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

    Gene ID: 72843, updated on 9-Dec-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 (34) 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)
    • Endonuclease-mediated (3) 
    • Targeted (6)  1 citation

    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 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 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
    		  
    Process Evidence Code Pubs
    involved_in 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 gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    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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