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

    Gene ID: 94030, updated on 2-Nov-2024

    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 postsynaptic density membrane. [provided by Alliance of Genome Resources, Nov 2024]
    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_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (50516892..50568435, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (53605741..53657264, complement)
    RS_2024_09 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 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. Protein interaction landscapes revealed by advanced in vivo cross-linking-mass spectrometry. Wheat A, et al. Proc Natl Acad Sci U S A, 2021 Aug 10. PMID 34349018, Free PMC Article
    5. 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

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    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 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_2024_08

    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

    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

    Gene LinkOut

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