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LRRTM4 leucine rich repeat transmembrane neuronal 4 [ Homo sapiens (human) ]

Gene ID: 80059, updated on 5-Sep-2021

Summary

Official Symbol
LRRTM4provided by HGNC
Official Full Name
leucine rich repeat transmembrane neuronal 4provided by HGNC
Primary source
HGNC:HGNC:19411
See related
Ensembl:ENSG00000176204 MIM:610870
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
Expression
Biased expression in brain (RPKM 5.6) and lung (RPKM 0.2) See more
Orthologs
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Genomic context

See LRRTM4 in Genome Data Viewer
Location:
2p12
Exon count:
4
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (76747685..77522376, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (76974811..77749502, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374814 Neighboring gene RN7SK pseudogene 164 Neighboring gene uncharacterized LOC105374815 Neighboring gene RNA, 5S ribosomal pseudogene 98 Neighboring gene LRRTM4 antisense RNA 1 Neighboring gene 2p12 distal HERV-mediated recombination region Neighboring gene tRNA-Pro (anticodon AGG) 5-1 Neighboring gene uncharacterized LOC101927967 Neighboring gene RPL38 pseudogene 2

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

Associated conditions

Description Tests
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ12568, MGC120633, MGC120636

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in synapse organization IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
located_in integral component of postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
leucine-rich repeat transmembrane neuronal protein 4

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.

Genomic

  1. NG_053082.1 RefSeqGene

    Range
    5001..779711
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001134745.3NP_001128217.1  leucine-rich repeat transmembrane neuronal protein 4 isoform a precursor

    See identical proteins and their annotated locations for NP_001128217.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) and variant 3 encode the same isoform (a).
    Source sequence(s)
    AC068616, AI079273, AK126961, AY358324
    Consensus CDS
    CCDS46346.1
    UniProtKB/Swiss-Prot
    Q86VH4
    UniProtKB/TrEMBL
    Q6ZT31
    Related
    ENSP00000387297.1, ENST00000409884.6
    Conserved Domains (3) summary
    sd00031
    Location:303315
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:6486
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:133193
    LRR_8; Leucine rich repeat
  2. NM_001282924.3NP_001269853.1  leucine-rich repeat transmembrane neuronal protein 4 isoform a precursor

    See identical proteins and their annotated locations for NP_001269853.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has an alternate splice site in the 5' UTR, compared to variant 1. Variants 1 and 3 encode the same isoform a.
    Source sequence(s)
    AC068616, AC079614, AI079273, AK122612, AY358324
    Consensus CDS
    CCDS46346.1
    UniProtKB/Swiss-Prot
    Q86VH4
    UniProtKB/TrEMBL
    B3KV11
    Related
    ENSP00000386357.1, ENST00000409093.1
    Conserved Domains (3) summary
    sd00031
    Location:303315
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:6486
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:133193
    LRR_8; Leucine rich repeat
  3. NM_001282928.3NP_001269857.1  leucine-rich repeat transmembrane neuronal protein 4 isoform c precursor

    See identical proteins and their annotated locations for NP_001269857.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an exon in the 5' region and its transcription extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR. It initiates translation at an alternate start codon compared to variant 1 and encodes isoform c, which distinct N- and C-termini and is shorter than isoform a.
    Source sequence(s)
    AC079614, AK122612, BC098301
    Consensus CDS
    CCDS74530.1
    UniProtKB/TrEMBL
    B3KV11, Q4KMX1
    Related
    ENSP00000386286.1, ENST00000409282.1
    Conserved Domains (3) summary
    sd00031
    Location:304316
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:6587
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:134194
    LRR_8; Leucine rich repeat
  4. NM_001330370.2NP_001317299.1  leucine-rich repeat transmembrane neuronal protein 4 isoform d precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an exon in the 5' region and initiates translation at an alternate start codon compared to variant 1. The encoded isoform (d) has a distinct N-terminus and is longer than isoform a.
    Source sequence(s)
    AC068616, AC079614
    Consensus CDS
    CCDS82475.1
    UniProtKB/TrEMBL
    B8ZZ84
    Related
    ENSP00000387228.1, ENST00000409911.5
    Conserved Domains (4) summary
    cd00116
    Location:85291
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00031
    Location:304316
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:6587
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:134194
    LRR_8; Leucine rich repeat
  5. NM_024993.6NP_079269.4  leucine-rich repeat transmembrane neuronal protein 4 isoform b precursor

    See identical proteins and their annotated locations for NP_079269.4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks the 3' terminal exon and its transcription extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR compared to variant 1. It encodes isoform b which is shorter and has a distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AC079614
    Consensus CDS
    CCDS46347.1
    UniProtKB/Swiss-Prot
    Q86VH4
    Related
    ENSP00000386236.3, ENST00000409088.3
    Conserved Domains (3) summary
    sd00031
    Location:303315
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:6486
    LRR_RI; leucine-rich repeat [structural motif]
    cd21340
    Location:90311
    PPP1R42; protein phosphatase 1 regulatory subunit 42

RNA

  1. NR_146416.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC068616, AC079614

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    76747685..77522376 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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