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

Gene ID: 84708, updated on 7-Jun-2020

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
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

Genomic context

See LNX1 in Genome Data Viewer
Location:
4q12
Exon count:
15
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (53458264..53652525, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (54326437..54518653, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene sec1 family domain containing 2 Neighboring gene RNA, U6 small nuclear 310, pseudogene Neighboring gene uncharacterized LOC105377654 Neighboring gene factor interacting with PAPOLA and CPSF1 Neighboring gene LNX1 antisense RNA 1 Neighboring gene COMM domain-containing protein 5-like Neighboring gene LNX1 antisense RNA 2 Neighboring gene uncharacterized LOC100506444 Neighboring gene nucleic acid binding protein 2 pseudogene

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

NHGRI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
PDZ domain binding IEA
Inferred from Electronic Annotation
more info
 
identical protein binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin-protein transferase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
protein ubiquitination IEA
Inferred from Electronic Annotation
more info
 
ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
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_016864265.1
XP_024310029.1
XP_024310030.1

NCBI Reference Sequences (RefSeq)

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
    Q8TBB1
    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_032622.2NP_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)
    BC034737, DA154083
    Consensus CDS
    CCDS3492.1
    UniProtKB/Swiss-Prot
    Q8TBB1
    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: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    53458264..53652525 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017008776.1XP_016864265.1  E3 ubiquitin-protein ligase LNX isoform X1

    UniProtKB/Swiss-Prot
    Q8TBB1
    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_024454261.1XP_024310029.1  E3 ubiquitin-protein ligase LNX isoform X1

    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_005265785.5XP_005265842.1  E3 ubiquitin-protein ligase LNX isoform X1

    See identical proteins and their annotated locations for XP_005265842.1

    UniProtKB/Swiss-Prot
    Q8TBB1
    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)
  4. XM_024454262.1XP_024310030.1  E3 ubiquitin-protein ligase LNX isoform X1

    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)
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