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    ARLNC1 androgen receptor regulated long noncoding RNA 1 [ Homo sapiens (human) ]

    Gene ID: 100996425, updated on 17-Sep-2024

    Summary

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    Official Symbol
    ARLNC1provided by HGNC
    Official Full Name
    androgen receptor regulated long noncoding RNA 1provided by HGNC
    Primary source
    HGNC:HGNC:53032
    See related
    Ensembl:ENSG00000260896 MIM:618053; AllianceGenome:HGNC:53032
    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
    PRCAT47; LINC02170
    Expression
    Biased expression in prostate (RPKM 1.3), testis (RPKM 0.3) and 8 other tissues See more
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    Genomic context

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    See ARLNC1 in Genome Data Viewer
    Location:
    16q23.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (80828735..80892596, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (86890597..86954461, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (80862632..80926493, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11168 Neighboring gene long intergenic non-protein coding RNA 1227 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:80641586-80642086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:80642087-80642587 Neighboring gene chromodomain Y like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11170 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:80700312-80701272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11171 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:80760822-80761322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:80761323-80761823 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7745 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7747 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11172 Neighboring gene Sharpr-MPRA regulatory region 7727 Neighboring gene NANOG hESC enhancer GRCh37_chr16:81032399-81032965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7748 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11175 Neighboring gene C-X9-C motif containing 2 Neighboring gene CENPN antisense RNA 1 Neighboring gene centromere protein N

    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. LOC100996425 acts as a promoter in prostate cancer by mediating hepatocyte nuclear factor 4A and the AMPK/mTOR pathway. Wang X, et al. J Cell Mol Med, 2021 Sep. PMID 34309216, Free PMC Article
    2. Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression. Zhang Y, et al. Nat Genet, 2018 Jun. PMID 29808028, Free PMC Article
    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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LOC100996425 acts as a promoter in prostate cancer by mediating hepatocyte nuclear factor 4A and the AMPK/mTOR pathway.
      Title: LOC100996425 acts as a promoter in prostate cancer by mediating hepatocyte nuclear factor 4A and the AMPK/mTOR pathway.
    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

    General gene information

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    Other Names

    • AR-regulated long noncoding RNA 1
    • long intergenic non-protein coding RNA 2170
    • prostate cancer-associated 47

    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_131947.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AA876610, AC009070, AK093002, BG166652, CR748417, DA950319
      Related
      ENST00000651582.1

    2. NR_131948.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an internal exon, compared to variant 1.
      Source sequence(s)
      AA876610, AC009070, AK093002, BG166652, DA950319
      Related
      ENST00000562231.6

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      80828735..80892596 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      86890597..86954461 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.

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    Research Materials