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Phf8 PHD finger protein 8 [ Mus musculus (house mouse) ]

Gene ID: 320595, updated on 27-Nov-2024

Summary

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Official Symbol
Phf8provided by MGI
Official Full Name
PHD finger protein 8provided by MGI
Primary source
MGI:MGI:2444341
See related
Ensembl:ENSMUSG00000041229 AllianceGenome:MGI:2444341
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
mKIAA1111; 9830141C09Rik
Summary
Predicted to enable several functions, including histone demethylase activity; methylated histone binding activity; and transition metal ion binding activity. Predicted to be involved in several processes, including G1/S transition of mitotic cell cycle; chromatin remodeling; and positive regulation of macromolecule biosynthetic process. Predicted to be located in nuclear membrane; nucleolus; and nucleoplasm. Is expressed in several structures, including brain; early conceptus; olfactory epithelium; ovary; and vibrissa follicle. Used to study syndromic X-linked intellectual disability Siderius type. Human ortholog(s) of this gene implicated in syndromic X-linked intellectual disability Siderius type. Orthologous to human PHF8 (PHD finger protein 8). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in genital fat pad adult (RPKM 7.8), thymus adult (RPKM 4.9) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Phf8 in Genome Data Viewer
Location:
X F3; X 68.46 cM
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (150303621..150416855)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (151520641..151633859)

Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 120, member C Neighboring gene NSA2 ribosome biogenesis homolog pseudogene Neighboring gene STARR-seq mESC enhancer starr_48081 Neighboring gene ribosomal protein L39 pseudogene Neighboring gene predicted gene, 24460 Neighboring gene STARR-seq mESC enhancer starr_48082 Neighboring gene STARR-seq mESC enhancer starr_48083 Neighboring gene aldo-keto reductase family 1, member B3 pseudogene Neighboring gene STARR-seq mESC enhancer starr_48084 Neighboring gene STARR-seq mESC enhancer starr_48086 Neighboring gene predicted gene 15151

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 histone demethylase PHF8 represses cardiac hypertrophy upon pressure overload. Liu X, et al. Exp Cell Res, 2015 Jul 1. PMID 25921086
  2. The histone demethylase PHF8 regulates astrocyte differentiation and function. Iacobucci S, et al. Development, 2021 Jun 15. PMID 34081130
  3. Phf8 histone demethylase deficiency causes cognitive impairments through the mTOR pathway. Chen X, et al. Nat Commun, 2018 Jan 9. PMID 29317619, Free PMC Article
  4. Mutations in PHF8 are associated with X linked mental retardation and cleft lip/cleft palate. Laumonnier F, et al. J Med Genet, 2005 Oct. PMID 16199551, Free PMC Article
  5. Loss of PHF8 induces a viral mimicry response by activating endogenous retrotransposons. Liu Y, et al. Nat Commun, 2023 Jul 15. PMID 37454216, Free PMC Article

See all (42) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Homocysteine metabolites impair the PHF8/H4K20me1/mTOR/autophagy pathway by upregulating the expression of histone demethylase PHF8-targeting microRNAs in human vascular endothelial cells and mice.
    Title: Homocysteine metabolites impair the PHF8/H4K20me1/mTOR/autophagy pathway by upregulating the expression of histone demethylase PHF8-targeting microRNAs in human vascular endothelial cells and mice.
  2. Homocysteine metabolites inhibit autophagy, elevate amyloid beta, and induce neuropathy by impairing Phf8/H4K20me1-dependent epigenetic regulation of mTOR in cystathionine beta-synthase-deficient mice.
    Title: Homocysteine metabolites inhibit autophagy, elevate amyloid beta, and induce neuropathy by impairing Phf8/H4K20me1-dependent epigenetic regulation of mTOR in cystathionine β-synthase-deficient mice.
  3. Loss of PHF8 induces a viral mimicry response by activating endogenous retrotransposons.
    Title: Loss of PHF8 induces a viral mimicry response by activating endogenous retrotransposons.
  4. Functional Characterization of a Phf8 Processed Pseudogene in the Mouse Genome.
    Title: Functional Characterization of a Phf8 Processed Pseudogene in the Mouse Genome.
  5. The role of PHF8 and TLR4 in osteogenic differentiation of periodontal ligament cells in inflammatory environment.
    Title: The role of PHF8 and TLR4 in osteogenic differentiation of periodontal ligament cells in inflammatory environment.
  6. The histone demethylase PHF8 regulates astrocyte differentiation and function.
    Title: The histone demethylase PHF8 regulates astrocyte differentiation and function.
  7. Histone demethylase PHF8 drives neuroendocrine prostate cancer progression by epigenetically upregulating FOXA2.
    Title: Histone demethylase PHF8 drives neuroendocrine prostate cancer progression by epigenetically upregulating FOXA2.
  8. These results clarify the functional role of Phf8 in mammalian development and behavior.
    Title: Phf8 loss confers resistance to depression-like and anxiety-like behaviors in mice.
  9. PHD zinc finger 8 protein (Phf8) knockout mice display normal brain development but impaired learning and memory, and compromised long-term potentiation (LTP) in the hippocampus.
    Title: Phf8 histone demethylase deficiency causes cognitive impairments through the mTOR pathway.
  10. knockdown of pmaip1 mimicked the phenotype of ph8(-/Y) by showing the decreased apoptosis during early differentiation of embryonic stem cells and promoted mesodermal and cardiac commitment.
    Title: Plant Homeo Domain Finger Protein 8 Regulates Mesodermal and Cardiac Differentiation of Embryonic Stem Cells Through Mediating the Histone Demethylation of pmaip1.
Submit: New GeneRIF Correction See all GeneRIFs (13)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (4) 
  • Targeted (4)  1 citation

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

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables 2-oxoglutarate-dependent dioxygenase activity ISO
Inferred from Sequence Orthology
more info
  
enables 2-oxoglutarate-dependent dioxygenase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables FAD-dependent histone H3K9me/H3K9me2 demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables chromatin binding ISO
Inferred from Sequence Orthology
more info
  
enables chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables histone H3K27me2/H3K27me3 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H3K27me2/H3K27me3 demethylase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables histone H3K36 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H3K36 demethylase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables histone H3K36me/H3K36me2 demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K9 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H3K9 demethylase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables histone H3K9me/H3K9me2 demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H4K20 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H4K20 demethylase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone demethylase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables iron ion binding ISO
Inferred from Sequence Orthology
more info
  
enables iron ion binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables methylated histone binding ISO
Inferred from Sequence Orthology
more info
  
enables methylated histone binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables transcription coregulator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables zinc ion binding ISO
Inferred from Sequence Orthology
more info
  
enables zinc ion binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in G1/S transition of mitotic cell cycle ISO
Inferred from Sequence Orthology
more info
  
involved_in G1/S transition of mitotic cell cycle ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in brain development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of rDNA heterochromatin formation ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of rDNA heterochromatin formation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of transcription by RNA polymerase I ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of transcription by RNA polymerase I ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II 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
  
Component Evidence Code Pubs
located_in nuclear membrane IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear membrane ISO
Inferred from Sequence Orthology
more info
  
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleolus ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
histone lysine demethylase PHF8
Names
[histone H3]-dimethyl-L-lysine(36) demethylase PHF8
[histone H3]-dimethyl-L-lysine(9) demethylase PHF8
NP_001106825.1
NP_796175.1
XP_006528938.1
XP_006528940.1
XP_006528941.1
XP_006528942.1
XP_006528943.1
XP_030107232.1
XP_030107233.1

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.

mRNA and Protein(s)

  1. NM_001113354.1 → NP_001106825.1  histone lysine demethylase PHF8 isoform b

    See identical proteins and their annotated locations for NP_001106825.1

    Status: VALIDATED

    Source sequence(s)
    AK040969, AK122447
    Consensus CDS
    CCDS53223.1
    UniProtKB/Swiss-Prot
    A2ABU8, A2ABV0, A2ABV2, Q80TJ7, Q8BLX8, Q8BLY0, Q8BZ61, Q8CG26
    UniProtKB/TrEMBL
    Z4YL84
    Related
    ENSMUSP00000127653.2, ENSMUST00000168501.8
    Conserved Domains (4) summary
    smart00558
    Location:199 → 262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:6 → 57
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    pfam17811
    Location:338 → 441
    JHD; Jumonji helical domain
    cl21464
    Location:234 → 334
    cupin_like; Conserved domain found in cupin and related proteins

  2. NM_177201.5 → NP_796175.1  histone lysine demethylase PHF8 isoform a

    See identical proteins and their annotated locations for NP_796175.1

    Status: VALIDATED

    Source sequence(s)
    AK036609, AK040969, AK122447, AL662922
    Consensus CDS
    CCDS30470.1
    UniProtKB/TrEMBL
    A2ABV3, Z4YL84
    Related
    ENSMUSP00000108281.3, ENSMUST00000112662.9
    Conserved Domains (3) summary
    smart00558
    Location:199 → 262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:6 → 57
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    cl21464
    Location:234 → 334
    cupin_like; Conserved domain found in cupin and related proteins

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_000086.8 Reference GRCm39 C57BL/6J

    Range
    150303621..150416855
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030251373.2 → XP_030107233.1  histone lysine demethylase PHF8 isoform X2

    Conserved Domains (4) summary
    smart00558
    Location:199 → 262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:6 → 57
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    pfam17811
    Location:338 → 441
    JHD; Jumonji helical domain
    cl21464
    Location:234 → 334
    cupin_like; Conserved domain found in cupin and related proteins

  2. XM_030251372.2 → XP_030107232.1  histone lysine demethylase PHF8 isoform X1

    UniProtKB/Swiss-Prot
    A2ABU8, A2ABV0, A2ABV2, Q80TJ7, Q8BLX8, Q8BLY0, Q8BZ61, Q8CG26
    UniProtKB/TrEMBL
    Z4YL84
    Conserved Domains (4) summary
    smart00558
    Location:199 → 262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:6 → 57
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    pfam17811
    Location:338 → 441
    JHD; Jumonji helical domain
    cl21464
    Location:234 → 334
    cupin_like; Conserved domain found in cupin and related proteins

  3. XM_006528879.5 → XP_006528942.1  histone lysine demethylase PHF8 isoform X2

    See identical proteins and their annotated locations for XP_006528942.1

    Conserved Domains (4) summary
    smart00558
    Location:199 → 262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:6 → 57
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    pfam17811
    Location:338 → 441
    JHD; Jumonji helical domain
    cl21464
    Location:234 → 334
    cupin_like; Conserved domain found in cupin and related proteins

  4. XM_006528878.5 → XP_006528941.1  histone lysine demethylase PHF8 isoform X2

    See identical proteins and their annotated locations for XP_006528941.1

    Conserved Domains (4) summary
    smart00558
    Location:199 → 262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:6 → 57
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    pfam17811
    Location:338 → 441
    JHD; Jumonji helical domain
    cl21464
    Location:234 → 334
    cupin_like; Conserved domain found in cupin and related proteins

  5. XM_006528875.5 → XP_006528938.1  histone lysine demethylase PHF8 isoform X1

    See identical proteins and their annotated locations for XP_006528938.1

    UniProtKB/Swiss-Prot
    A2ABU8, A2ABV0, A2ABV2, Q80TJ7, Q8BLX8, Q8BLY0, Q8BZ61, Q8CG26
    UniProtKB/TrEMBL
    Z4YL84
    Related
    ENSMUSP00000040765.7, ENSMUST00000046950.13
    Conserved Domains (4) summary
    smart00558
    Location:199 → 262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:6 → 57
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    pfam17811
    Location:338 → 441
    JHD; Jumonji helical domain
    cl21464
    Location:234 → 334
    cupin_like; Conserved domain found in cupin and related proteins

  6. XM_006528877.5 → XP_006528940.1  histone lysine demethylase PHF8 isoform X1

    See identical proteins and their annotated locations for XP_006528940.1

    UniProtKB/Swiss-Prot
    A2ABU8, A2ABV0, A2ABV2, Q80TJ7, Q8BLX8, Q8BLY0, Q8BZ61, Q8CG26
    UniProtKB/TrEMBL
    Z4YL84
    Conserved Domains (4) summary
    smart00558
    Location:199 → 262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:6 → 57
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    pfam17811
    Location:338 → 441
    JHD; Jumonji helical domain
    cl21464
    Location:234 → 334
    cupin_like; Conserved domain found in cupin and related proteins

  7. XM_006528880.5 → XP_006528943.1  histone lysine demethylase PHF8 isoform X1

    See identical proteins and their annotated locations for XP_006528943.1

    UniProtKB/Swiss-Prot
    A2ABU8, A2ABV0, A2ABV2, Q80TJ7, Q8BLX8, Q8BLY0, Q8BZ61, Q8CG26
    UniProtKB/TrEMBL
    Z4YL84
    Conserved Domains (4) summary
    smart00558
    Location:199 → 262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:6 → 57
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    pfam17811
    Location:338 → 441
    JHD; Jumonji helical domain
    cl21464
    Location:234 → 334
    cupin_like; Conserved domain found in cupin and related proteins
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q80TJ7.2 GenPept UniProtKB/Swiss-Prot:Q80TJ7

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