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

Gene ID: 283902, updated on 10-Oct-2023

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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Location:
16q22.3
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (73092349..73093774)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (78910078..78911503)
105.20220307 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
  • 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_2023_10

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

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