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

Gene ID: 70998, updated on 12-May-2024

Summary

Official Symbol
Phf6provided by MGI
Official Full Name
PHD finger protein 6provided by MGI
Primary source
MGI:MGI:1918248
See related
Ensembl:ENSMUSG00000025626 AllianceGenome:MGI:1918248
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
Summary
Predicted to enable several functions, including histone deacetylase binding activity; phosphoprotein binding activity; and scaffold protein binding activity. Acts upstream of or within blastocyst hatching. Located in nucleus. Is expressed in several structures, including alimentary system; nervous system; sensory organ; skin; and testis. Used to study Borjeson-Forssman-Lehmann syndrome. Human ortholog(s) of this gene implicated in Borjeson-Forssman-Lehmann syndrome. Orthologous to human PHF6 (PHD finger protein 6). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in CNS E11.5 (RPKM 18.3), whole brain E14.5 (RPKM 16.6) and 14 other tissues See more
Orthologs
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Genomic context

See Phf6 in Genome Data Viewer
Location:
X A5; X 29.28 cM
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (52001091..52045838)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (52912214..52956961)

Chromosome X - NC_000086.8Genomic 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 phosphoribosyltransferase 1 Neighboring gene predicted gene, 57846 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 Functions

What's a GeneRIF?

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables enzyme binding ISO
Inferred from Sequence Orthology
more info
 
enables histone binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables histone binding ISO
Inferred from Sequence Orthology
more info
 
enables histone deacetylase binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables histone deacetylase binding ISO
Inferred from Sequence Orthology
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables phosphoprotein binding ISO
Inferred from Sequence Orthology
more info
 
enables ribonucleoprotein complex binding ISO
Inferred from Sequence Orthology
more info
 
enables scaffold protein binding ISO
Inferred from Sequence Orthology
more info
 
enables tubulin binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within blastocyst hatching IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
located_in chromosome, centromeric region IEA
Inferred from Electronic Annotation
more info
 
located_in kinetochore IEA
Inferred from Electronic Annotation
more info
 
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

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_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
    ENSMUSP00000130358.2, ENSMUST00000154864.4
    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
    Q80T86, Q8BYT8, Q8C1B5, Q9D4J7
    UniProtKB/TrEMBL
    E9QAG2
    Related
    ENSMUSP00000077971.7, ENSMUST00000078944.13
    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: 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_000086.8 Reference GRCm39 C57BL/6J

    Range
    52001091..52045838
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)