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    Phf8 PHD finger protein 8 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 317425, updated on 9-Dec-2024

    Summary

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    Symbol
    Phf8provided by RGD
    Full Name
    PHD finger protein 8provided by RGD
    Primary source
    RGD:1561065
    See related
    EnsemblRapid:ENSRNOG00000002708 AllianceGenome:RGD:1561065
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1561065
    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 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. 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, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 153.0), Spleen (RPKM 77.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Phf8 in Genome Data Viewer
    Location:
    Xq12
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (23967126..24066473)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (20524103..20623459)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (21063487..21168750)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 120 member C Neighboring gene ribosomal protein L18, pseudogene 14 Neighboring gene similar to human chromosome 3 open reading frame 38 Neighboring gene ubiquitin domain containing 2, pseudogene 2 Neighboring gene enolase 1, pseudogene 6

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. PHF8, a gene associated with cleft lip/palate and mental retardation, encodes for an Nepsilon-dimethyl lysine demethylase. Loenarz C, et al. Hum Mol Genet, 2010 Jan 15. PMID 19843542, Free PMC Article
    2. Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Horton JR, et al. Nat Struct Mol Biol, 2010 Jan. PMID 20023638, Free PMC Article
    3. Systematic knockdown of epigenetic enzymes identifies a novel histone demethylase PHF8 overexpressed in prostate cancer with an impact on cell proliferation, migration and invasion. Björkman M, et al. Oncogene, 2012 Jul 19. PMID 22120715
    4. A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation. Kleine-Kohlbrecher D, et al. Mol Cell, 2010 Apr 23. PMID 20346720, Free PMC Article
    5. PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation. Feng W, et al. Nat Struct Mol Biol, 2010 Apr. PMID 20208542

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables 2-oxoglutarate-dependent dioxygenase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K27me2/H3K27me3 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K36 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K9 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H4K20 demethylase activity ISO
    Inferred from Sequence Orthology
    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 iron ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables methylated histone binding ISO
    Inferred from Sequence Orthology
    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
    		  
    Process Evidence Code Pubs
    involved_in G1/S transition of mitotic cell cycle ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of rDNA heterochromatin formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    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 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    histone lysine demethylase PHF8
    NP_001101723.1
    XP_006256854.1
    XP_008771341.1
    XP_017457561.1
    XP_038955735.1
    XP_038955736.1
    XP_038955738.1
    XP_038955741.1
    XP_038955742.1
    XP_063136134.1
    XP_063136135.1
    XP_063136136.1
    XP_063136137.1

    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_001108253.2 → NP_001101723.1  histone lysine demethylase PHF8 isoform 1

      See identical proteins and their annotated locations for NP_001101723.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A6KLA6, D4AD31
      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
      cl40423
      Location:234 → 334
      cupin_RmlC-like; RmlC-like cupin superfamily

    2. NM_001434155.1 → NP_001421084.1  histone lysine demethylase PHF8 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A0A8I6AC06

    3. NM_001434156.1 → NP_001421085.1  histone lysine demethylase PHF8 isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021

    4. NM_001434157.1 → NP_001421086.1  histone lysine demethylase PHF8 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A6KLA6, D4AD31

    5. NM_001434159.1 → NP_001421088.1  histone lysine demethylase PHF8 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A6KLA6, D4AD31

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086039.1 Reference GRCr8

      Range
      23967126..24066473
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063280065.1 → XP_063136135.1  histone lysine demethylase PHF8 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AC06

    2. XM_006256792.4 → XP_006256854.1  histone lysine demethylase PHF8 isoform X1

      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
      cl40423
      Location:234 → 334
      cupin_RmlC-like; RmlC-like cupin superfamily

    3. XM_063280067.1 → XP_063136137.1  histone lysine demethylase PHF8 isoform X4

    4. XM_063280066.1 → XP_063136136.1  histone lysine demethylase PHF8 isoform X3

    5. XM_039099808.2 → XP_038955736.1  histone lysine demethylase PHF8 isoform X1

      UniProtKB/TrEMBL
      A6KLA6, D4AD31
      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
      cl40423
      Location:234 → 334
      cupin_RmlC-like; RmlC-like cupin superfamily

    6. XM_017602072.3 → XP_017457561.1  histone lysine demethylase PHF8 isoform X1

      UniProtKB/TrEMBL
      A6KLA6, D4AD31
      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
      cl40423
      Location:234 → 334
      cupin_RmlC-like; RmlC-like cupin superfamily

    7. XM_039099807.2 → XP_038955735.1  histone lysine demethylase PHF8 isoform X1

      Related
      ENSRNOP00000040672.4, ENSRNOT00000045708.7
      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
      cl40423
      Location:234 → 334
      cupin_RmlC-like; RmlC-like cupin superfamily

    8. XM_039099810.2 → XP_038955738.1  histone lysine demethylase PHF8 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AC06
      Related
      ENSRNOP00000090968.1, ENSRNOT00000093422.3
      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
      cl40423
      Location:234 → 334
      cupin_RmlC-like; RmlC-like cupin superfamily

    9. XM_063280064.1 → XP_063136134.1  histone lysine demethylase PHF8 isoform X2

    10. XM_008773119.2 → XP_008771341.1  histone lysine demethylase PHF8 isoform X1

      See identical proteins and their annotated locations for XP_008771341.1

      UniProtKB/TrEMBL
      A6KLA6, D4AD31
      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
      cl40423
      Location:234 → 334
      cupin_RmlC-like; RmlC-like cupin superfamily

    11. XM_039099813.2 → XP_038955741.1  histone lysine demethylase PHF8 isoform X5

      Conserved Domains (1) summary
      pfam17811
      Location:1 → 34
      JHD; Jumonji helical domain

    12. XM_039099814.1 → XP_038955742.1  histone lysine demethylase PHF8 isoform X6

      Conserved Domains (1) summary
      pfam17811
      Location:1 → 34
      JHD; Jumonji helical domain
    Nucleotide Protein Strain
    Heading Accession and Version

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