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    LNCAROD lncRNA activating regulator of DKK1 [ Homo sapiens (human) ]

    Gene ID: 101928687, updated on 10-Oct-2023

    Summary

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    Official Symbol
    LNCARODprovided by HGNC
    Official Full Name
    lncRNA activating regulator of DKK1provided by HGNC
    Primary source
    HGNC:HGNC:50913
    See related
    Ensembl:ENSG00000231131 AllianceGenome:HGNC:50913
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    A-ROD; LINC01468; lnc-MBL2-4
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See LNCAROD in Genome Data Viewer
    Location:
    10q21.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (52450877..52470533, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (53297467..53317123, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (54210637..54230293, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L31 pseudogene 44 Neighboring gene THAP domain containing 12 pseudogene 3 Neighboring gene NANOG hESC enhancer GRCh37_chr10:54212085-54212953 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:54229543-54230135 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:54258936-54260135 Neighboring gene uncharacterized LOC124902426 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:54315609-54315769 Neighboring gene uncharacterized LOC105378305 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:54421868-54422425 Neighboring gene mannose binding lectin 2

    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. Analysis of lncRNA sequences: FAM3D-AS1, LINC01230, LINC01315 and LINC01468 in endometrial cancer. Bieńkiewicz J, et al. BMC Cancer, 2022 Mar 29. PMID 35351056, Free PMC Article
    2. Long ncRNA A-ROD activates its target gene DKK1 at its release from chromatin. Ntini E, et al. Nat Commun, 2018 Apr 24. PMID 29691407, Free PMC Article
    3. Genetic Association of a Gain-of-Function IFNGR1 Polymorphism and the Intergenic Region LNCAROD/DKK1 With Behçet's Disease. Ortiz Fernández L, et al. Arthritis Rheumatol, 2021 Jul. PMID 33393726, Free PMC Article
    4. LNCAROD is stabilized by m6A methylation and promotes cancer progression via forming a ternary complex with HSPA1A and YBX1 in head and neck squamous cell carcinoma. Ban Y, et al. Mol Oncol, 2020 Jun. PMID 32216017, Free PMC Article
    5. Long non-coding RNA deregulation in tongue squamous cell carcinoma. Gao W, et al. Biomed Res Int, 2014. PMID 25045670, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Analysis of lncRNA sequences: FAM3D-AS1, LINC01230, LINC01315 and LINC01468 in endometrial cancer.
      Title: Analysis of lncRNA sequences: FAM3D-AS1, LINC01230, LINC01315 and LINC01468 in endometrial cancer.
    2. Genetic Association of a Gain-of-Function IFNGR1 Polymorphism and the Intergenic Region LNCAROD/DKK1 With Behcet's Disease.
      Title: Genetic Association of a Gain-of-Function IFNGR1 Polymorphism and the Intergenic Region LNCAROD/DKK1 With Behçet's Disease.
    3. LNCAROD is stabilized by m6A methylation and promotes cancer progression via forming a ternary complex with HSPA1A and YBX1 in head and neck squamous cell carcinoma.
      Title: LNCAROD is stabilized by m6A methylation and promotes cancer progression via forming a ternary complex with HSPA1A and YBX1 in head and neck squamous cell carcinoma.
    4. A-ROD enhances DKK1 transcription via its nascent spliced released form.
      Title: Long ncRNA A-ROD activates its target gene DKK1 at its release from chromatin.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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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    Other Names

    • Activating Regulator of DKK1
    • long intergenic non-protein coding RNA 1468

    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.

    RNA

    1. NR_120641.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AC009986, AL731545

    2. NR_120642.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two exons and contains an alternate 5' terminal exon, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AC009986
      Related
      ENST00000435813.6

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      52450877..52470533 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      53297467..53317123 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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

    Other Literature Sources
    Molecular Biology Databases
    Research Materials