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    Phf12 PHD finger protein 12 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 303274, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Phf12provided by RGD
    Official Full Name
    PHD finger protein 12provided by RGD
    Primary source
    RGD:1305731
    See related
    EnsemblRapid:ENSRNOG00000009566 AllianceGenome:RGD:1305731
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable phosphatidylinositol binding activity; transcription corepressor activity; and transcription corepressor binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of Sin3-type complex and transcription repressor complex. Predicted to be active in nucleus. Orthologous to human PHF12 (PHD finger protein 12). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 82.5), Spleen (RPKM 75.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Phf12 in Genome Data Viewer
    Location:
    10q25
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (63368547..63417079)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (62871309..62919026)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (64815462..64863514, complement)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102551552 Neighboring gene pipecolic acid and sarcosine oxidase Neighboring gene uncharacterized LOC134480828 Neighboring gene seizure related 6 homolog Neighboring gene dehydrogenase/reductase 13 Neighboring gene flotillin 2

    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 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. The polybasic region that follows the plant homeodomain zinc finger 1 of Pf1 is necessary and sufficient for specific phosphoinositide binding. Kaadige MR, et al. J Biol Chem, 2006 Sep 29. PMID 16893883
    2. Peptidoglycan recognition protein Pglyrp2 protects mice from psoriasis-like skin inflammation by promoting regulatory T cells and limiting Th17 responses. Park SY, et al. J Immunol, 2011 Dec 1. PMID 22048773, Free PMC Article
    3. Pf1, a novel PHD zinc finger protein that links the TLE corepressor to the mSin3A-histone deacetylase complex. Yochum GS, et al. Mol Cell Biol, 2001 Jul. PMID 11390640, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC109651

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription corepressor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription corepressor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription corepressor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of Sin3-type complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Sin3-type complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of transcription repressor complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    PHD finger protein 12

    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_001013117.2 → NP_001013135.2  PHD finger protein 12

      See identical proteins and their annotated locations for NP_001013135.2

      Status: PROVISIONAL

      Source sequence(s)
      CH473948
      UniProtKB/TrEMBL
      A0A1W2Q657, A6HGZ8, F1LM99
      Related
      ENSRNOP00000053077.3, ENSRNOT00000056234.7
      Conserved Domains (4) summary
      cd00060
      Location:813 → 868
      FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
      cd15533
      Location:58 → 102
      PHD1_PHF12; PHD finger 1 found in PHD finger protein 12 (PHF12)
      cd15534
      Location:273 → 318
      PHD2_PHF12_Rco1; PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins
      pfam16737
      Location:203 → 241
      PHF12_MRG_bd; PHD finger protein 12 MRG binding domain

    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_086028.1 Reference GRCr8

      Range
      63368547..63417079
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063269041.1 → XP_063125111.1  PHD finger protein 12 isoform X4

    2. XM_063269042.1 → XP_063125112.1  PHD finger protein 12 isoform X5

    3. XM_039085997.2 → XP_038941925.1  PHD finger protein 12 isoform X3

      Conserved Domains (3) summary
      cd00060
      Location:596 → 651
      FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
      cd15534
      Location:56 → 101
      PHD2_PHF12_Rco1; PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins
      pfam16737
      Location:1 → 24
      PHF12_MRG_bd; PHD finger protein 12 MRG binding domain

    4. XM_039085995.2 → XP_038941923.1  PHD finger protein 12 isoform X1

      UniProtKB/TrEMBL
      A0A1W2Q657
      Related
      ENSRNOP00000076149.3, ENSRNOT00000093678.3
      Conserved Domains (4) summary
      cd00060
      Location:759 → 814
      FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
      cd15534
      Location:219 → 264
      PHD2_PHF12_Rco1; PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins
      pfam16737
      Location:149 → 187
      PHF12_MRG_bd; PHD finger protein 12 MRG binding domain
      cl22851
      Location:30 → 48
      PHD_SF; PHD finger superfamily

    5. XM_039085996.2 → XP_038941924.1  PHD finger protein 12 isoform X2

      UniProtKB/TrEMBL
      A0A1W2Q657
      Conserved Domains (3) summary
      cd00060
      Location:723 → 778
      FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
      cd15534
      Location:183 → 228
      PHD2_PHF12_Rco1; PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins
      pfam16737
      Location:113 → 151
      PHF12_MRG_bd; PHD finger protein 12 MRG binding domain
    Nucleotide Protein Strain
    Heading Accession and Version

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