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    Phf14 PHD finger protein 14 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 500030, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Phf14provided by RGD
    Official Full Name
    PHD finger protein 14provided by RGD
    Primary source
    RGD:1563764
    See related
    EnsemblRapid:ENSRNOG00000005775 AllianceGenome:RGD:1563764
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1563764
    Summary
    Predicted to enable histone binding activity. Predicted to be involved in germinal center B cell differentiation and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including lung alveolus development; negative regulation of mesenchymal cell proliferation involved in lung development; and negative regulation of platelet-derived growth factor receptor-alpha signaling pathway. Predicted to be located in chromatin; cytoplasm; and nucleus. Orthologous to human PHF14 (PHD finger protein 14). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 161.3), Thymus (RPKM 109.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Phf14 in Genome Data Viewer
    Location:
    4q21
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (40975897..41162043)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (40009691..40195877)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (38241189..38420199)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene stathmin like, pseudogene 2 Neighboring gene Ndufa4, mitochondrial complex associated Neighboring gene uncharacterized LOC120102235 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene thrombospondin type 1 domain containing 7A Neighboring gene ribosomal protein S2, pseudogene 40

    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. Phf14, a novel regulator of mesenchyme growth via platelet-derived growth factor (PDGF) receptor-α. Kitagawa M, et al. J Biol Chem, 2012 Aug 10. PMID 22730381, Free PMC Article
    2. 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
    3. 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 histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in germinal center B cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within lung alveolus development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of mesenchymal cell proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of mesenchymal cell proliferation involved in lung development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of mesenchymal cell proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of mesenchymal cell proliferation involved in lung development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of platelet-derived growth factor receptor-alpha signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    PHD finger protein 14

    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_001110492.1 → NP_001103962.1  PHD finger protein 14 isoform 2

      See identical proteins and their annotated locations for NP_001103962.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473959
      UniProtKB/TrEMBL
      A0A8I5ZNB3, A6IDZ1, G3V9T6
      Related
      ENSRNOP00000059404.1, ENSRNOT00000065649.4
      Conserved Domains (3) summary
      cd15561
      Location:313 → 369
      PHD1_PHF14; PHD finger 1 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15562
      Location:719 → 768
      PHD2_PHF14; PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15674
      Location:377 → 490
      ePHD_PHF14; Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins

    2. NM_001398908.1 → NP_001385837.1  PHD finger protein 14 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/TrEMBL
      A0A0G2K7P2
      Conserved Domains (4) summary
      cd15561
      Location:313 → 369
      PHD1_PHF14; PHD finger 1 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15562
      Location:719 → 768
      PHD2_PHF14; PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15563
      Location:862 → 910
      PHD3_PHF14; PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15674
      Location:377 → 490
      ePHD_PHF14; Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins

    3. NM_001398909.1 → NP_001385838.1  PHD finger protein 14 isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/TrEMBL
      B2GUY7
      Conserved Domains (3) summary
      cd15561
      Location:313 → 369
      PHD1_PHF14; PHD finger 1 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15562
      Location:719 → 768
      PHD2_PHF14; PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15674
      Location:377 → 490
      ePHD_PHF14; Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins

    RNA

    1. NR_174140.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004

    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_086022.1 Reference GRCr8

      Range
      40975897..41162043
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006236105.5 → XP_006236167.1  PHD finger protein 14 isoform X2

      See identical proteins and their annotated locations for XP_006236167.1

      UniProtKB/TrEMBL
      A0A8I6ASZ4
      Conserved Domains (4) summary
      cd15561
      Location:313 → 369
      PHD1_PHF14; PHD finger 1 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15562
      Location:719 → 768
      PHD2_PHF14; PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15563
      Location:862 → 920
      PHD3_PHF14; PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15674
      Location:377 → 490
      ePHD_PHF14; Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins

    2. XM_063286469.1 → XP_063142539.1  PHD finger protein 14 isoform X4

      UniProtKB/TrEMBL
      A0A0G2K7P2

    3. XM_063286474.1 → XP_063142544.1  PHD finger protein 14 isoform X9

      UniProtKB/TrEMBL
      A0A8I5Y7V8
      Related
      ENSRNOP00000089184.2, ENSRNOT00000094938.2

    4. XM_006236104.5 → XP_006236166.1  PHD finger protein 14 isoform X1

      See identical proteins and their annotated locations for XP_006236166.1

      UniProtKB/TrEMBL
      A0A8I6ASZ4
      Related
      ENSRNOP00000074287.3, ENSRNOT00000089897.3
      Conserved Domains (4) summary
      cd15561
      Location:313 → 369
      PHD1_PHF14; PHD finger 1 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15562
      Location:719 → 768
      PHD2_PHF14; PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15563
      Location:862 → 920
      PHD3_PHF14; PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15674
      Location:377 → 490
      ePHD_PHF14; Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins

    5. XM_063286468.1 → XP_063142538.1  PHD finger protein 14 isoform X3

    6. XM_063286472.1 → XP_063142542.1  PHD finger protein 14 isoform X7

    7. XM_039108097.2 → XP_038964025.1  PHD finger protein 14 isoform X10

      UniProtKB/TrEMBL
      A6IDZ2
      Related
      ENSRNOP00000095907.1, ENSRNOT00000106332.2
      Conserved Domains (4) summary
      cd15561
      Location:36 → 92
      PHD1_PHF14; PHD finger 1 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15562
      Location:442 → 491
      PHD2_PHF14; PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15563
      Location:585 → 643
      PHD3_PHF14; PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins
      cd15674
      Location:100 → 213
      ePHD_PHF14; Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins

    8. XM_063286470.1 → XP_063142540.1  PHD finger protein 14 isoform X5

      Related
      ENSRNOP00000079696.2, ENSRNOT00000103513.2

    9. XM_063286471.1 → XP_063142541.1  PHD finger protein 14 isoform X6

      Related
      ENSRNOP00000098004.2, ENSRNOT00000120231.2

    10. XM_063286473.1 → XP_063142543.1  PHD finger protein 14 isoform X8

      UniProtKB/TrEMBL
      A0A8I5Y7V8
      Related
      ENSRNOP00000077762.1, ENSRNOT00000108109.2

    RNA

    1. XR_010065688.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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