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    Phf21b PHD finger protein 21B [ Mus musculus (house mouse) ]

    Gene ID: 271305, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Phf21bprovided by MGI
    Official Full Name
    PHD finger protein 21Bprovided by MGI
    Primary source
    MGI:MGI:2443812
    See related
    Ensembl:ENSMUSG00000016624 AllianceGenome:MGI:2443812
    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
    A730032D07Rik
    Summary
    Predicted to enable metal ion binding activity. Is expressed in several structures, including central nervous system; dorsal root ganglion; lens; and lower urinary tract. Orthologous to human PHF21B (PHD finger protein 21B). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in CNS E11.5 (RPKM 19.3), whole brain E14.5 (RPKM 16.1) and 13 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    15 E2; 15 40.08 cM
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (84669577..84740330, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (84785376..84856129, complement)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 41374 Neighboring gene STARR-seq mESC enhancer starr_39372 Neighboring gene predicted gene, 20556 Neighboring gene Rho GTPase activating protein 8 Neighboring gene predicted gene, 52202 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene predicted gene, 46528

    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. The epigenetic reader PHF21B modulates murine social memory and synaptic plasticity-related genes. Chin EW, et al. JCI Insight, 2022 Jul 22. PMID 35866480, Free PMC Article
    2. Phf21b imprints the spatiotemporal epigenetic switch essential for neural stem cell differentiation. Basu A, et al. Genes Dev, 2020 Sep 1. PMID 32820037, Free PMC Article
    3. Analysis of HSF4 binding regions reveals its necessity for gene regulation during development and heat shock response in mouse lenses. Fujimoto M, et al. J Biol Chem, 2008 Oct 31. PMID 18755693, Free PMC Article
    4. The AERO system: a 3D-like approach for recording gene expression patterns in the whole mouse embryo. Shimizu H, et al. PLoS One, 2013. PMID 24146773, Free PMC Article
    5. A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58. Yokoyama S, et al. Dev Cell, 2009 Dec. PMID 20059953, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The epigenetic reader PHF21B modulates murine social memory and synaptic plasticity-related genes.
      Title: The epigenetic reader PHF21B modulates murine social memory and synaptic plasticity-related genes.
    2. Phf21b imprints the spatiotemporal epigenetic switch essential for neural stem cell differentiation.
      Title: Phf21b imprints the spatiotemporal epigenetic switch essential for neural stem cell differentiation.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    PHD finger protein 21B

    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_001081166.2 → NP_001074635.2  PHD finger protein 21B isoform 1

      See identical proteins and their annotated locations for NP_001074635.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer protein.
      Source sequence(s)
      AK046530, AL513352, BM936475
      Consensus CDS
      CCDS37169.2
      UniProtKB/Swiss-Prot
      Q8C966
      UniProtKB/TrEMBL
      B2RXP2
      Related
      ENSMUSP00000125355.2, ENSMUST00000159939.8
      Conserved Domains (1) summary
      cl22851
      Location:309 → 351
      PHD_SF; PHD finger superfamily

    2. NM_001356573.1 → NP_001343502.1  PHD finger protein 21B isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL513352
      Consensus CDS
      CCDS88821.1
      UniProtKB/TrEMBL
      B2RXP2, F8WGM2
      Related
      ENSMUSP00000016768.6, ENSMUST00000016768.12
      Conserved Domains (4) summary
      COG5118
      Location:132 → 252
      BDP1; Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
      cl22851
      Location:297 → 339
      PHD_SF; PHD finger superfamily
      cl26267
      Location:241 → 343
      ING; Inhibitor of growth proteins N-terminal histone-binding
      cl26464
      Location:50 → 161
      Atrophin-1; Atrophin-1 family

    RNA

    1. NR_030731.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK046530, AL513352, BM936475

    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_000081.7 Reference GRCm39 C57BL/6J

      Range
      84669577..84740330 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006521034.4 → XP_006521097.1  PHD finger protein 21B isoform X1

      UniProtKB/TrEMBL
      B2RXP2
      Conserved Domains (4) summary
      PHA03247
      Location:40 → 151
      PHA03247; large tegument protein UL36; Provisional
      COG5034
      Location:231 → 333
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      COG5118
      Location:122 → 242
      BDP1; Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
      cl22851
      Location:287 → 329
      PHD_SF; PHD finger superfamily

    2. XM_036159445.1 → XP_036015338.1  PHD finger protein 21B isoform X2

      Conserved Domains (2) summary
      PHA03247
      Location:15 → 279
      PHA03247; large tegument protein UL36; Provisional
      cl22851
      Location:355 → 397
      PHD_SF; PHD finger superfamily

    3. XM_017316655.3 → XP_017172144.1  PHD finger protein 21B isoform X3

      Conserved Domains (1) summary
      PHA03247
      Location:15 → 279
      PHA03247; large tegument protein UL36; Provisional

    RNA

    1. XR_003951399.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8C966.1 GenPept UniProtKB/Swiss-Prot:Q8C966

    Gene LinkOut

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

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