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    Phf3 PHD finger protein 3 [ Mus musculus (house mouse) ]

    Gene ID: 213109, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Phf3provided by MGI
    Official Full Name
    PHD finger protein 3provided by MGI
    Primary source
    MGI:MGI:2446126
    See related
    Ensembl:ENSMUSG00000048874 AllianceGenome:MGI:2446126
    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
    2310061N19Rik
    Summary
    Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Is expressed in central nervous system; genitourinary system; and retina. Orthologous to human PHF3 (PHD finger protein 3). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 9.6), CNS E14 (RPKM 8.9) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Phf3 in Genome Data Viewer
    Location:
    1 A5- B; 1 11.45 cM
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (30841417..30912989, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (30802342..30873922, complement)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_00508 Neighboring gene cyclin-dependent kinase 10 pseudogene Neighboring gene predicted gene 2914 Neighboring gene STARR-seq mESC enhancer starr_00509 Neighboring gene STARR-seq mESC enhancer starr_00510 Neighboring gene STARR-seq mESC enhancer starr_00512 Neighboring gene STARR-seq mESC enhancer starr_00514 Neighboring gene STARR-seq mESC enhancer starr_00515 Neighboring gene STARR-seq mESC enhancer starr_00516 Neighboring gene protein tyrosine phosphatase 4a1 Neighboring gene predicted gene, 53209

    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. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Appel LM, et al. Nat Commun, 2021 Oct 19. PMID 34667177, Free PMC Article
    2. Evolutionary diversification of the BetaM interactome acquired through co-option of the ATP1B4 gene in placental mammals. Korneenko TV, et al. Sci Rep, 2016 Mar 4. PMID 26939788, Free PMC Article
    3. The ubiquitin ligase Uhrf2 is a master regulator of cholesterol biosynthesis and is essential for liver regeneration. Slabber CF, et al. Sci Signal, 2023 May 30. PMID 37253089
    4. Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of trophoblast stem cells. Latos PA, et al. Nat Commun, 2015 Jul 24. PMID 26206133, Free PMC Article
    5. Oct4 links multiple epigenetic pathways to the pluripotency network. Ding J, et al. Cell Res, 2012 Jan. PMID 22083510, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC.
      Title: PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0244

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    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_001081080.2 → NP_001074549.1  PHD finger protein 3 isoform 1

      See identical proteins and their annotated locations for NP_001074549.1

      Status: VALIDATED

      Source sequence(s)
      AC124469, AC153137
      Consensus CDS
      CCDS35530.1
      UniProtKB/TrEMBL
      B2RQG2
      Related
      ENSMUSP00000139610.2, ENSMUST00000186733.7
      Conserved Domains (5) summary
      PHA03369
      Location:983 → 1184
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1916 → 2025
      SF-CC1; splicing factor, CC1-like family
      cd15638
      Location:697 → 747
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:904 → 1017
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1181 → 1327
      SPOC; SPOC domain

    2. NM_001403128.1 → NP_001390057.1  PHD finger protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC124469, AC153137

    3. NM_001403130.1 → NP_001390059.1  PHD finger protein 3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC124469, AC153137

    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_000067.7 Reference GRCm39 C57BL/6J

      Range
      30841417..30912989 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011238471.4 → XP_011236773.1  PHD finger protein 3 isoform X4

      Conserved Domains (5) summary
      PHA03369
      Location:895 → 1096
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1828 → 1937
      SF-CC1; splicing factor, CC1-like family
      cd15638
      Location:609 → 659
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:816 → 929
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1093 → 1239
      SPOC; SPOC domain

    2. XM_030252760.1 → XP_030108620.1  PHD finger protein 3 isoform X6

      Conserved Domains (5) summary
      PHA03369
      Location:778 → 979
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1711 → 1820
      SF-CC1; splicing factor, CC1-like family
      cd15638
      Location:492 → 542
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:699 → 812
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:976 → 1122
      SPOC; SPOC domain

    3. XM_036163369.1 → XP_036019262.1  PHD finger protein 3 isoform X5

      Conserved Domains (5) summary
      PHA03369
      Location:882 → 1083
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1815 → 1924
      SF-CC1; splicing factor, CC1-like family
      cd15638
      Location:596 → 646
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:803 → 916
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1079 → 1227
      SPOC; SPOC domain

    4. XM_011238470.4 → XP_011236772.1  PHD finger protein 3 isoform X2

      Conserved Domains (5) summary
      PHA03369
      Location:936 → 1137
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1869 → 1978
      SF-CC1; splicing factor, CC1-like family
      cd15638
      Location:650 → 700
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:857 → 970
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1134 → 1280
      SPOC; SPOC domain

    5. XM_006495840.5 → XP_006495903.1  PHD finger protein 3 isoform X7

      See identical proteins and their annotated locations for XP_006495903.1

      UniProtKB/TrEMBL
      Q80U54
      Conserved Domains (5) summary
      PHA03369
      Location:274 → 475
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1207 → 1316
      SF-CC1; splicing factor, CC1-like family
      pfam07500
      Location:195 → 308
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:471 → 619
      SPOC; SPOC domain
      cl22851
      Location:1 → 38
      PHD_SF; PHD finger superfamily

    6. XM_036163374.1 → XP_036019267.1  PHD finger protein 3 isoform X7

      UniProtKB/TrEMBL
      Q80U54
      Conserved Domains (5) summary
      PHA03369
      Location:274 → 475
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1207 → 1316
      SF-CC1; splicing factor, CC1-like family
      pfam07500
      Location:195 → 308
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:471 → 619
      SPOC; SPOC domain
      cl22851
      Location:1 → 38
      PHD_SF; PHD finger superfamily

    7. XM_006495839.4 → XP_006495902.1  PHD finger protein 3 isoform X7

      See identical proteins and their annotated locations for XP_006495902.1

      UniProtKB/TrEMBL
      Q80U54
      Conserved Domains (5) summary
      PHA03369
      Location:274 → 475
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1207 → 1316
      SF-CC1; splicing factor, CC1-like family
      pfam07500
      Location:195 → 308
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:471 → 619
      SPOC; SPOC domain
      cl22851
      Location:1 → 38
      PHD_SF; PHD finger superfamily

    8. XM_030252767.1 → XP_030108627.1  PHD finger protein 3 isoform X7

      UniProtKB/TrEMBL
      Q80U54
      Conserved Domains (5) summary
      PHA03369
      Location:274 → 475
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1207 → 1316
      SF-CC1; splicing factor, CC1-like family
      pfam07500
      Location:195 → 308
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:471 → 619
      SPOC; SPOC domain
      cl22851
      Location:1 → 38
      PHD_SF; PHD finger superfamily

    9. XM_030252757.2 → XP_030108617.1  PHD finger protein 3 isoform X2

      Conserved Domains (5) summary
      PHA03369
      Location:936 → 1137
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1869 → 1978
      SF-CC1; splicing factor, CC1-like family
      cd15638
      Location:650 → 700
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:857 → 970
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1134 → 1280
      SPOC; SPOC domain

    10. XM_030252758.2 → XP_030108618.1  PHD finger protein 3 isoform X3

      Conserved Domains (5) summary
      PHA03369
      Location:929 → 1130
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1862 → 1971
      SF-CC1; splicing factor, CC1-like family
      cd15638
      Location:643 → 693
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:850 → 963
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1127 → 1273
      SPOC; SPOC domain

    11. XM_030252762.2 → XP_030108622.1  PHD finger protein 3 isoform X7

      UniProtKB/TrEMBL
      Q80U54
      Conserved Domains (5) summary
      PHA03369
      Location:274 → 475
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1207 → 1316
      SF-CC1; splicing factor, CC1-like family
      pfam07500
      Location:195 → 308
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:471 → 619
      SPOC; SPOC domain
      cl22851
      Location:1 → 38
      PHD_SF; PHD finger superfamily

    12. XM_006495837.4 → XP_006495900.1  PHD finger protein 3 isoform X1

      See identical proteins and their annotated locations for XP_006495900.1

      UniProtKB/TrEMBL
      B2RQG2
      Conserved Domains (5) summary
      PHA03369
      Location:983 → 1184
      PHA03369; capsid maturational protease; Provisional
      TIGR01622
      Location:1916 → 2025
      SF-CC1; splicing factor, CC1-like family
      cd15638
      Location:697 → 747
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:904 → 1017
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1181 → 1327
      SPOC; SPOC domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_025871.1: Suppressed sequence

      Description
      NM_025871.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.
    Nucleotide Protein Strain
    Heading Accession and Version

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