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    COL18A1-AS1 COL18A1 antisense RNA 1 [ Homo sapiens (human) ]

    Gene ID: 378832, updated on 8-Nov-2023

    Summary

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    Official Symbol
    COL18A1-AS1provided by HGNC
    Official Full Name
    COL18A1 antisense RNA 1provided by HGNC
    Primary source
    HGNC:HGNC:23132
    See related
    Ensembl:ENSG00000183535 AllianceGenome:HGNC:23132
    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
    PRED80; C21orf123; NCRNA00175
    Expression
    Restricted expression toward kidney (RPKM 1.7) See more
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    Genomic context

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    Location:
    21q22.3
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (45419716..45425070, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (43785552..43790906, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (46839631..46844985, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46824235-46824935 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46827875-46828666 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46828667-46829459 Neighboring gene COL18A1 antisense RNA 2 Neighboring gene collagen type XVIII alpha 1 chain Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46833102-46833725 Neighboring gene breast cancer associated ESR1 regulating natural antisense transcript 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46834349-46834972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46834973-46835596 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46838464-46839218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46839219-46839973 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46839974-46840729 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46841485-46842239 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46844008-46844605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46844606-46845204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46847276-46847948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46850948-46851946 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46851947-46852943 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46854143-46854992 Neighboring gene uncharacterized LOC124905042 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46858777-46859506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46859507-46860236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46860237-46860966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46862147-46862656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46870853-46871354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46871355-46871854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46874827-46875383 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46885176-46885740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46885741-46886304 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46894762-46895262 Neighboring gene microRNA 6815

    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. Restoring the epigenetically silenced lncRNA COL18A1-AS1 represses ccRCC progression by lipid browning via miR-1286/KLF12 axis. Liu Y, et al. Cell Death Dis, 2022 Jul 4. PMID 35787628, Free PMC Article
    2. Multiple loci influencing hippocampal degeneration identified by genome scan. Melville SA, et al. Ann Neurol, 2012 Jul. PMID 22745009, Free PMC Article
    3. Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. Warnatz HJ, et al. Nucleic Acids Res, 2010 Oct. PMID 20494980, 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. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Restoring the epigenetically silenced lncRNA COL18A1-AS1 represses ccRCC progression by lipid browning via miR-1286/KLF12 axis.
      Title: Restoring the epigenetically silenced lncRNA COL18A1-AS1 represses ccRCC progression by lipid browning via miR-1286/KLF12 axis.
    2. The COL18A1-AS1/C21orf123 promoter is activated by serum depletion according to promoter reporter assays in HEK 293 cells.
      Title: Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Multiple loci influencing hippocampal degeneration identified by genome scan.
    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

    General gene information

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    Other Names

    • COL18A1 antisense RNA 1 (non-protein coding)

    Clone Names

    • MGC129884, MGC129885

    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_027498.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternative splice site compared to variant 1.
      Source sequence(s)
      AK096071, BC111539, BX322563
      Related
      ENST00000485206.1

    2. NR_028082.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AK096071, BC111539, BX322563
      Related
      ENST00000397787.5

    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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      45419716..45425070 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791815.1 Reference GRCh38.p14 PATCHES

      Range
      36951..42305 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      43785552..43790906 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_199175.1: Suppressed sequence

      Description
      NM_199175.1: This RefSeq was permanently suppressed because it is now thought that this gene does not encode a protein.
    Nucleotide Protein
    Heading Accession and Version

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