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    LNX2 ligand of numb-protein X 2 [ Homo sapiens (human) ]

    Gene ID: 222484, updated on 3-Apr-2024

    Summary

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    Official Symbol
    LNX2provided by HGNC
    Official Full Name
    ligand of numb-protein X 2provided by HGNC
    Primary source
    HGNC:HGNC:20421
    See related
    Ensembl:ENSG00000139517 MIM:609733; AllianceGenome:HGNC:20421
    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
    PDZRN1
    Summary
    Predicted to enable ubiquitin-protein transferase activity. Predicted to be involved in protein ubiquitination. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 9.5), small intestine (RPKM 7.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LNX2 in Genome Data Viewer
    Location:
    13q12.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (27545913..27621107, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (26766973..26842233, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (28120050..28194666, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:28008622-28009821 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32805 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:28023938-28024852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7507 Neighboring gene general transcription factor IIIA Neighboring gene Sharpr-MPRA regulatory region 13742 Neighboring gene mitochondrial translational initiation factor 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7508 Neighboring gene RNA, U6 small nuclear 63, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32806 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32807 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32809 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:28107144-28107644 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:28107645-28108145 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32810 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:28194694-28195422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5204 Neighboring gene RNA polymerase I and III subunit D Neighboring gene nucleophosmin 1 pseudogene 4 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr13:28302713-28303912 Neighboring gene uncharacterized LOC105370129

    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. Genetic amplification of the NOTCH modulator LNX2 upregulates the WNT/β-catenin pathway in colorectal cancer. Camps J, et al. Cancer Res, 2013 Mar 15. PMID 23319804, Free PMC Article
    2. The ligands of Numb proteins X1 and X2 are specific markers for chronic Q fever. Mehraj V, et al. FEMS Immunol Med Microbiol, 2012 Feb. PMID 22066909
    3. E3 ubiquitin ligases LNX1 and LNX2 localize at neuronal gap junctions formed by connexin36 in rodent brain and molecularly interact with connexin36. Lynn BD, et al. Eur J Neurosci, 2018 Nov. PMID 30295974
    4. Structural basis for the indispensable role of a unique zinc finger motif in LNX2 ubiquitination. Nayak D, et al. Oncotarget, 2015 Oct 27. PMID 26451611, Free PMC Article
    5. Ligand of Numb proteins LNX1p80 and LNX2 interact with the human glycoprotein CD8α and promote its ubiquitylation and endocytosis. D'Agostino M, et al. J Cell Sci, 2011 Nov 1. PMID 22045731

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LNX2 involves in the role of ghrelin to promote the neuronal differentiation of adipose tissue-derived mesenchymal stem cells.
      Title: LNX2 involves in the role of ghrelin to promote the neuronal differentiation of adipose tissue-derived mesenchymal stem cells.
    2. FOXC2 or its associated gene expression program may provide an effective target for anti-EMT-based therapies for the treatment of claudin-low/basal B breast tumors or other EMT-/CSC-enriched tumors
      Title: Genetic amplification of the NOTCH modulator LNX2 upregulates the WNT/β-catenin pathway in colorectal cancer.
    3. The authors found a high level of LNX1 and LNX2 mRNAs in endocarditis, the principal manifestation of chronic Q fever, but not in acute Q fever.
      Title: The ligands of Numb proteins X1 and X2 are specific markers for chronic Q fever.
    4. LNX1 and LNX2 interact with CD8alpha and promote its ubiquitylation and endocytosis
      Title: Ligand of Numb proteins LNX1p80 and LNX2 interact with the human glycoprotein CD8α and promote its ubiquitylation and endocytosis.
    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
    Common variants on 14q32 and 13q12 are associated with DLBCL susceptibility.
    EBI GWAS Catalog
    Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines.
    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of ligand of numb-protein X 2 (LNX2) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells 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

    Clone Names

    • FLJ12933, FLJ23932, FLJ38000, MGC46315

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables PDZ domain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin-protein transferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in neural precursor cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ligand of Numb protein X 2
    Names
    PDZ domain containing ring finger 1
    PDZ domain-containing RING finger protein 1
    numb-binding protein 2

    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_153371.4 → NP_699202.1  ligand of Numb protein X 2

      See identical proteins and their annotated locations for NP_699202.1

      Status: VALIDATED

      Source sequence(s)
      AK022995, BC036755, DB220129, DN990012
      Consensus CDS
      CCDS9323.1
      UniProtKB/Swiss-Prot
      Q5W0P0, Q6ZMH2, Q8N448, Q96SH4
      UniProtKB/TrEMBL
      B2R8J5
      Related
      ENSP00000325929.3, ENST00000316334.5
      Conserved Domains (3) summary
      smart00228
      Location:230 → 316
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:599 → 683
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd16780
      Location:45 → 89
      mRING-HC-C3HC3D_LNX2; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 2 (LNX2)

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      27545913..27621107 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017020434.2 → XP_016875923.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5W0P0, Q6ZMH2, Q8N448, Q96SH4
      UniProtKB/TrEMBL
      B2R8J5
      Conserved Domains (3) summary
      smart00228
      Location:230 → 316
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:599 → 683
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd16780
      Location:45 → 89
      mRING-HC-C3HC3D_LNX2; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 2 (LNX2)

    2. XM_011534995.3 → XP_011533297.1  ligand of Numb protein X 2 isoform X2

      UniProtKB/TrEMBL
      B2R8J5
      Conserved Domains (3) summary
      smart00184
      Location:50 → 86
      RING; Ring finger
      smart00228
      Location:230 → 299
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:476 → 560
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

    3. XM_047430148.1 → XP_047286104.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5W0P0, Q6ZMH2, Q8N448, Q96SH4

    4. XM_047430150.1 → XP_047286106.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5W0P0, Q6ZMH2, Q8N448, Q96SH4

    5. XM_047430151.1 → XP_047286107.1  ligand of Numb protein X 2 isoform X2

    6. XM_047430145.1 → XP_047286101.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5W0P0, Q6ZMH2, Q8N448, Q96SH4

    7. XM_047430147.1 → XP_047286103.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5W0P0, Q6ZMH2, Q8N448, Q96SH4
      Related
      ENSP00000497224.1, ENST00000649248.1

    8. XM_047430149.1 → XP_047286105.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5W0P0, Q6ZMH2, Q8N448, Q96SH4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      26766973..26842233 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374213.1 → XP_054230188.1  ligand of Numb protein X 2 isoform X1

    2. XM_054374212.1 → XP_054230187.1  ligand of Numb protein X 2 isoform X1

    3. XM_054374215.1 → XP_054230190.1  ligand of Numb protein X 2 isoform X1

    4. XM_054374219.1 → XP_054230194.1  ligand of Numb protein X 2 isoform X2

    5. XM_054374218.1 → XP_054230193.1  ligand of Numb protein X 2 isoform X1

    6. XM_054374220.1 → XP_054230195.1  ligand of Numb protein X 2 isoform X2

    7. XM_054374214.1 → XP_054230189.1  ligand of Numb protein X 2 isoform X1

    8. XM_054374217.1 → XP_054230192.1  ligand of Numb protein X 2 isoform X1

    9. XM_054374216.1 → XP_054230191.1  ligand of Numb protein X 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N448.1 GenPept UniProtKB/Swiss-Prot:Q8N448

    Gene LinkOut

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

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