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

Gene ID: 363210, updated on 27-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
  • 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 DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
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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