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    Phrf1 PHD and ring finger domains 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 245925, updated on 10-Oct-2024

    Summary

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    Official Symbol
    Phrf1provided by RGD
    Official Full Name
    PHD and ring finger domains 1provided by RGD
    Primary source
    RGD:708360
    See related
    EnsemblRapid:ENSRNOG00000017299 AllianceGenome:RGD:708360
    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
    Summary
    Enables RNA polymerase binding activity and protein domain specific binding activity. Involved in mRNA processing and transcription by RNA polymerase II. Orthologous to human PHRF1 (PHD and ring finger domains 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 114.2), Spleen (RPKM 102.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Phrf1 in Genome Data Viewer
    Location:
    1q41
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (205763264..205796478)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (196333663..196366901)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (214215673..214248906)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene lamin tail domain containing 2 Neighboring gene Ras association domain family member 7 Neighboring gene uncharacterized LOC102553043 Neighboring gene microRNA 3574 Neighboring gene microRNA 210 Neighboring gene interferon regulatory factor 7 Neighboring gene cadherin-related family member 5

    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. The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Yuryev A, et al. Proc Natl Acad Sci U S A, 1996 Jul 9. PMID 8692929, Free PMC Article
    2. Defining the membrane proteome of NK cells. Ghosh D, et al. J Mass Spectrom, 2010 Jan. PMID 19946888

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA polymerase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein domain specific binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    PHD and RING finger domain-containing protein 1
    Names
    CTD-binding SR-like protein rA9

    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_001401353.1 → NP_001388282.1  PHD and RING finger domain-containing protein 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001

    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_086019.1 Reference GRCr8

      Range
      205763264..205796478
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039098028.2 → XP_038953956.1  PHD and RING finger domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A6HXS0
      Conserved Domains (4) summary
      PHA03247
      Location:1291 → 1598
      PHA03247; large tegument protein UL36; Provisional
      cd15536
      Location:189 → 234
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      cd16635
      Location:106 → 149
      mRING-HC-C3HC3D_PHRF1; Modified RING finger, HC subclass (C3HC3D-type), found in PHD and RING finger domain-containing protein 1(PHRF1) and similar proteins
      NF033845
      Location:13 → 107
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    2. XM_006230511.5 → XP_006230573.1  PHD and RING finger domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006230573.1

      UniProtKB/TrEMBL
      A6HXS0
      Conserved Domains (2) summary
      cd15536
      Location:190 → 235
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      pfam13639
      Location:107 → 150
      zf-RING_2; Ring finger domain

    3. XM_063280803.1 → XP_063136873.1  PHD and RING finger domain-containing protein 1 isoform X3

      UniProtKB/Swiss-Prot
      Q63625
      Related
      ENSRNOP00000023376.1, ENSRNOT00000023376.6

    4. XM_006230510.5 → XP_006230572.1  PHD and RING finger domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006230572.1

      UniProtKB/TrEMBL
      A6HXS0
      Conserved Domains (2) summary
      cd15536
      Location:190 → 235
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      pfam13639
      Location:107 → 150
      zf-RING_2; Ring finger domain

    5. XM_006230515.5 → XP_006230577.1  PHD and RING finger domain-containing protein 1 isoform X5

      UniProtKB/TrEMBL
      A6HXS0
      Conserved Domains (2) summary
      cd15536
      Location:190 → 235
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      pfam13639
      Location:107 → 150
      zf-RING_2; Ring finger domain

    6. XM_006230514.5 → XP_006230576.1  PHD and RING finger domain-containing protein 1 isoform X3

      See identical proteins and their annotated locations for XP_006230576.1

      UniProtKB/Swiss-Prot
      Q63625
      UniProtKB/TrEMBL
      A6HXS0
      Related
      ENSRNOP00000101712.1, ENSRNOT00000150569.1
      Conserved Domains (2) summary
      cd15536
      Location:190 → 235
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      pfam13639
      Location:107 → 150
      zf-RING_2; Ring finger domain

    7. XM_006230513.5 → XP_006230575.1  PHD and RING finger domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A6HXS0
      Conserved Domains (4) summary
      PHA03247
      Location:1291 → 1598
      PHA03247; large tegument protein UL36; Provisional
      cd15536
      Location:189 → 234
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      cd16635
      Location:106 → 149
      mRING-HC-C3HC3D_PHRF1; Modified RING finger, HC subclass (C3HC3D-type), found in PHD and RING finger domain-containing protein 1(PHRF1) and similar proteins
      NF033845
      Location:13 → 107
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    8. XM_063280804.1 → XP_063136874.1  PHD and RING finger domain-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      A0A8L2QQ15
      Related
      ENSRNOP00000046880.3, ENSRNOT00000051755.6

    9. XM_006230517.5 → XP_006230579.1  PHD and RING finger domain-containing protein 1 isoform X6

      UniProtKB/TrEMBL
      A6HXS0
      Conserved Domains (2) summary
      cd15536
      Location:189 → 234
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      pfam13639
      Location:106 → 149
      zf-RING_2; Ring finger domain

    10. XM_063280805.1 → XP_063136875.1  PHD and RING finger domain-containing protein 1 isoform X7

    11. XM_063280808.1 → XP_063136878.1  PHD and RING finger domain-containing protein 1 isoform X8

    12. XM_039098067.2 → XP_038953995.1  PHD and RING finger domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A6HXS0
      Conserved Domains (4) summary
      PHA03247
      Location:1291 → 1598
      PHA03247; large tegument protein UL36; Provisional
      cd15536
      Location:189 → 234
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      cd16635
      Location:106 → 149
      mRING-HC-C3HC3D_PHRF1; Modified RING finger, HC subclass (C3HC3D-type), found in PHD and RING finger domain-containing protein 1(PHRF1) and similar proteins
      NF033845
      Location:13 → 107
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    13. XM_017588782.3 → XP_017444271.1  PHD and RING finger domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A6HXS0
      Conserved Domains (2) summary
      cd15536
      Location:190 → 235
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      pfam13639
      Location:107 → 150
      zf-RING_2; Ring finger domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_139093.1: Suppressed sequence

      Description
      NM_139093.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q63625.2 GenPept UniProtKB/Swiss-Prot:Q63625

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