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    PRDM4 PR/SET domain 4 [ Homo sapiens (human) ]

    Gene ID: 11108, updated on 14-Nov-2024

    Summary

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    Official Symbol
    PRDM4provided by HGNC
    Official Full Name
    PR/SET domain 4provided by HGNC
    Primary source
    HGNC:HGNC:9348
    See related
    Ensembl:ENSG00000110851 MIM:605780; AllianceGenome:HGNC:9348
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PFM1
    Summary
    The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorigenesis. An elevated expression level of this gene has been observed in PC12 cells treated with nerve growth factor, beta polypeptide (NGF). This gene is located in a chromosomal region that is thought to contain tumor suppressor genes. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in kidney (RPKM 10.4), esophagus (RPKM 8.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PRDM4 in Genome Data Viewer
    Location:
    12q23.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (107732871..107761137, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (107696363..107724788, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (108126648..108154914, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene PWP1 homolog, endonuclein Neighboring gene uncharacterized LOC124903010 Neighboring gene ribosomal protein L17 pseudogene 38 Neighboring gene PRDM4 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6956 Neighboring gene achaete-scute family bHLH transcription factor 4 Neighboring gene uncharacterized LOC105369963

    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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. results demonstrate that YAP promotes cell invasion by inducing leukocyte-specific integrin expression, and identify PRDM4 as a novel transcription factor for YAP targets.
      Title: PRDM4 mediates YAP-induced cell invasion by activating leukocyte-specific integrin β2 expression.
    2. Both Prdm 4 and Prdm 5 are expressed in human corneal endothelium, primary hCECs and in HCECs-12 cells, characterised by expression of the Na(+)/K(+)-ATPase.
      Title: Identification of Prdm genes in human corneal endothelium.
    3. PRDM4 zinc knuckle by NMR spectroscopy.
      Title: The PR/SET domain in PRDM4 is preceded by a zinc knuckle.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC45046

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables histone methyltransferase binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of histone methyltransferase complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    PR domain zinc finger protein 4
    Names
    PR domain 4
    PR domain containing 4
    PR domain-containing protein 4
    PR-domain zinc-finger protein PFM1

    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.

    mRNA and Protein(s)

    1. NM_012406.4 → NP_036538.3  PR domain zinc finger protein 4

      See identical proteins and their annotated locations for NP_036538.3

      Status: REVIEWED

      Source sequence(s)
      AK056378, AL133083, BU502236
      Consensus CDS
      CCDS9115.1
      UniProtKB/Swiss-Prot
      Q9UFA6, Q9UKN5
      UniProtKB/TrEMBL
      B3KPI0
      Related
      ENSP00000228437.5, ENST00000228437.10
      Conserved Domains (4) summary
      sd00017
      Location:620 → 640
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:618 → 640
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:632 → 657
      zf-H2C2_2; Zinc-finger double domain
      cl02566
      Location:426 → 533
      SET; SET domain

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      107732871..107761137 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005268593.2 → XP_005268650.1  PR domain zinc finger protein 4 isoform X1

      See identical proteins and their annotated locations for XP_005268650.1

      UniProtKB/TrEMBL
      B3KPI0
      Conserved Domains (4) summary
      sd00017
      Location:627 → 647
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:625 → 647
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:639 → 664
      zf-H2C2_2; Zinc-finger double domain
      cl02566
      Location:433 → 540
      SET; SET domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      107696363..107724788 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370847.1 → XP_054226822.1  PR domain zinc finger protein 4 isoform X2

      UniProtKB/Swiss-Prot
      Q9UFA6, Q9UKN5

    2. XM_054370846.1 → XP_054226821.1  PR domain zinc finger protein 4 isoform X1

    3. XM_054370845.1 → XP_054226820.1  PR domain zinc finger protein 4 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UKN5.3 GenPept UniProtKB/Swiss-Prot:Q9UKN5

    Gene LinkOut

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