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    Phf6 PHD finger protein 6 [ Mus musculus (house mouse) ]

    Gene ID: 70998, updated on 2-Oct-2018

    Summary

    Official Symbol
    Phf6provided by MGI
    Official Full Name
    PHD finger protein 6provided by MGI
    Primary source
    MGI:MGI:1918248
    See related
    Ensembl:ENSMUSG00000025626 Vega:OTTMUSG00000017343
    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
    Also known as
    mKIAA1823; 2700007B13Rik; 4931428F02Rik
    Expression
    Biased expression in CNS E11.5 (RPKM 18.3), whole brain E14.5 (RPKM 16.6) and 14 other tissues See more
    Orthologs

    Genomic context

    See Phf6 in Genome Data Viewer
    Location:
    X; X A5
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) X NC_000086.7 (52912214..52956961)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) X NC_000086.6 (50265443..50310120)

    Chromosome X - NC_000086.7Genomic Context describing neighboring genes Neighboring gene POU domain, class 5, transcription factor 1, related sequence 8 Neighboring gene ribosomal protein S2, pseudogene 13 Neighboring gene hypoxanthine guanine phosphoribosyl transferase Neighboring gene microRNA 450b

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (2) 

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
     
    enzyme binding ISO
    Inferred from Sequence Orthology
    more info
     
    histone binding ISO
    Inferred from Sequence Orthology
    more info
     
    histone deacetylase binding ISO
    Inferred from Sequence Orthology
    more info
     
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    phosphoprotein binding ISO
    Inferred from Sequence Orthology
    more info
     
    ribonucleoprotein complex binding ISO
    Inferred from Sequence Orthology
    more info
     
    scaffold protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    tubulin binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    blastocyst hatching IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    chromosome, centromeric region IEA
    Inferred from Electronic Annotation
    more info
     
    kinetochore IEA
    Inferred from Electronic Annotation
    more info
     
    nucleolus ISO
    Inferred from Sequence Orthology
    more info
     
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    NCBI Reference Sequences (RefSeq)

    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_001290546.1NP_001277475.1  PHD finger protein 6 isoform 2

      See identical proteins and their annotated locations for NP_001277475.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AK016480, AK028498, BC055330, CJ287261
      Consensus CDS
      CCDS72380.1
      UniProtKB/Swiss-Prot
      Q9D4J7
      Related
      ENSMUSP00000130358.1, OTTMUSP00000049153, ENSMUST00000154864.3, OTTMUST00000042252
      Conserved Domains (2) summary
      cd15711
      Location:132249
      ePHD2_PHF6; Extended PHD finger 2 found in PHD finger protein 6 (PHF6)
      cl22851
      Location:151
      PHD_SF; PHD finger superfamily
    2. NM_027642.2NP_081918.1  PHD finger protein 6 isoform 1

      See identical proteins and their annotated locations for NP_081918.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK016480, BC055330, CJ287261
      Consensus CDS
      CCDS30127.1
      UniProtKB/Swiss-Prot
      Q9D4J7
      Related
      ENSMUSP00000077971.6, OTTMUSP00000018937, ENSMUST00000078944.12, OTTMUST00000042126
      Conserved Domains (2) summary
      cd15710
      Location:17131
      ePHD1_PHF6; Extended PHD finger 1 found in PHD finger protein 6 (PHF6)
      cd15711
      Location:212329
      ePHD2_PHF6; Extended PHD finger 2 found in PHD finger protein 6 (PHF6)

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000086.7 Reference GRCm38.p4 C57BL/6J

      Range
      52912214..52956961
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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