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

Gene ID: 213109, updated on 2-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 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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