlin-3 isoform X6

    3. XM_054329461.1 → XP_054185436.1  derlin-3 isoform X5

    4. XM_054329459.1 → XP_054185434.1  derlin-3 isoform X3

    5. XM_054329457.1 → XP_054185432.1  derlin-3 isoform X1

    6. XM_054329458.1 → XP_054185433.1  derlin-3 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      24281689..24286190 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326128.1 → XP_054182103.1  derlin-3 isoform X4

    2. XM_054326130.1 → XP_054182105.1  derlin-3 isoform X6

    3. XM_054326129.1 → XP_054182104.1  derlin-3 isoform X5

    4. XM_054326127.1 → XP_054182102.1  derlin-3 isoform X3

    5. XM_054326125.1 → XP_054182100.1  derlin-3 isoform X1

    6. XM_054326126.1 → XP_054182101.1  derlin-3 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96Q80.2 GenPept UniProtKB/Swiss-Prot:Q96Q80

    Gene LinkOut

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

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