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LRTM2 leucine rich repeats and transmembrane domains 2 [ Homo sapiens (human) ]

Gene ID: 654429, updated on 11-Apr-2024

Summary

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Official Symbol
LRTM2provided by HGNC
Official Full Name
leucine rich repeats and transmembrane domains 2provided by HGNC
Primary source
HGNC:HGNC:32443
See related
Ensembl:ENSG00000166159 AllianceGenome:HGNC:32443
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
Summary
Predicted to enable Roundabout binding activity and heparin binding activity. Predicted to be involved in axon guidance and negative chemotaxis. Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Restricted expression toward brain (RPKM 3.3) See more
Orthologs
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Genomic context

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Location:
12p13.33
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (1820565..1836753)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (1816705..1832896)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (1929731..1945919)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene calcium voltage-gated channel auxiliary subunit alpha2delta 4 Neighboring gene uncharacterized LOC105369602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1913659-1914581 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5812 Neighboring gene uncharacterized LOC105369601 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1929301-1930047 Neighboring gene Sharpr-MPRA regulatory region 2999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1937325-1937864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1939727-1940340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1944610-1945110 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1953159-1954115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1979781-1980282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1980283-1980782 Neighboring gene lysosomal associated membrane protein 1 pseudogene 1 Neighboring gene uncharacterized LOC124902858

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. A genome-wide association study of behavioral disinhibition. McGue M, et al. Behav Genet, 2013 Sep. PMID 23942779, Free PMC Article
  2. Sequential genome-wide CRISPR-Cas9 screens identify genes regulating cell-surface expression of tetraspanins. Yang J, et al. Cell Rep, 2023 Feb 28. PMID 36724073
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
  5. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Huttlin EL, et al. Cell, 2021 May 27. PMID 33961781, Free PMC Article

See all (7) 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

EBI GWAS Catalog

Description
A genome-wide association study of behavioral disinhibition.
EBI GWAS Catalog

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Clone Names

  • FLJ42697

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables Roundabout binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables heparin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of synapse assembly IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
leucine-rich repeat and transmembrane domain-containing protein 2

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_001039029.3 → NP_001034118.1  leucine-rich repeat and transmembrane domain-containing protein 2 precursor

    See identical proteins and their annotated locations for NP_001034118.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the shortest transcript. Variants 1-3 encode the same protein.
    Source sequence(s)
    AC005343, AK095610, BC036868, BX115405, DA336140, DA418133
    Consensus CDS
    CCDS31726.1
    UniProtKB/Swiss-Prot
    A7E2U6, Q8N967
    Related
    ENSP00000299194.1, ENST00000299194.6
    Conserved Domains (6) summary
    TIGR00864
    Location:174 → 261
    PCC; polycystin cation channel protein
    smart00013
    Location:39 → 70
    LRRNT; Leucine rich repeat N-terminal domain
    sd00033
    Location:51 → 72
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:92 → 152
    LRR_8; Leucine rich repeat
    cl26018
    Location:57 → 202
    NEL; C-terminal novel E3 ligase, LRR-interacting
    cl27544
    Location:265 → 335
    Herpes_glycop_D; Herpesvirus glycoprotein D/GG/GX domain

  2. NM_001163925.2 → NP_001157397.1  leucine-rich repeat and transmembrane domain-containing protein 2 precursor

    See identical proteins and their annotated locations for NP_001157397.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1-3 encode the same protein.
    Source sequence(s)
    AC005343, AK095610, AK124687, BC036868, BX115405, DA336140
    Consensus CDS
    CCDS31726.1
    UniProtKB/Swiss-Prot
    A7E2U6, Q8N967
    Related
    ENSP00000446278.1, ENST00000543818.5
    Conserved Domains (6) summary
    TIGR00864
    Location:174 → 261
    PCC; polycystin cation channel protein
    smart00013
    Location:39 → 70
    LRRNT; Leucine rich repeat N-terminal domain
    sd00033
    Location:51 → 72
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:92 → 152
    LRR_8; Leucine rich repeat
    cl26018
    Location:57 → 202
    NEL; C-terminal novel E3 ligase, LRR-interacting
    cl27544
    Location:265 → 335
    Herpes_glycop_D; Herpesvirus glycoprotein D/GG/GX domain

  3. NM_001163926.2 → NP_001157398.1  leucine-rich repeat and transmembrane domain-containing protein 2 precursor

    See identical proteins and their annotated locations for NP_001157398.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1-3 encode the same protein.
    Source sequence(s)
    AC005343, AK095610, BC146894, BX115405, DA336140
    Consensus CDS
    CCDS31726.1
    UniProtKB/Swiss-Prot
    A7E2U6, Q8N967
    Related
    ENSP00000444737.1, ENST00000535041.5
    Conserved Domains (6) summary
    TIGR00864
    Location:174 → 261
    PCC; polycystin cation channel protein
    smart00013
    Location:39 → 70
    LRRNT; Leucine rich repeat N-terminal domain
    sd00033
    Location:51 → 72
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:92 → 152
    LRR_8; Leucine rich repeat
    cl26018
    Location:57 → 202
    NEL; C-terminal novel E3 ligase, LRR-interacting
    cl27544
    Location:265 → 335
    Herpes_glycop_D; Herpesvirus glycoprotein D/GG/GX domain

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    1820565..1836753
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047429421.1 → XP_047285377.1  leucine-rich repeat and transmembrane domain-containing protein 2 isoform X1

  2. XM_011521015.2 → XP_011519317.1  leucine-rich repeat and transmembrane domain-containing protein 2 isoform X2

    See identical proteins and their annotated locations for XP_011519317.1

    UniProtKB/Swiss-Prot
    A7E2U6, Q8N967
    Conserved Domains (6) summary
    TIGR00864
    Location:174 → 261
    PCC; polycystin cation channel protein
    smart00013
    Location:39 → 70
    LRRNT; Leucine rich repeat N-terminal domain
    sd00033
    Location:51 → 72
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:92 → 152
    LRR_8; Leucine rich repeat
    cl26018
    Location:57 → 202
    NEL; C-terminal novel E3 ligase, LRR-interacting
    cl27544
    Location:265 → 335
    Herpes_glycop_D; Herpesvirus glycoprotein D/GG/GX domain

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654718.1 Reference GRCh38.p14 PATCHES

    Range
    162709..178897
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054332284.1 → XP_054188259.1  leucine-rich repeat and transmembrane domain-containing protein 2 isoform X1

  2. XM_054332285.1 → XP_054188260.1  leucine-rich repeat and transmembrane domain-containing protein 2 isoform X2

    UniProtKB/Swiss-Prot
    A7E2U6, Q8N967

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    1816705..1832896
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373008.1 → XP_054228983.1  leucine-rich repeat and transmembrane domain-containing protein 2 isoform X1

  2. XM_054373009.1 → XP_054228984.1  leucine-rich repeat and transmembrane domain-containing protein 2 isoform X2

    UniProtKB/Swiss-Prot
    A7E2U6, Q8N967
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N967.1 GenPept UniProtKB/Swiss-Prot:Q8N967

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