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    Phf3 PHD finger protein 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 363210, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Phf3provided by RGD
    Official Full Name
    PHD finger protein 3provided by RGD
    Primary source
    RGD:1304925
    See related
    EnsemblRapid:ENSRNOG00000011756 AllianceGenome:RGD:1304925
    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 metal ion binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Orthologous to human PHF3 (PHD finger protein 3). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 220.2), Thymus (RPKM 174.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Phf3 in Genome Data Viewer
    Location:
    9q21
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (40559929..40632096, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (33063855..33136013, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (37073514..37144027, complement)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene zinc finger protein 706, pseudogene 1 Neighboring gene eukaryotic translation initiation factor 4, gamma 2, pseudogene 1 Neighboring gene protein tyrosine phosphatase 4A1 Neighboring gene uncharacterized LOC102548289

    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. 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

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    PHD finger protein 3

    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_001108791.1 → NP_001102261.1  PHD finger protein 3

      See identical proteins and their annotated locations for NP_001102261.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473965
      UniProtKB/TrEMBL
      A0A8I6AS20, A6IN78, D3ZKI5
      Related
      ENSRNOP00000015638.5, ENSRNOT00000015638.7
      Conserved Domains (3) summary
      cd15638
      Location:698 → 748
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:908 → 1018
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1193 → 1299
      SPOC; SPOC 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_086027.1 Reference GRCr8

      Range
      40559929..40632096 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039083830.2 → XP_038939758.1  PHD finger protein 3 isoform X7

      Conserved Domains (5) summary
      PHA03369
      Location:277 → 479
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1173 → 1269
      SF-CC1; splicing factor, CC1-like family
      pfam07500
      Location:198 → 311
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:475 → 623
      SPOC; SPOC domain
      cl22851
      Location:1 → 38
      PHD_SF; PHD finger superfamily

    2. XM_039083827.2 → XP_038939755.1  PHD finger protein 3 isoform X6

      UniProtKB/TrEMBL
      A0A8I6AS20
      Conserved Domains (5) summary
      PTZ00121
      Location:545 → 890
      PTZ00121; MAEBL; Provisional
      TIGR01622
      Location:1678 → 1774
      SF-CC1; splicing factor, CC1-like family
      cd15638
      Location:493 → 543
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:703 → 816
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:980 → 1128
      SPOC; SPOC domain

    3. XM_006244676.5 → XP_006244738.1  PHD finger protein 3 isoform X4

      See identical proteins and their annotated locations for XP_006244738.1

      UniProtKB/TrEMBL
      A0A8I6AS20
      Conserved Domains (3) summary
      cd15638
      Location:610 → 660
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:820 → 930
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1105 → 1211
      SPOC; SPOC domain

    4. XM_063267363.1 → XP_063123433.1  PHD finger protein 3 isoform X5

    5. XM_039083826.2 → XP_038939754.1  PHD finger protein 3 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AS20
      Conserved Domains (5) summary
      PTZ00121
      Location:703 → 1048
      PTZ00121; MAEBL; Provisional
      TIGR01622
      Location:1836 → 1932
      SF-CC1; splicing factor, CC1-like family
      cd15638
      Location:651 → 701
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:861 → 974
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1138 → 1286
      SPOC; SPOC domain

    6. XM_006244675.5 → XP_006244737.1  PHD finger protein 3 isoform X3

      UniProtKB/TrEMBL
      A0A8I6ARM7, A0A8I6AS20
      Related
      ENSRNOP00000096905.1, ENSRNOT00000119509.2
      Conserved Domains (3) summary
      cd15638
      Location:644 → 694
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:854 → 964
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1139 → 1245
      SPOC; SPOC domain

    7. XM_006244673.5 → XP_006244735.1  PHD finger protein 3 isoform X1

      See identical proteins and their annotated locations for XP_006244735.1

      UniProtKB/TrEMBL
      A0A8I6AS20, A6IN78, D3ZKI5
      Conserved Domains (3) summary
      cd15638
      Location:698 → 748
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:908 → 1018
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1193 → 1299
      SPOC; SPOC domain

    8. XM_039083829.2 → XP_038939757.1  PHD finger protein 3 isoform X7

      Conserved Domains (5) summary
      PHA03369
      Location:277 → 479
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1173 → 1269
      SF-CC1; splicing factor, CC1-like family
      pfam07500
      Location:198 → 311
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:475 → 623
      SPOC; SPOC domain
      cl22851
      Location:1 → 38
      PHD_SF; PHD finger superfamily

    9. XM_006244677.5 → XP_006244739.1  PHD finger protein 3 isoform X4

      See identical proteins and their annotated locations for XP_006244739.1

      UniProtKB/TrEMBL
      A0A8I6AS20
      Conserved Domains (3) summary
      cd15638
      Location:610 → 660
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:820 → 930
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1105 → 1211
      SPOC; SPOC domain

    10. XM_039083828.2 → XP_038939756.1  PHD finger protein 3 isoform X7

      Conserved Domains (5) summary
      PHA03369
      Location:277 → 479
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1173 → 1269
      SF-CC1; splicing factor, CC1-like family
      pfam07500
      Location:198 → 311
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:475 → 623
      SPOC; SPOC domain
      cl22851
      Location:1 → 38
      PHD_SF; PHD finger superfamily
    Nucleotide Protein Strain
    Heading Accession and Version

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