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

Gene ID: 271305, updated on 2-Nov-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, Nov 2024]
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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See Phf21b in Genome Data Viewer
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 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. 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
  2. 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
  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 (23) 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

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