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    LRATD1 LRAT domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 151354, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LRATD1provided by HGNC
    Official Full Name
    LRAT domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:20743
    See related
    Ensembl:ENSG00000162981 MIM:611234; AllianceGenome:HGNC:20743
    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
    NSE1; FAM84A; PP11517
    Summary
    Involved in cell morphogenesis and cell motility. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in colon (RPKM 29.3), small intestine (RPKM 11.3) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRATD1 in Genome Data Viewer
    Location:
    2p24.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (14632717..14651916)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (14663504..14682703)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (14772841..14792040)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985854 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_52900 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_52953 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_52989 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_52999 Neighboring gene NANOG hESC enhancer GRCh37_chr2:14337206-14337732 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:14371872-14372508 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:14372509-14373144 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:14394929-14395543 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:14395544-14396157 Neighboring gene long intergenic non-protein coding RNA 276 Neighboring gene RNA, U6 small nuclear 1288, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr2:14472914-14473113 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:14541927-14542484 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:14654042-14654593 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:14988479-14989049 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11184 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:15100270-15101469 Neighboring gene NBAS subunit of NRZ tethering complex Neighboring gene H3K4me1 hESC enhancers GRCh37_chr2:15182798-15183298 and GRCh37_chr2:15183299-15183799 Neighboring gene Sharpr-MPRA regulatory region 966 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:15213063-15213219 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:15224708-15225393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:15225394-15226078 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:15281925-15283124 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:15315340-15315550 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:15399317-15400143 Neighboring gene NANOG hESC enhancer GRCh37_chr2:15589330-15589831 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:15606309-15606502 Neighboring gene ribosomal protein S26 pseudogene 18 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:15672530-15672745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15346 Neighboring gene uncharacterized LOC105373440

    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. The direct miR-874-3p-target FAM84A promotes tumor development in papillary thyroid cancer. Ding Y, et al. Mol Oncol, 2021 May. PMID 33751775, Free PMC Article
    2. A gene encoding a family with sequence similarity 84, member A (FAM84A) enhanced migration of human colon cancer cells. Kobayashi T, et al. Int J Oncol, 2006 Aug. PMID 16820875
    3. Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. Fox CS, et al. PLoS Genet, 2012. PMID 22589738, Free PMC Article
    4. Bcl2-associated athanogene 3 interactome analysis reveals a new role in modulating proteasome activity. Chen Y, et al. Mol Cell Proteomics, 2013 Oct. PMID 23824909, Free PMC Article
    5. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Hillier LW, et al. Nature, 2005 Apr 7. PMID 15815621

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The direct miR-874-3p-target FAM84A promotes tumor development in papillary thyroid cancer.
      Title: The direct miR-874-3p-target FAM84A promotes tumor development in papillary thyroid cancer.
    2. up-regulation of FAM84A may play a critical role in progression of colon cancer
      Title: A gene encoding a family with sequence similarity 84, member A (FAM84A) enhanced migration of human colon cancer cells.
    Submit: New GeneRIF Correction

    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
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    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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    Markers

    Homology

    Clone Names

    • FLJ35392

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cell motility IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell motility IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein LRATD1
    Names
    family with sequence similarity 84 member A
    neurologic sensory protein 1
    neurological/sensory 1
    protein FAM84A

    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_001369364.1 → NP_001356293.1  protein LRATD1

      Status: VALIDATED

      Source sequence(s)
      AC011897
      Consensus CDS
      CCDS1684.1
      UniProtKB/Swiss-Prot
      A6NP76, Q86UZ2, Q8NAH7, Q8TAM5, Q96KN4
      UniProtKB/TrEMBL
      B2RB24
      Related
      ENSP00000330681.4, ENST00000331243.4
      Conserved Domains (1) summary
      cl21534
      Location:143 → 223
      NLPC_P60; NlpC/P60 family

    2. NM_145175.4 → NP_660158.2  protein LRATD1

      See identical proteins and their annotated locations for NP_660158.2

      Status: VALIDATED

      Source sequence(s)
      AC011897, AJ417080, BX113099, HY017941
      Consensus CDS
      CCDS1684.1
      UniProtKB/Swiss-Prot
      A6NP76, Q86UZ2, Q8NAH7, Q8TAM5, Q96KN4
      UniProtKB/TrEMBL
      B2RB24
      Related
      ENSP00000295092.2, ENST00000295092.3
      Conserved Domains (1) summary
      cl21534
      Location:143 → 223
      NLPC_P60; NlpC/P60 family

    RNA

    1. NR_144632.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC011897, BM998595

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      14632717..14651916
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      14663504..14682703
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001291410.1: Suppressed sequence

      Description
      NM_001291410.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96KN4.2 GenPept UniProtKB/Swiss-Prot:Q96KN4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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