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

Gene ID: 317425, updated on 27-Nov-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, Nov 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

  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

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

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000021

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

    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

  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

    UniProtKB/TrEMBL
    A6KLA6, D4AD31
    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

    UniProtKB/TrEMBL
    A0A8I6AC06

  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
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