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    Phrf1 PHD and ring finger domains 1 [ Mus musculus (house mouse) ]

    Gene ID: 101471, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Phrf1provided by MGI
    Official Full Name
    PHD and ring finger domains 1provided by MGI
    Primary source
    MGI:MGI:2141847
    See related
    Ensembl:ENSMUSG00000038611 AllianceGenome:MGI:2141847
    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
    Summary
    Predicted to enable RNA polymerase binding activity and protein domain specific binding activity. Predicted to be involved in mRNA processing and transcription by RNA polymerase II. Is expressed in several structures, including central nervous system and retina. Orthologous to human PHRF1 (PHD and ring finger domains 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thymus adult (RPKM 11.5), CNS E11.5 (RPKM 7.5) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    7 F5; 7 86.53 cM
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (140808373..140842664)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (141228477..141262751)

    Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene lamin tail domain containing 2 Neighboring gene STARR-positive B cell enhancer ABC_E1749 Neighboring gene Ras association (RalGDS/AF-6) domain family (N-terminal) member 7 Neighboring gene STARR-positive B cell enhancer ABC_E2854 Neighboring gene microRNA 210 Neighboring gene STARR-positive B cell enhancer ABC_E11376 Neighboring gene predicted gene, 51460 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: 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. An important role of PHRF1 in dendritic architecture and memory formation by modulating TGF-β signaling. Shih TW, et al. Sci Rep, 2020 Jul 2. PMID 32616804, Free PMC Article
    2. Laser capture microdissection and cDNA array analysis for identification of mouse KIAA/FLJ genes differentially expressed in the embryonic dorsal spinal cord. Masuda T, et al. Brain Res, 2009 Jan 16. PMID 19026994
    3. Tagging genes with cassette-exchange sites. Cobellis G, et al. Nucleic Acids Res, 2005 Mar 1. PMID 15741177, Free PMC Article
    4. Prediction of the coding sequences of mouse homologues of KIAA gene: III. the complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries. Okazaki N, et al. DNA Res, 2003 Aug 31. PMID 14621295
    5. Genomic analysis of mouse retinal development. Blackshaw S, et al. PLoS Biol, 2004 Sep. PMID 15226823, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PHRF1 promotes the class switch recombination of IgA in CH12F3-2A cells.
      Title: PHRF1 promotes the class switch recombination of IgA in CH12F3-2A cells.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA polymerase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein domain specific binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    PHD and RING finger domain-containing protein 1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001081118.2 → NP_001074587.1  PHD and RING finger domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001074587.1

      Status: VALIDATED

      Source sequence(s)
      AC108908, AC163434
      Consensus CDS
      CCDS52441.1
      UniProtKB/Swiss-Prot
      A6H619, Q505G1, Q6ZPN4
      Related
      ENSMUSP00000101648.3, ENSMUST00000106027.9
      Conserved Domains (5) summary
      PHA03247
      Location:1175 → 1518
      PHA03247; large tegument protein UL36; Provisional
      PHA03307
      Location:561 → 773
      PHA03307; transcriptional regulator ICP4; Provisional
      cd15536
      Location:187 → 232
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      cd16635
      Location:107 → 150
      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 → 108
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    2. NM_001419133.1 → NP_001406062.1  PHD and RING finger domain-containing protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC108908, AC163434

    3. NM_001419134.1 → NP_001406063.1  PHD and RING finger domain-containing protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC108908, AC163434

    4. NM_001419136.1 → NP_001406065.1  PHD and RING finger domain-containing protein 1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC108908, AC163434

    5. NM_001419137.1 → NP_001406066.1  PHD and RING finger domain-containing protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC108908, AC163434

    6. NM_001419138.1 → NP_001406067.1  PHD and RING finger domain-containing protein 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC108908, AC163434
      Related
      ENSMUSP00000113195.2, ENSMUST00000122143.8

    RNA

    1. NR_185020.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC108908, AC163434

    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_000073.7 Reference GRCm39 C57BL/6J

      Range
      140808373..140842664
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006536137.5 → XP_006536200.1  PHD and RING finger domain-containing protein 1 isoform X1

      Conserved Domains (4) summary
      PHA03247
      Location:1306 → 1614
      PHA03247; large tegument protein UL36; Provisional
      PHA03307
      Location:579 → 791
      PHA03307; transcriptional regulator ICP4; Provisional
      cd15536
      Location:205 → 250
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      cd16635
      Location:125 → 168
      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

    2. XM_006536143.5 → XP_006536206.1  PHD and RING finger domain-containing protein 1 isoform X6

      Conserved Domains (4) summary
      PHA03247
      Location:1193 → 1532
      PHA03247; large tegument protein UL36; Provisional
      PHA03307
      Location:579 → 785
      PHA03307; transcriptional regulator ICP4; Provisional
      cd15536
      Location:205 → 250
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      cd16635
      Location:125 → 168
      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

    3. XM_006536139.5 → XP_006536202.1  PHD and RING finger domain-containing protein 1 isoform X3

      Conserved Domains (5) summary
      PHA03247
      Location:1193 → 1536
      PHA03247; large tegument protein UL36; Provisional
      PHA03307
      Location:579 → 791
      PHA03307; transcriptional regulator ICP4; Provisional
      cd15536
      Location:205 → 250
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      cd16635
      Location:125 → 168
      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
      pfam03154
      Location:1475 → 1601
      Atrophin-1; Atrophin-1 family

    4. XM_006536144.5 → XP_006536207.1  PHD and RING finger domain-containing protein 1 isoform X9

      Conserved Domains (4) summary
      PHA03247
      Location:1186 → 1578
      PHA03247; large tegument protein UL36; Provisional
      PHA03307
      Location:579 → 791
      PHA03307; transcriptional regulator ICP4; Provisional
      cd15536
      Location:205 → 250
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      cd16635
      Location:125 → 168
      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

    5. XM_006536138.5 → XP_006536201.1  PHD and RING finger domain-containing protein 1 isoform X2

      Conserved Domains (4) summary
      PHA03247
      Location:1305 → 1613
      PHA03247; large tegument protein UL36; Provisional
      PHA03307
      Location:578 → 790
      PHA03307; transcriptional regulator ICP4; Provisional
      cd15536
      Location:204 → 249
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      cd16635
      Location:124 → 167
      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

    6. XM_006536145.5 → XP_006536208.1  PHD and RING finger domain-containing protein 1 isoform X10

      Conserved Domains (4) summary
      PHA03247
      Location:1185 → 1577
      PHA03247; large tegument protein UL36; Provisional
      PHA03307
      Location:578 → 790
      PHA03307; transcriptional regulator ICP4; Provisional
      cd15536
      Location:204 → 249
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      cd16635
      Location:124 → 167
      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

    7. XM_006536141.4 → XP_006536204.1  PHD and RING finger domain-containing protein 1 isoform X4

      See identical proteins and their annotated locations for XP_006536204.1

      Conserved Domains (4) summary
      PHA03247
      Location:1288 → 1596
      PHA03247; large tegument protein UL36; Provisional
      PHA03307
      Location:561 → 773
      PHA03307; transcriptional regulator ICP4; Provisional
      cd15536
      Location:187 → 232
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      cd16635
      Location:107 → 150
      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

    8. XM_036152509.1 → XP_036008402.1  PHD and RING finger domain-containing protein 1 isoform X7

      UniProtKB/Swiss-Prot
      A6H619, Q505G1, Q6ZPN4
      Conserved Domains (5) summary
      PHA03247
      Location:1175 → 1518
      PHA03247; large tegument protein UL36; Provisional
      PHA03307
      Location:561 → 773
      PHA03307; transcriptional regulator ICP4; Provisional
      cd15536
      Location:187 → 232
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      cd16635
      Location:107 → 150
      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 → 108
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    9. XM_006536142.2 → XP_006536205.1  PHD and RING finger domain-containing protein 1 isoform X5

      Conserved Domains (4) summary
      PHA03247
      Location:1287 → 1595
      PHA03247; large tegument protein UL36; Provisional
      PHA03307
      Location:560 → 772
      PHA03307; transcriptional regulator ICP4; Provisional
      cd15536
      Location:186 → 231
      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

    10. XM_030241933.1 → XP_030097793.1  PHD and RING finger domain-containing protein 1 isoform X5

      Conserved Domains (4) summary
      PHA03247
      Location:1287 → 1595
      PHA03247; large tegument protein UL36; Provisional
      PHA03307
      Location:560 → 772
      PHA03307; transcriptional regulator ICP4; Provisional
      cd15536
      Location:186 → 231
      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

    11. XM_011249837.4 → XP_011248139.1  PHD and RING finger domain-containing protein 1 isoform X4

      See identical proteins and their annotated locations for XP_011248139.1

      Conserved Domains (4) summary
      PHA03247
      Location:1288 → 1596
      PHA03247; large tegument protein UL36; Provisional
      PHA03307
      Location:561 → 773
      PHA03307; transcriptional regulator ICP4; Provisional
      cd15536
      Location:187 → 232
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      cd16635
      Location:107 → 150
      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

    12. XM_036152511.1 → XP_036008404.1  PHD and RING finger domain-containing protein 1 isoform X8

      Conserved Domains (5) summary
      PHA03247
      Location:1174 → 1517
      PHA03247; large tegument protein UL36; Provisional
      PHA03307
      Location:560 → 772
      PHA03307; transcriptional regulator ICP4; Provisional
      cd15536
      Location:186 → 231
      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_036152515.1 → XP_036008408.1  PHD and RING finger domain-containing protein 1 isoform X14

      Conserved Domains (2) summary
      PHA03247
      Location:639 → 1031
      PHA03247; large tegument protein UL36; Provisional
      PHA03307
      Location:32 → 244
      PHA03307; transcriptional regulator ICP4; Provisional

    RNA

    1. XR_004933983.1 RNA Sequence

    2. XR_004933984.1 RNA Sequence

    3. XR_004933985.1 RNA Sequence

    4. XR_004933987.1 RNA Sequence

    5. XR_004933986.1 RNA Sequence

    6. XR_389947.4 RNA Sequence

    7. XR_004933988.1 RNA Sequence

      Related
      ENSMUST00000155123.8

    8. XR_004933990.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_207211.1: Suppressed sequence

      Description
      NM_207211.1: 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
    Protein Accession Links
    GenPept Link UniProtKB Link
    A6H619.2 GenPept UniProtKB/Swiss-Prot:A6H619

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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