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    PCAT4 prostate cancer associated transcript 4 [ Homo sapiens (human) ]

    Gene ID: 118425, updated on 10-Oct-2023

    Summary

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    Official Symbol
    PCAT4provided by HGNC
    Official Full Name
    prostate cancer associated transcript 4provided by HGNC
    Primary source
    HGNC:HGNC:24853
    See related
    Ensembl:ENSG00000251321 MIM:609717; AllianceGenome:HGNC:24853
    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
    GDEP; PCA4; PCAN1
    Expression
    Restricted expression toward prostate (RPKM 24.7) See more
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    Genomic context

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    See PCAT4 in Genome Data Viewer
    Location:
    4q21.21
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (79827471..79863247)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (83163872..83199659)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (80748625..80784401)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2469 Neighboring gene uncharacterized LOC105377302 Neighboring gene Sharpr-MPRA regulatory region 5843 Neighboring gene small nucleolar RNA SNORA75 Neighboring gene MPRA-validated peak5063 silencer Neighboring gene ANTXR cell adhesion molecule 2 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:80859151-80859758 Neighboring gene MPRA-validated peak5064 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr4:80885254-80885815 Neighboring gene uncharacterized LOC124900918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21653 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:80997503-80998702 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:81002404-81003603 Neighboring gene karyopherin subunit alpha 2 pseudogene 1

    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. Functional characterization of the GDEP promoter and three enhancer elements in retinoblastoma and prostate cell lines. Cross DS, et al. Med Oncol, 2008. PMID 18188713
    2. Molecular cloning and analysis of the human PCAN1 (GDEP) promoter. Liu W, et al. Cell Mol Biol Lett, 2007. PMID 17468839, Free PMC Article
    3. Expression and initial promoter characterization of PCAN1 in retinal tissue and prostate cell lines. Cross D, et al. Med Oncol, 2004. PMID 15299187
    4. Identification of a gene frequently mutated in prostate tumors. Reding DJ, et al. Med Oncol, 2001. PMID 11917942
    5. GDEP, a new gene differentially expressed in normal prostate and prostate cancer. Olsson P, et al. Prostate, 2001 Sep 15. PMID 11536302

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. These results suggested that two functional NKX3.1 binding sites located at -1848 to -1836 and -803 to -791 upstream of the PCAN1 gene were involved in the positive regulation of PCAN1 gene transcription by NKX3.1.
      Title: Characterization of two functional NKX3.1 binding sites upstream of the PCAN1 gene that are involved in the positive regulation of PCAN1 gene transcription.
    2. Study reports cloning a 2.6-kb fragment of the 5' flanking region of the PCAN1 gene which represented promoter activity and was regulated by NKX3.1, p53, Sp1, Pten and 9-cis-RA in the luciferase reporter assay.
      Title: Molecular cloning and analysis of the human PCAN1 (GDEP) promoter.
    3. a 1.5 kb prostate-specific promoter from the proximal region of the GDEP gene was identified. A smaller 0.5 kb promoter exhibited minimal activity in the retinoblastoma cell line Y79, but not in the prostate cells tested.
      Title: Functional characterization of the GDEP promoter and three enhancer elements in retinoblastoma and prostate cell lines.
    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

    Other Names

    • gene differentially expressed in prostate
    • prostate cancer associated transcript 4 (non-protein coding)
    • prostate cancer gene 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_026555.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC118141, AK056825
      Related
      ENST00000504263.1

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      79827471..79863247
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      83163872..83199659
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_058168.2: Suppressed sequence

      Description
      NM_058168.2: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
    Nucleotide Protein
    Heading Accession and Version

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