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    LNX1 ligand of numb-protein X 1 [ Homo sapiens (human) ]

    Gene ID: 84708, updated on 7-Apr-2024

    Summary

    Official Symbol
    LNX1provided by HGNC
    Official Full Name
    ligand of numb-protein X 1provided by HGNC
    Primary source
    HGNC:HGNC:6657
    See related
    Ensembl:ENSG00000072201 MIM:609732; AllianceGenome:HGNC:6657
    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
    LNX; MPDZ; PDZRN2
    Summary
    This gene encodes a membrane-bound protein that is involved in signal transduction and protein interactions. The encoded product is an E3 ubiquitin-protein ligase, which mediates ubiquitination and subsequent proteasomal degradation of proteins containing phosphotyrosine binding (PTB) domains. This protein may play an important role in tumorogenesis. Alternatively spliced transcript variants encoding distinct isoforms have been described. A pseudogene, which is located on chromosome 17, has been identified for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 10.1), esophagus (RPKM 8.0) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See LNX1 in Genome Data Viewer
    Location:
    4q12
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (53459301..53652477, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (56946519..57139835, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (54325468..54457653, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene sec1 family domain containing 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:54140029-54140243 Neighboring gene RNA, U6 small nuclear 310, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:54195258-54195835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21562 Neighboring gene uncharacterized LOC105377654 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:54243526-54244074 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:54244075-54244623 Neighboring gene factor interacting with PAPOLA and CPSF1 Neighboring gene LNX1 antisense RNA 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:54458833-54459745 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:54467685-54468184 Neighboring gene COMMD5 pseudogene 1 Neighboring gene LNX1 antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21566 Neighboring gene uncharacterized LOC100506444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21567 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21568 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:54584896-54585497 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21570 Neighboring gene Sharpr-MPRA regulatory region 11224 Neighboring gene uncharacterized LOC124900702

    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
    GWAS of DNA methylation variation within imprinting control regions suggests parent-of-origin association.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    E3 ubiquitin-protein ligase LNX
    Names
    PDZ domain-containing ring finger protein 2
    RING-type E3 ubiquitin transferase LNX
    ligand of numb-protein X 1, E3 ubiquitin protein ligase
    multi-PDZ-domain-containing protein, E3 ubiquitin-protein ligase LNX
    numb-binding protein 1
    NP_001119800.1
    NP_116011.2
    XP_005265842.1
    XP_024310030.1
    XP_047272284.1
    XP_054207084.1
    XP_054207085.1
    XP_054207086.1
    XP_054207087.1
    XP_054207088.1
    XP_054207089.1

    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_001126328.3NP_001119800.1  E3 ubiquitin-protein ligase LNX isoform a

      See identical proteins and their annotated locations for NP_001119800.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a, also known as LNXp80).
      Source sequence(s)
      AC058822, BC022983, BC034737, DB159390
      Consensus CDS
      CCDS47057.1
      UniProtKB/Swiss-Prot
      Q4W5K7, Q8N4C2, Q8TBB1, Q96MJ7, Q9BY20
      Related
      ENSP00000263925.7, ENST00000263925.8
      Conserved Domains (2) summary
      cd00992
      Location:637721
      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) ...
      cd16779
      Location:3879
      mRING-HC-C3HC3D_LNX1; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1)
    2. NM_032622.3NP_116011.2  E3 ubiquitin-protein ligase LNX isoform b precursor

      See identical proteins and their annotated locations for NP_116011.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region, compared to variant 1. The resulting isoform (b, also known as LNXp70) contains a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AC058822, BC034737, DA154083
      Consensus CDS
      CCDS3492.1
      UniProtKB/TrEMBL
      B4DGI5
      Related
      ENSP00000302879.2, ENST00000306888.6
      Conserved Domains (1) summary
      cd00992
      Location:541625
      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) ...

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      53459301..53652477 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005265785.6XP_005265842.1  E3 ubiquitin-protein ligase LNX isoform X1

      See identical proteins and their annotated locations for XP_005265842.1

      UniProtKB/Swiss-Prot
      Q4W5K7, Q8N4C2, Q8TBB1, Q96MJ7, Q9BY20
      Conserved Domains (2) summary
      cd00992
      Location:637721
      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) ...
      cd16779
      Location:3879
      mRING-HC-C3HC3D_LNX1; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1)
    2. XM_024454262.2XP_024310030.1  E3 ubiquitin-protein ligase LNX isoform X1

      UniProtKB/Swiss-Prot
      Q4W5K7, Q8N4C2, Q8TBB1, Q96MJ7, Q9BY20
      Conserved Domains (2) summary
      cd00992
      Location:637721
      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) ...
      cd16779
      Location:3879
      mRING-HC-C3HC3D_LNX1; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1)
    3. XM_047416328.1XP_047272284.1  E3 ubiquitin-protein ligase LNX isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      56946519..57139835 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351114.1XP_054207089.1  E3 ubiquitin-protein ligase LNX isoform X1

      UniProtKB/Swiss-Prot
      Q4W5K7, Q8N4C2, Q8TBB1, Q96MJ7, Q9BY20
    2. XM_054351111.1XP_054207086.1  E3 ubiquitin-protein ligase LNX isoform X1

      UniProtKB/Swiss-Prot
      Q4W5K7, Q8N4C2, Q8TBB1, Q96MJ7, Q9BY20
    3. XM_054351113.1XP_054207088.1  E3 ubiquitin-protein ligase LNX isoform X1

      UniProtKB/Swiss-Prot
      Q4W5K7, Q8N4C2, Q8TBB1, Q96MJ7, Q9BY20
    4. XM_054351112.1XP_054207087.1  E3 ubiquitin-protein ligase LNX isoform X1

      UniProtKB/Swiss-Prot
      Q4W5K7, Q8N4C2, Q8TBB1, Q96MJ7, Q9BY20
    5. XM_054351110.1XP_054207085.1  E3 ubiquitin-protein ligase LNX isoform X1

      UniProtKB/Swiss-Prot
      Q4W5K7, Q8N4C2, Q8TBB1, Q96MJ7, Q9BY20
    6. XM_054351109.1XP_054207084.1  E3 ubiquitin-protein ligase LNX isoform X1

      UniProtKB/Swiss-Prot
      Q4W5K7, Q8N4C2, Q8TBB1, Q96MJ7, Q9BY20