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    ERLEC1 endoplasmic reticulum lectin 1 [ Homo sapiens (human) ]

    Gene ID: 27248, updated on 11-Apr-2024

    Summary

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    Official Symbol
    ERLEC1provided by HGNC
    Official Full Name
    endoplasmic reticulum lectin 1provided by HGNC
    Primary source
    HGNC:HGNC:25222
    See related
    Ensembl:ENSG00000068912 MIM:611229; AllianceGenome:HGNC:25222
    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
    CIM; HEL117; XTP3-B; C2orf30; CL24936; CL25084; XTP3TPB
    Summary
    This gene encodes a resident endoplasmic reticulum (ER) protein that functions in N-glycan recognition. This protein is thought to be involved in ER-associated degradation via its interaction with the membrane-associated ubiquitin ligase complex. It also functions as a regulator of multiple cellular stress-response pathways in a manner that promotes metastatic cell survival. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 21. [provided by RefSeq, Aug 2011]
    Expression
    Ubiquitous expression in thyroid (RPKM 36.0), prostate (RPKM 29.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ERLEC1 in Genome Data Viewer
    Location:
    2p16.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (53787044..53818796)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (53783247..53814984)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (54014181..54045933)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374600 Neighboring gene GPR75-ASB3 readthrough Neighboring gene ankyrin repeat and SOCS box containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15754 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:54013580-54014238 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:54019308-54019522 Neighboring gene ChaC glutathione specific gamma-glutamylcyclotransferase 2 Neighboring gene uncharacterized LOC112268415 Neighboring gene Sharpr-MPRA regulatory region 2358 Neighboring gene uncharacterized LOC124906183 Neighboring gene microRNA 3682

    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. Identification of pathogenic variants of ERLEC1 in individuals with Class III malocclusion by exome sequencing. Rao C, et al. Hum Mutat, 2020 Aug. PMID 32442352
    2. Mannose 6-phosphate receptor homology (MRH) domain-containing lectins in the secretory pathway. Castonguay AC, et al. Biochim Biophys Acta, 2011 Sep. PMID 21723917, Free PMC Article
    3. Mannose 6-phosphate receptor homology domain-containing lectins in mammalian endoplasmic reticulum-associated degradation. Hosokawa N, et al. Methods Enzymol, 2010. PMID 20816211
    4. Sweet bays of ERAD. Tamura T, et al. Trends Biochem Sci, 2008 Jul. PMID 18538572
    5. Redundant and Antagonistic Roles of XTP3B and OS9 in Decoding Glycan and Non-glycan Degrons in ER-Associated Degradation. van der Goot AT, et al. Mol Cell, 2018 May 3. PMID 29706535, Free PMC Article

    See all (64) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of pathogenic variants of ERLEC1 in individuals with Class III malocclusion by exome sequencing.
      Title: Identification of pathogenic variants of ERLEC1 in individuals with Class III malocclusion by exome sequencing.
    2. The relative expression of OS9 and XTP3B and the distribution of glycan and non-glycan degrons within the same protein contribute to the fidelity.
      Title: Redundant and Antagonistic Roles of XTP3B and OS9 in Decoding Glycan and Non-glycan Degrons in ER-Associated Degradation.
    3. Data indicate that the interaction of OS-9 and XTP3-B with CD147(CG) was inhibited by mutations to conserved residues in their lectin domains.
      Title: Unassembled CD147 is an endogenous endoplasmic reticulum-associated degradation substrate.
    4. Lectin activity of XTP3-B is required for its interaction with the misfolded glycoprotein alpha1-antitrypsin variant.
      Title: Endoplasmic reticulum lectin XTP3-B inhibits endoplasmic reticulum-associated degradation of a misfolded α1-antitrypsin variant.
    5. It regulates endoplasmic reticulum-associated degradation. (review)
      Title: [OS-9 and XTP3-B: lectins that regulate endoplasmic reticulum-associated degradation (ERAD)].
    6. mannose trimming enables delivery of a substrate glycoprotein from EDEM1 to late endoplsmic reticulum degredation steps through association with XTP3-B
      Title: Mannose trimming is required for delivery of a glycoprotein from EDEM1 to XTP3-B and to late endoplasmic reticulum-associated degradation steps.
    7. Findings shed light on how tolerance to multiple cellular stresses at a metastatic site can be evoked by an integrated mechanism involving CIM, ERLEC1, which can function to coordinate those responses in a manner that promotes metastatic cell survival.
      Title: Novel metastasis-related gene CIM functions in the regulation of multiple cellular stress-response pathways.
    8. XTP3-B specifically binds to AT(NHK), which is a well-known substrate of ERAD, via a C-terminal MRH domain in a glycan-dependent manner.
      Title: Human XTP3-B binds to alpha1-antitrypsin variant null(Hong Kong) via the C-terminal MRH domain in a glycan-dependent manner.
    9. XTP3-B forms an endoplasmic reticulum quality control scaffold with the HRD1-SEL1L ubiquitin ligase complex and BiP
      Title: Human XTP3-B forms an endoplasmic reticulum quality control scaffold with the HRD1-SEL1L ubiquitin ligase complex and BiP.
    10. Erlectin functions in N-glycan recognition in the endoplasmic reticulum and may regulate glycoprotein traffic
      Title: The MRH protein Erlectin is a member of the endoplasmic reticulum synexpression group and functions in N-glycan recognition.
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 is identified to have a physical interaction with endoplasmic reticulum lectin 1 (ERLEC1; XTP3B) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
    Envelope transmembrane glycoprotein gp41 env HIV-1 gp41 is identified to have a physical interaction with endoplasmic reticulum lectin 1 (ERLEC1; XTP3B) 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

    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 protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables unfolded protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in ERAD pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in endoplasmic reticulum unfolded protein response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of retrograde protein transport, ER to cytosol IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in retrograde protein transport, ER to cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum lumen IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum lumen IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum quality control compartment TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    endoplasmic reticulum lectin 1
    Names
    ER lectin
    XTP3-transactivated gene B protein
    XTP3-transactivated protein B
    cancer invasion and metastasis-related
    epididymis luminal protein 117
    erlectin 1

    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.

    Genomic

    1. NG_029742.1 RefSeqGene

      Range
      5114..36866
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001127397.3 → NP_001120869.1  endoplasmic reticulum lectin 1 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
      Source sequence(s)
      BC013129, BQ017438, DB451941
      Consensus CDS
      CCDS46283.1
      UniProtKB/TrEMBL
      A0A8I5KWJ1
      Related
      ENSP00000385629.3, ENST00000405123.7
      Conserved Domains (2) summary
      pfam07915
      Location:111 → 199
      PRKCSH; Glucosidase II beta subunit-like protein
      cl06793
      Location:206 → 250
      PRKCSH; Glucosidase II beta subunit-like protein

    2. NM_001127398.3 → NP_001120870.1  endoplasmic reticulum lectin 1 isoform 3 precursor

      See identical proteins and their annotated locations for NP_001120870.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (3, also known as hXTP3-B-short) that is shorter than isoform 1.
      Source sequence(s)
      AY358717, DB451941
      Consensus CDS
      CCDS46284.1
      UniProtKB/TrEMBL
      A0A8I5KTC7
      Related
      ENSP00000367485.5, ENST00000378239.5
      Conserved Domains (2) summary
      pfam07915
      Location:294 → 367
      PRKCSH; Glucosidase II beta subunit-like protein
      cl06793
      Location:206 → 250
      PRKCSH; Glucosidase II beta subunit-like protein

    3. NM_015701.5 → NP_056516.2  endoplasmic reticulum lectin 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_056516.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1, also known as hXTP3-B-long).
      Source sequence(s)
      BC013129, DB451941
      Consensus CDS
      CCDS1848.1
      UniProtKB/Swiss-Prot
      B2RDB4, B5MC72, O95901, Q6UWN7, Q96DZ1, Q9NUY7, Q9UQL4
      UniProtKB/TrEMBL
      A0A8I5KWJ1, V9HWD3
      Related
      ENSP00000185150.4, ENST00000185150.9
      Conserved Domains (2) summary
      pfam07915
      Location:342 → 421
      PRKCSH; Glucosidase II beta subunit-like protein
      cl06793
      Location:206 → 250
      PRKCSH; Glucosidase II beta subunit-like protein

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      53787044..53818796
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      53783247..53814984
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96DZ1.1 GenPept UniProtKB/Swiss-Prot:Q96DZ1

    Gene LinkOut

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