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

    Gene ID: 654429, updated on 27-Nov-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 located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward brain (RPKM 3.3) See more
    Orthologs
    mouse all
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    Genomic context

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    See LRTM2 in Genome Data Viewer
    Location:
    12p13.33
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (1820565..1836753)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (1816705..1832896)
    RS_2024_09 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)

    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

    Process Evidence Code Pubs
    involved_in positive regulation of synapse assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane 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_2024_08

    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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