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    APTR Alu-mediated CDKN1A/p21 transcriptional regulator [ Homo sapiens (human) ]

    Gene ID: 100505854, updated on 8-Mar-2024

    Summary

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    Official Symbol
    APTRprovided by HGNC
    Official Full Name
    Alu-mediated CDKN1A/p21 transcriptional regulatorprovided by HGNC
    Primary source
    HGNC:HGNC:44173
    See related
    Ensembl:ENSG00000214293 MIM:616048; AllianceGenome:HGNC:44173
    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
    RSBN1L-AS1
    Expression
    Ubiquitous expression in thyroid (RPKM 5.3), testis (RPKM 4.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See APTR in Genome Data Viewer
    Location:
    7q11.23
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (77657660..77697345, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (78909575..78949254, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (77286977..77326662, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901681 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77154891-77155392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77155393-77155892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26206 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18324 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18325 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18326 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:77169285-77169866 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:77185513-77186127 Neighboring gene protein tyrosine phosphatase non-receptor type 12 Neighboring gene uncharacterized LOC105375363 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:77305655-77305829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77321385-77321884 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:77324871-77325766 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:77325767-77326662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18329 Neighboring gene round spermatid basic protein 1 like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77393580-77394080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26209 Neighboring gene transmembrane protein 60 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18331 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:77464234-77464734 Neighboring gene putative homeodomain transcription factor 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:77501601-77502172 Neighboring gene uncharacterized LOC124901682

    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. Down-Regulation of APTR and it's Diagnostic Value in Papillary and Anaplastic Thyroid Cancer. Zhang K, et al. Pathol Oncol Res, 2020 Jan. PMID 30539519
    2. Long noncoding RNA APTR contributes to osteosarcoma progression through repression of miR-132-3p and upregulation of yes-associated protein 1. Guan H, et al. J Cell Physiol, 2019 Jun. PMID 30317613
    3. APTR is a prognostic marker in cirrhotic patients with portal hypertension during TIPS procedure. Yu S, et al. Gene, 2018 Mar 1. PMID 29274906
    4. A new lncRNA, APTR, associates with and represses the CDKN1A/p21 promoter by recruiting polycomb proteins. Negishi M, et al. PLoS One, 2014. PMID 24748121, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Down-Regulation of APTR and it's Diagnostic Value in Papillary and Anaplastic Thyroid Cancer.
      Title: Down-Regulation of APTR and it's Diagnostic Value in Papillary and Anaplastic Thyroid Cancer.
    2. APTR contributed to osteosarcoma progression through repression of miR-132-3p and upregulation of YAP1 expression.
      Title: Long noncoding RNA APTR contributes to osteosarcoma progression through repression of miR-132-3p and upregulation of yes-associated protein 1.
    3. Results show that portal venous levels of APTR was significantly decreased after TIPS treatment and its aberrant expression levels were positively correlated with Model for End Stage Liver Disease (MELD), portal hepatic venous pressure gradient (PHPG) in patients. Higher APTR expression in portal vein was associated with poor prognosis.
      Title: APTR is a prognostic marker in cirrhotic patients with portal hypertension during TIPS procedure.
    4. APTR associates with the promoter of CDKN1A/p21 and this association requires a complementary-Alu sequence encoded in APTR. A different module of APTR associates with and recruits the Polycomb repressive complex 2 (PRC2) to repress the p21 promote
      Title: A new lncRNA, APTR, associates with and represses the CDKN1A/p21 promoter by recruiting polycomb proteins.
    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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    Markers

    Homology

    Other Names

    • Alu-mediated CDKN1A/p21 transcriptional regulator (non-protein coding)
    • RSBN1L antisense RNA 1 (non-protein coding)

    Clone Names

    • AC090421.1

    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_038361.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the shortest transcript.
      Source sequence(s)
      AC004955, AC090421

    2. NR_134251.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 5' region and contains two alternate 3' exons, compared to variant 1.
      Source sequence(s)
      AC004955, AC090421
      Related
      ENST00000430801.6

    3. NR_134253.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate 3'-terminal exon, compared to variant 1.
      Source sequence(s)
      AC004955, AC090421
      Related
      ENST00000665948.1

    4. NR_134254.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an internal exon and uses an alternate 3'-terminal exon, compared to variant 1.
      Source sequence(s)
      AC004955, AC090421
      Related
      ENST00000440088.5

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      77657660..77697345 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      78909575..78949254 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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