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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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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

Gene LinkOut

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