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LRRC4B leucine rich repeat containing 4B [ Homo sapiens (human) ]

Gene ID: 94030, updated on 23-Nov-2023

Summary

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Official Symbol
LRRC4Bprovided by HGNC
Official Full Name
leucine rich repeat containing 4Bprovided by HGNC
Primary source
HGNC:HGNC:25042
See related
Ensembl:ENSG00000131409 AllianceGenome:HGNC:25042
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
HSM; LRIG4; NGL-3
Summary
Predicted to enable signaling receptor binding activity. Predicted to be involved in regulation of synapse assembly and synaptic membrane adhesion. Predicted to be located in cerebellar mossy fiber and presynaptic membrane. Predicted to be active in glutamatergic synapse and plasma membrane. Predicted to be integral component of postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in brain (RPKM 11.1), endometrium (RPKM 2.3) and 4 other tissues See more
Orthologs
mouse all
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Genomic context

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See LRRC4B in Genome Data Viewer
Location:
19q13.33
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (50516892..50568435, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (53605741..53657264, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (51020149..51071692, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:51013121-51013628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:51013629-51014135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14992 Neighboring gene uncharacterized LOC124904747 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:51015053-51015642 Neighboring gene Josephin domain containing 2 Neighboring gene aspartate dehydrogenase domain containing Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14993 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:51055019-51055930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10972 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10973 Neighboring gene CRISPRi-validated cis-regulatory element chr19.5650 Neighboring gene small NF90 (ILF3) associated RNA F Neighboring gene synaptotagmin 3 Neighboring gene Sharpr-MPRA regulatory region 12037 Neighboring gene Sharpr-MPRA regulatory region 12891 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14995 Neighboring gene chromosome 19 open reading frame 81

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution. Dehal P, et al. Science, 2001 Jul 6. PMID 11441184
  2. MxA interacts with and is modified by the SUMOylation machinery. Brantis-de-Carvalho CE, et al. Exp Cell Res, 2015 Jan 1. PMID 25447205
  3. The DNA sequence and biology of human chromosome 19. Grimwood J, et al. Nature, 2004 Apr 1. PMID 15057824
  4. Histone deacetylase inhibitors inhibit cervical cancer growth through Parkin acetylation-mediated mitophagy. Sun X, et al. Acta Pharm Sin B, 2022 Feb. PMID 35256949, Free PMC Article
  5. A proximity-dependent biotinylation map of a human cell. Go CD, et al. Nature, 2021 Jul. PMID 34079125

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp761A179

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables signaling receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in positive regulation of synapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of postsynaptic density assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of presynapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in synaptic membrane adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cerebellar mossy fiber IEA
Inferred from Electronic Annotation
more info
  
is_active_in glutamatergic synapse IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
is_active_in postsynaptic density membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
  
located_in presynaptic membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
leucine-rich repeat-containing protein 4B
Names
leucine-rich repeats and immunoglobulin-like domains 4
netrin-G ligand-3
netrin-G3 ligand

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_001080457.2 → NP_001073926.1  leucine-rich repeat-containing protein 4B precursor

    See identical proteins and their annotated locations for NP_001073926.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    AC008743
    Consensus CDS
    CCDS42595.1
    UniProtKB/Swiss-Prot
    Q3ZCQ4, Q58F20, Q9NT99
    UniProtKB/TrEMBL
    A0PJJ4
    Related
    ENSP00000498662.1, ENST00000652263.1
    Conserved Domains (5) summary
    smart00013
    Location:57 → 90
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:311 → 361
    LRRCT; Leucine rich repeat C-terminal domain
    COG4886
    Location:76 → 297
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    pfam07679
    Location:364 → 453
    I-set; Immunoglobulin I-set domain
    sd00033
    Location:88 → 111
    LRR_RI; leucine-rich repeat [structural motif]

  2. NM_001348568.1 → NP_001335497.1  leucine-rich repeat-containing protein 4B precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    AC008743
    Consensus CDS
    CCDS42595.1
    UniProtKB/Swiss-Prot
    Q3ZCQ4, Q58F20, Q9NT99
    UniProtKB/TrEMBL
    A0PJJ4
    Related
    ENSP00000471502.1, ENST00000599957.5
    Conserved Domains (5) summary
    smart00013
    Location:57 → 90
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:311 → 361
    LRRCT; Leucine rich repeat C-terminal domain
    COG4886
    Location:76 → 297
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    pfam07679
    Location:364 → 453
    I-set; Immunoglobulin I-set domain
    sd00033
    Location:88 → 111
    LRR_RI; leucine-rich repeat [structural motif]

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    50516892..50568435 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006723506.4 → XP_006723569.1  leucine-rich repeat-containing protein 4B isoform X1

    See identical proteins and their annotated locations for XP_006723569.1

    UniProtKB/Swiss-Prot
    Q3ZCQ4, Q58F20, Q9NT99
    UniProtKB/TrEMBL
    A0PJJ4
    Conserved Domains (5) summary
    smart00013
    Location:57 → 90
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:311 → 361
    LRRCT; Leucine rich repeat C-terminal domain
    COG4886
    Location:76 → 297
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    pfam07679
    Location:364 → 453
    I-set; Immunoglobulin I-set domain
    sd00033
    Location:88 → 111
    LRR_RI; leucine-rich repeat [structural motif]

  2. XM_011527520.4 → XP_011525822.1  leucine-rich repeat-containing protein 4B isoform X1

    See identical proteins and their annotated locations for XP_011525822.1

    UniProtKB/Swiss-Prot
    Q3ZCQ4, Q58F20, Q9NT99
    UniProtKB/TrEMBL
    A0PJJ4
    Conserved Domains (5) summary
    smart00013
    Location:57 → 90
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:311 → 361
    LRRCT; Leucine rich repeat C-terminal domain
    COG4886
    Location:76 → 297
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    pfam07679
    Location:364 → 453
    I-set; Immunoglobulin I-set domain
    sd00033
    Location:88 → 111
    LRR_RI; leucine-rich repeat [structural motif]

  3. XM_005259429.6 → XP_005259486.1  leucine-rich repeat-containing protein 4B isoform X1

    See identical proteins and their annotated locations for XP_005259486.1

    UniProtKB/Swiss-Prot
    Q3ZCQ4, Q58F20, Q9NT99
    UniProtKB/TrEMBL
    A0PJJ4
    Conserved Domains (5) summary
    smart00013
    Location:57 → 90
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:311 → 361
    LRRCT; Leucine rich repeat C-terminal domain
    COG4886
    Location:76 → 297
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    pfam07679
    Location:364 → 453
    I-set; Immunoglobulin I-set domain
    sd00033
    Location:88 → 111
    LRR_RI; leucine-rich repeat [structural motif]

  4. XM_047439720.1 → XP_047295676.1  leucine-rich repeat-containing protein 4B isoform X1

    UniProtKB/Swiss-Prot
    Q3ZCQ4, Q58F20, Q9NT99
    UniProtKB/TrEMBL
    A0PJJ4

  5. XM_047439721.1 → XP_047295677.1  leucine-rich repeat-containing protein 4B isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    53605741..53657264 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NT99.3 GenPept UniProtKB/Swiss-Prot:Q9NT99

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