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

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. Involved in synapse maturation. Acts upstream of or within ubiquitin-dependent protein catabolic process. Located in cytoplasm. Is active in hippocampal mossy fiber to CA3 synapse and postsynapse. Is expressed in several structures, including brain; genitourinary system; liver; nasal epithelium; and spleen. Orthologous to human LNX1 (ligand of numb-protein X 1). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Broad expression in frontal lobe adult (RPKM 6.0), cortex adult (RPKM 5.8) and 23 other tissues See more
Orthologs: human all
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Genomic context

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_000071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Ligand-of-Numb protein X1 controls the coxsackievirus B3-induced myocarditis via regulating the stability of coxsackievirus and adenovirus receptor.
Title: Ligand-of-Numb protein X1 controls the coxsackievirus B3-induced myocarditis via regulating the stability of coxsackievirus and adenovirus receptor.
Hippocampal Lnx1-NMDAR multiprotein complex mediates initial social memory.
Title: Hippocampal Lnx1-NMDAR multiprotein complex mediates initial social memory.
MicroRNA-325-3p Facilitates Immune Escape of Mycobacterium tuberculosis through Targeting LNX1 via NEK6 Accumulation to Promote Anti-Apoptotic STAT3 Signaling.
Title: MicroRNA-325-3p Facilitates Immune Escape of Mycobacterium tuberculosis through Targeting LNX1 via NEK6 Accumulation to Promote Anti-Apoptotic STAT3 Signaling.
Retrograde regulation of mossy fiber axon targeting and terminal maturation via postsynaptic Lnx1.
Title: Retrograde regulation of mossy fiber axon targeting and terminal maturation via postsynaptic Lnx1.
These findings provide functional insights into the LNX protein family, particularly the neuronal LNX1p70 isoform.
Title: Proteomic analysis reveals novel ligands and substrates for LNX1 E3 ubiquitin ligase.
LNX1p80 is involved in the ubiquitylation, endocytosis and lysosomal degradation of claudins, and the turnover of tight junctions is regulated by ubiquitylation.
Title: The E3 ubiquitin ligase LNX1p80 promotes the removal of claudins from tight junctions in MDCK cells.
LNX1 provides an endocytic scaffold for JAM4 that is implicated in the reorganization of cell junctions.
Title: Ligand-of-Numb protein X is an endocytic scaffold for junctional adhesion molecule 4.
the PDZ domain-containing protein ligand-of-numb protein-X (LNX) is found in complex with the coxsackievirus and adenovirus receptor (CAR)
Title: The Coxsackievirus and adenovirus receptor (CAR) forms a complex with the PDZ domain-containing protein ligand-of-numb protein-X (LNX).
LNX1 may play a role in regulating neuregulin-1/ErbB signaling in perisynaptic Schwann cells.
Title: LNX1 is a perisynaptic Schwann cell specific E3 ubiquitin ligase that interacts with ErbB2.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (4)
Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D5Jcs312 (e-PCR), detects polymorphism
- UniSTS:479321

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 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 protein ubiquitination	IEA Inferred from Electronic Annotation more info
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

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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

EC 2.3.2.27

NP_001153050.1

EC 2.3.2.27

NP_001153051.1

EC 2.3.2.27

NP_001153052.1

EC 2.3.2.27

NP_001346003.1

EC 2.3.2.27

NP_034857.3

EC 2.3.2.27

XP_006504317.1

EC 2.3.2.27

XP_017176180.1

EC 2.3.2.27

XP_036020727.1

EC 2.3.2.27

XP_036020728.1

EC 2.3.2.27

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)

NM_001159577.1 → NP_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:637 → 721

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:42 → 83

mRING-HC-C3HC3D_LNX1; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1)
NM_001159578.1 → NP_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:478 → 562

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) ...
NM_001159579.1 → NP_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:537 → 621

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) ...
NM_001159580.1 → NP_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:527 → 611

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) ...
NM_001359074.1 → NP_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:478 → 562

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) ...
NM_010727.4 → NP_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:537 → 621

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

NC_000071.7 Reference GRCm39 C57BL/6J

Range

74753108..74865203 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036164834.1 → XP_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:637 → 721

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:42 → 83

mRING-HC-C3HC3D_LNX1; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1)
XM_006504254.4 → XP_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:637 → 721

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:42 → 83

mRING-HC-C3HC3D_LNX1; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1)
XM_036164835.1 → XP_036020728.1 E3 ubiquitin-protein ligase LNX isoform X2

UniProtKB/TrEMBL

D3YTM4, E9Q4N3, Q3UUJ9

Conserved Domains (1) summary

cd00992
Location:478 → 562

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) ...
XM_017320691.3 → XP_017176180.1 E3 ubiquitin-protein ligase LNX isoform X2

UniProtKB/TrEMBL

D3YTM4, E9Q4N3, Q3UUJ9

Conserved Domains (1) summary

cd00992
Location:478 → 562

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) ...