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    HCCAT5 hepatocellular carcinoma associated transcript 5 [ Homo sapiens (human) ]

    Gene ID: 283902, updated on 17-Sep-2024

    Summary

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    Official Symbol
    HCCAT5provided by HGNC
    Official Full Name
    hepatocellular carcinoma associated transcript 5provided by HGNC
    Primary source
    HGNC:HGNC:48612
    See related
    Ensembl:ENSG00000260880 MIM:615613; AllianceGenome:HGNC:48612
    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
    HTA; FJ222407
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See HCCAT5 in Genome Data Viewer
    Location:
    16q22.3
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (73092349..73093774)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (78910078..78911503)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (73126248..73127673)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903715 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:72910943-72912142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72912157-72912658 Neighboring gene zinc finger homeobox 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72923795-72924295 Neighboring gene Sharpr-MPRA regulatory region 11593 Neighboring gene Sharpr-MPRA regulatory region 14271 Neighboring gene VISTA enhancer hs16 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72995175-72995675 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73049174-73049674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11101 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73066446-73067008 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:73069350-73070204 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:73070205-73071057 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73074111-73074623 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:73078457-73078957 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:73081321-73081856 Neighboring gene uncharacterized LOC124903719 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:73082393-73082928 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73087036-73087536 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73087537-73088037 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:73089102-73089614 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7694 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7692 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:73091454-73092186 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7693 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73098351-73098972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73126852-73127352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73127353-73127853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11103 Neighboring gene HCCAT5-C16orf47 intergenic CAGE-defined high expression enhancer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:73186584-73187107 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73190308-73190808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73190809-73191309 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73204295-73204796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73204797-73205296 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:73205367-73206216 Neighboring gene NANOG hESC enhancer GRCh37_chr16:73230564-73231065 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:73266082-73267281 Neighboring gene uncharacterized LOC124903716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11105 Neighboring gene VISTA enhancer hs1724 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:73368016-73368182 Neighboring gene lncRNA oncogene in head and neck cancer 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 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. Molecular clone and functional study of a novel hepatoma associated gene. Liu Y, et al. Int J Oncol, 2013 Mar. PMID 23314567
    2. Identification of HTA as a novel-specific marker for human hepatocellular carcinoma. Liu Y, et al. J Cancer Res Clin Oncol, 2010 Aug. PMID 20130911
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    GeneRIFs: Gene References Into Functions

    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

    • hepatocellular carcinoma associated transcript 5 (non-protein coding)
    • hepatoma associated protein

    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_027756.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      FJ222407
      Related
      ENST00000569990.2

    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
      73092349..73093774
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      78910078..78911503
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001101347.1: Suppressed sequence

      Description
      NM_001101347.1: This RefSeq was permanently suppressed because it is now thought that this gene does not encode a protein.
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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