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Prdm4 PR domain containing 4 [ Mus musculus (house mouse) ]

Gene ID: 72843, updated on 5-Mar-2024

Summary

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Official Symbol
Prdm4provided by MGI
Official Full Name
PR domain containing 4provided by MGI
Primary source
MGI:MGI:1920093
See related
Ensembl:ENSMUSG00000035529 AllianceGenome:MGI:1920093
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
SC1; SC-1; 1700031E19Rik; 2810470D21Rik
Summary
This gene encodes a member of the PR/SET family of zinc finger proteins. This protein has been shown to bind DNA in a sequence-specific manner and has been implicated in neural stem cell proliferation and differentiation. Pseudogenes have been identified on chromosomes 14 and X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
Expression
Ubiquitous expression in testis adult (RPKM 15.6), whole brain E14.5 (RPKM 14.9) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Prdm4 in Genome Data Viewer
Location:
10 C1; 10 41.75 cM
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (85727828..85752958, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (85891964..85917152, complement)

Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene uncharacterized protein C12orf73 homolog Neighboring gene PWP1 homolog, endonuclein Neighboring gene STARR-positive B cell enhancer ABC_E723 Neighboring gene achaete-scute family bHLH transcription factor 4 Neighboring gene STARR-seq mESC enhancer starr_27454 Neighboring gene RNA 2',3'-cyclic phosphate and 5'-OH ligase Neighboring gene predicted gene, 48175

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. The overexpression of peroxiredoxin-4 affects the progression of idiopathic pulmonary fibrosis. Hanaka T, et al. BMC Pulm Med, 2019 Dec 30. PMID 31888585, Free PMC Article
  2. SC1/PRDM4 is a critical mediator for cell death, mitosis and differentiation of neural stem cells. Orel N, et al. J Stem Cells Regen Med, 2007. PMID 24693010
  3. PI3Ka-Akt1-mediated Prdm4 induction in adipose tissue increases energy expenditure, inhibits weight gain, and improves insulin resistance in diet-induced obese mice. Song NJ, et al. Cell Death Dis, 2018 Aug 29. PMID 30158592, Free PMC Article
  4. Overexpression of peroxiredoxin 4 attenuates atherosclerosis in apolipoprotein E knockout mice. Guo X, et al. Antioxid Redox Signal, 2012 Nov 15. PMID 22548251, Free PMC Article
  5. The PR/SET domain zinc finger protein Prdm4 regulates gene expression in embryonic stem cells but plays a nonessential role in the developing mouse embryo. Bogani D, et al. Mol Cell Biol, 2013 Oct. PMID 23918801, Free PMC Article

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The role of butein in obesity and metabolic diseases, further highlighting that adipose PI3Kalpha-Akt1-Prdm4 axis is a regulator of energy expenditure.
    Title: PI3Ka-Akt1-mediated Prdm4 induction in adipose tissue increases energy expenditure, inhibits weight gain, and improves insulin resistance in diet-induced obese mice.
  2. Results suggest that Prdm4 functions redundantly with other transcriptional partners to cooperatively regulate gene expression in the embryo and adult animal.
    Title: The PR/SET domain zinc finger protein Prdm4 regulates gene expression in embryonic stem cells but plays a nonessential role in the developing mouse embryo.
  3. SC1 and PRMT5 are components of an epigenetic regulatory complex that maintains the "stem-like" cellular state of the neural stem cells.
    Title: Transcription factor positive regulatory domain 4 (PRDM4) recruits protein arginine methyltransferase 5 (PRMT5) to mediate histone arginine methylation and control neural stem cell proliferation and differentiation.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (6)  1 citation
  • Endonuclease-mediated (2) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription activator activity, RNA polymerase II-specific IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables death receptor binding ISO
Inferred from Sequence Orthology
more info
  
enables histone methyltransferase binding IPI
Inferred from Physical Interaction
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 sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cell fate commitment IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of cell growth ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of gene expression ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of neural precursor cell proliferation ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of stem cell differentiation ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of transcription by RNA polymerase II 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
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
part_of histone methyltransferase complex IPI
Inferred from Physical Interaction
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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

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_001302886.1 → NP_001289815.1  PR domain zinc finger protein 4 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains a longer 5' UTR and uses an alternate in-frame splice site in the central coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AK028414, BC057596, CD350319
    Consensus CDS
    CCDS88065.1
    UniProtKB/TrEMBL
    A0A1X7SB67, B7ZP41
    Related
    ENSMUSP00000041942.9, ENSMUST00000037646.9
    Conserved Domains (5) summary
    sd00017
    Location:616 → 636
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:614 → 636
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:628 → 653
    zf-H2C2_2; Zinc-finger double domain
    pfam18445
    Location:361 → 398
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:401 → 533
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins

  2. NM_001302887.1 → NP_001289816.1  PR domain zinc finger protein 4 isoform 3

    See identical proteins and their annotated locations for NP_001289816.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate exon in the 5' region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    BC057596, CD350319
    UniProtKB/TrEMBL
    Q8C0V8
    Conserved Domains (5) summary
    sd00017
    Location:434 → 454
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:432 → 454
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:446 → 471
    zf-H2C2_2; Zinc-finger double domain
    pfam18445
    Location:172 → 209
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:212 → 351
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins

  3. NM_181650.3 → NP_857633.2  PR domain zinc finger protein 4 isoform 1

    See identical proteins and their annotated locations for NP_857633.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    BC057596, BC139409, CD350319
    Consensus CDS
    CCDS24093.1
    UniProtKB/Swiss-Prot
    B2RTL4, Q80V63
    UniProtKB/TrEMBL
    B7ZP41
    Conserved Domains (4) summary
    sd00017
    Location:623 → 643
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18445
    Location:361 → 398
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:401 → 540
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins
    pfam13465
    Location:635 → 660
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000076.7 Reference GRCm39 C57BL/6J

    Range
    85727828..85752958 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011243582.2 → XP_011241884.1  PR domain zinc finger protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011241884.1

    UniProtKB/Swiss-Prot
    B2RTL4, Q80V63
    UniProtKB/TrEMBL
    B7ZP41
    Related
    ENSMUSP00000151931.2, ENSMUST00000220032.2
    Conserved Domains (4) summary
    sd00017
    Location:623 → 643
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18445
    Location:361 → 398
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:401 → 540
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins
    pfam13465
    Location:635 → 660
    zf-H2C2_2; Zinc-finger double domain

  2. XM_006514194.4 → XP_006514257.1  PR domain zinc finger protein 4 isoform X1

    See identical proteins and their annotated locations for XP_006514257.1

    UniProtKB/Swiss-Prot
    B2RTL4, Q80V63
    UniProtKB/TrEMBL
    B7ZP41
    Conserved Domains (4) summary
    sd00017
    Location:623 → 643
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18445
    Location:361 → 398
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:401 → 540
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins
    pfam13465
    Location:635 → 660
    zf-H2C2_2; Zinc-finger double domain

  3. XM_006514197.4 → XP_006514260.1  PR domain zinc finger protein 4 isoform X3

    UniProtKB/TrEMBL
    Q8R3B9
    Conserved Domains (5) summary
    sd00017
    Location:557 → 577
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:555 → 577
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:569 → 594
    zf-H2C2_2; Zinc-finger double domain
    pfam18445
    Location:295 → 332
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:335 → 474
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins

  4. XM_030245304.1 → XP_030101164.1  PR domain zinc finger protein 4 isoform X2

    UniProtKB/TrEMBL
    A0A1X7SB67, B7ZP41
    Conserved Domains (5) summary
    sd00017
    Location:616 → 636
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:614 → 636
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:628 → 653
    zf-H2C2_2; Zinc-finger double domain
    pfam18445
    Location:361 → 398
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:401 → 533
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins

  5. XM_017314116.2 → XP_017169605.1  PR domain zinc finger protein 4 isoform X4

    UniProtKB/TrEMBL
    Q8R3B9
    Conserved Domains (5) summary
    sd00017
    Location:550 → 570
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:548 → 570
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:562 → 587
    zf-H2C2_2; Zinc-finger double domain
    pfam18445
    Location:295 → 332
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:335 → 467
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins

  6. XM_011243583.4 → XP_011241885.1  PR domain zinc finger protein 4 isoform X5

    See identical proteins and their annotated locations for XP_011241885.1

    UniProtKB/TrEMBL
    Q8C0V8
    Conserved Domains (5) summary
    sd00017
    Location:434 → 454
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:432 → 454
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:446 → 471
    zf-H2C2_2; Zinc-finger double domain
    pfam18445
    Location:172 → 209
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:212 → 351
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q80V63.2 GenPept UniProtKB/Swiss-Prot:Q80V63

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