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

Gene ID: 101471, updated on 2-Nov-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, Nov 2024]
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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See Phrf1 in Genome Data Viewer
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 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. PHRF1 promotes the class switch recombination of IgA in CH12F3-2A cells. Lee JY, et al. PLoS One, 2023. PMID 37540725, Free PMC Article
  3. 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
  4. Tagging genes with cassette-exchange sites. Cobellis G, et al. Nucleic Acids Res, 2005 Mar 1. PMID 15741177, Free PMC Article
  5. 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

See all (24) 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 RNA polymerase binding ISS
Inferred from Sequence or Structural Similarity
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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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

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