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

Gene ID: 151354, updated on 2-Nov-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, Nov 2024]
Expression
Broad expression in colon (RPKM 29.3), small intestine (RPKM 11.3) and 16 other tissues See more
Orthologs
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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 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)

Genotypes

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.

Chemical Information
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