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Lnx1 ligand of numb-protein X 1 [ Mus musculus (house mouse) ]

Gene ID: 16924, updated on 14-May-2024

Summary

Official Symbol
Lnx1provided by MGI
Official Full Name
ligand of numb-protein X 1provided by MGI
Primary source
MGI:MGI:1278335
See related
Ensembl:ENSMUSG00000029228 AllianceGenome:MGI:1278335
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Lnx
Summary
Enables PDZ domain binding activity; identical protein binding activity; and ubiquitin-protein transferase activity. Acts upstream of or within ubiquitin-dependent protein catabolic process. Located in cytoplasm. Is expressed in several structures, including brain; heart; lung; nasal epithelium; and spinal cord. Orthologous to human LNX1 (ligand of numb-protein X 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in frontal lobe adult (RPKM 6.0), cortex adult (RPKM 5.8) and 23 other tissues See more
Orthologs
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Genomic context

See Lnx1 in Genome Data Viewer
Location:
5 C3.3; 5 39.52 cM
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (74753108..74865203, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (74592447..74703043, complement)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:74596657-74596859 Neighboring gene RAS-like, family 11, member B Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:74656347-74656530 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:74656616-74656725 Neighboring gene Sec1 family domain containing 2 Neighboring gene STARR-seq mESC enhancer starr_13406 Neighboring gene VISTA enhancer mm139 Neighboring gene predicted gene, 32064 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:74762842-74763025 Neighboring gene STARR-seq mESC enhancer starr_13407 Neighboring gene STARR-positive B cell enhancer ABC_E2746 Neighboring gene STARR-positive B cell enhancer ABC_E6339 Neighboring gene factor interacting with PAPOLA and CPSF1 Neighboring gene STARR-seq mESC enhancer starr_13408 Neighboring gene STARR-seq mESC enhancer starr_13409 Neighboring gene predicted gene, 32304 Neighboring gene STARR-seq mESC enhancer starr_13410 Neighboring gene STARR-seq mESC enhancer starr_13411 Neighboring gene predicted gene 15984 Neighboring gene predicted gene 15985 Neighboring gene STARR-seq mESC enhancer starr_13412 Neighboring gene nucleophosmin 1 pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (4) 
  • Targeted (1)  1 citation

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables PDZ domain binding IDA
Inferred from Direct Assay
more info
PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
 
enables ubiquitin-protein transferase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in synapse maturation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in synapse maturation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in hippocampal mossy fiber to CA3 synapse IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in hippocampal mossy fiber to CA3 synapse IMP
Inferred from Mutant Phenotype
more info
PubMed 
is_active_in postsynapse IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in postsynapse IEP
Inferred from Expression Pattern
more info
PubMed 
is_active_in postsynapse IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
E3 ubiquitin-protein ligase LNX
Names
RING-type E3 ubiquitin transferase LNX
ligand of Numb protein X 1
ligand of Numb-binding protein 1
numb-binding protein 1
NP_001153049.1
NP_001153050.1
NP_001153051.1
NP_001153052.1
NP_001346003.1
NP_034857.3
XP_006504317.1
XP_017176180.1
XP_036020727.1
XP_036020728.1

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.

mRNA and Protein(s)

  1. NM_001159577.1NP_001153049.1  E3 ubiquitin-protein ligase LNX isoform 1

    See identical proteins and their annotated locations for NP_001153049.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC120865, AF034745, AI850871
    Consensus CDS
    CCDS51524.1
    UniProtKB/Swiss-Prot
    O70263, O70264, Q8BRI8, Q8CFR3
    UniProtKB/TrEMBL
    Q3UUJ9
    Related
    ENSMUSP00000113035.2, ENSMUST00000117388.8
    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:4283
    mRING-HC-C3HC3D_LNX1; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1)
  2. NM_001159578.1NP_001153050.1  E3 ubiquitin-protein ligase LNX isoform 3

    See identical proteins and their annotated locations for NP_001153050.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, 3' UTR and coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (3) with a shorter N-terminus compared to isoform 1. Variants 3 and 6 both encode the same isoform (3).
    Source sequence(s)
    AK044127, AK138326, AK161194
    Consensus CDS
    CCDS51522.1
    UniProtKB/TrEMBL
    D3YTM4, E9Q4N3, Q3UUJ9
    Related
    ENSMUSP00000109159.3, ENSMUST00000113531.9
    Conserved Domains (1) summary
    cd00992
    Location:478562
    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. NM_001159579.1NP_001153051.1  E3 ubiquitin-protein ligase LNX isoform 2 precursor

    See identical proteins and their annotated locations for NP_001153051.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus compared to isoform 1. Variants 2 and 4 encode the same isoform.
    Source sequence(s)
    AF034746, AI850871, AK138326
    Consensus CDS
    CCDS19347.1
    UniProtKB/TrEMBL
    A4QPD4, Q3UUJ9
    Related
    ENSMUSP00000113837.2, ENSMUST00000117525.8
    Conserved Domains (1) summary
    cd00992
    Location:537621
    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) ...
  4. NM_001159580.1NP_001153052.1  E3 ubiquitin-protein ligase LNX isoform 5 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (5) with a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AI850871, AK044127, AK138326
    Consensus CDS
    CCDS51523.1
    UniProtKB/TrEMBL
    E9Q6Q0, Q3UUJ9
    Related
    ENSMUSP00000113565.2, ENSMUST00000121690.8
    Conserved Domains (1) summary
    cd00992
    Location:527611
    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) ...
  5. NM_001359074.1NP_001346003.1  E3 ubiquitin-protein ligase LNX isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR, 3' UTR, and 5' coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1. Variants 3 and 6 both encode the same isoform (3).
    Source sequence(s)
    KJ418422
    Consensus CDS
    CCDS51522.1
    UniProtKB/TrEMBL
    D3YTM4, E9Q4N3, Q3UUJ9
    Conserved Domains (1) summary
    cd00992
    Location:478562
    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) ...
  6. NM_010727.4NP_034857.3  E3 ubiquitin-protein ligase LNX isoform 2 precursor

    See identical proteins and their annotated locations for NP_034857.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, 3' UTR and coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus compared to isoform 1. Variants 2 and 4 encode the same isoform.
    Source sequence(s)
    AK044127, AK138326, BC139771
    Consensus CDS
    CCDS19347.1
    UniProtKB/TrEMBL
    A4QPD4, Q3UUJ9
    Related
    ENSMUSP00000040098.7, ENSMUST00000039744.13
    Conserved Domains (1) summary
    cd00992
    Location:537621
    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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000071.7 Reference GRCm39 C57BL/6J

    Range
    74753108..74865203 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036164834.1XP_036020727.1  E3 ubiquitin-protein ligase LNX isoform X1

    UniProtKB/Swiss-Prot
    O70263, O70264, Q8BRI8, Q8CFR3
    UniProtKB/TrEMBL
    Q3UUJ9
    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:4283
    mRING-HC-C3HC3D_LNX1; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1)
  2. XM_006504254.4XP_006504317.1  E3 ubiquitin-protein ligase LNX isoform X1

    See identical proteins and their annotated locations for XP_006504317.1

    UniProtKB/Swiss-Prot
    O70263, O70264, Q8BRI8, Q8CFR3
    UniProtKB/TrEMBL
    Q3UUJ9
    Related
    ENSMUSP00000084405.4, ENSMUST00000087161.10
    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:4283
    mRING-HC-C3HC3D_LNX1; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1)
  3. XM_036164835.1XP_036020728.1  E3 ubiquitin-protein ligase LNX isoform X2

    UniProtKB/TrEMBL
    D3YTM4, E9Q4N3, Q3UUJ9
    Conserved Domains (1) summary
    cd00992
    Location:478562
    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) ...
  4. XM_017320691.3XP_017176180.1  E3 ubiquitin-protein ligase LNX isoform X2

    UniProtKB/TrEMBL
    D3YTM4, E9Q4N3, Q3UUJ9
    Conserved Domains (1) summary
    cd00992
    Location:478562
    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) ...

RNA

  1. XR_003955587.2 RNA Sequence

  2. XR_001784630.3 RNA Sequence

  3. XR_001784629.3 RNA Sequence

  4. XR_003955588.2 RNA Sequence

  5. XR_003955589.2 RNA Sequence

  6. XR_004942440.1 RNA Sequence