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

    Gene ID: 222484, updated on 17-Jun-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    HIV-1 interactions

    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

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    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_153371.4NP_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:230316
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:599683
      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:4589
      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_017020434.2XP_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:230316
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:599683
      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:4589
      mRING-HC-C3HC3D_LNX2; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 2 (LNX2)
    2. XM_011534995.3XP_011533297.1  ligand of Numb protein X 2 isoform X2

      UniProtKB/TrEMBL
      B2R8J5
      Conserved Domains (3) summary
      smart00184
      Location:5086
      RING; Ring finger
      smart00228
      Location:230299
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:476560
      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_047430148.1XP_047286104.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5W0P0, Q6ZMH2, Q8N448, Q96SH4
      UniProtKB/TrEMBL
      B2R8J5
    4. XM_047430150.1XP_047286106.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5W0P0, Q6ZMH2, Q8N448, Q96SH4
      UniProtKB/TrEMBL
      B2R8J5
    5. XM_047430151.1XP_047286107.1  ligand of Numb protein X 2 isoform X2

      UniProtKB/TrEMBL
      B2R8J5
    6. XM_047430145.1XP_047286101.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5W0P0, Q6ZMH2, Q8N448, Q96SH4
      UniProtKB/TrEMBL
      B2R8J5
    7. XM_047430147.1XP_047286103.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5W0P0, Q6ZMH2, Q8N448, Q96SH4
      UniProtKB/TrEMBL
      B2R8J5
      Related
      ENSP00000497224.1, ENST00000649248.1
    8. XM_047430149.1XP_047286105.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/Swiss-Prot
      Q5W0P0, Q6ZMH2, Q8N448, Q96SH4
      UniProtKB/TrEMBL
      B2R8J5

    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_054374213.1XP_054230188.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/TrEMBL
      B2R8J5
    2. XM_054374212.1XP_054230187.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/TrEMBL
      B2R8J5
    3. XM_054374215.1XP_054230190.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/TrEMBL
      B2R8J5
    4. XM_054374219.1XP_054230194.1  ligand of Numb protein X 2 isoform X2

      UniProtKB/TrEMBL
      B2R8J5
    5. XM_054374218.1XP_054230193.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/TrEMBL
      B2R8J5
    6. XM_054374220.1XP_054230195.1  ligand of Numb protein X 2 isoform X2

      UniProtKB/TrEMBL
      B2R8J5
    7. XM_054374214.1XP_054230189.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/TrEMBL
      B2R8J5
    8. XM_054374217.1XP_054230192.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/TrEMBL
      B2R8J5
    9. XM_054374216.1XP_054230191.1  ligand of Numb protein X 2 isoform X1

      UniProtKB/TrEMBL
      B2R8J5