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    PHF10 PHD finger protein 10 [ Homo sapiens (human) ]

    Gene ID: 55274, updated on 27-Nov-2024

    Summary

    Official Symbol
    PHF10provided by HGNC
    Official Full Name
    PHD finger protein 10provided by HGNC
    Primary source
    HGNC:HGNC:18250
    See related
    Ensembl:ENSG00000130024 MIM:613069; AllianceGenome:HGNC:18250
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BAF45A; XAP135; SMARCG4
    Summary
    This gene contains a predicted ORF that encodes a protein with two zinc finger domains. The function of the encoded protein is not known. Sequence analysis suggests that multiple alternatively spliced transcript variants are derived from this gene but the full-length nature of only two of them is known. These two splice variants encode different isoforms. A pseudogene for this gene is located on Xq28. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in adrenal (RPKM 31.1), ovary (RPKM 25.5) and 25 other tissues See more
    Orthologs
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    Genomic context

    See PHF10 in Genome Data Viewer
    Location:
    6q27
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (169703902..169724500, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (171057816..171078422, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (170103998..170124596, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169829202-169829769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169849141-169850015 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169850016-169850889 Neighboring gene WD repeat domain 27 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169952752-169953720 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:169956378-169956538 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169964074-169964574 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17796 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:170017112-170017650 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:170019030-170019674 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:170019675-170020319 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170024255-170024754 Neighboring gene uncharacterized LOC124901471 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170040667-170041282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170047131-170048124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25463 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:170056229-170057024 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:170057025-170057820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170061015-170061514 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:170062913-170064112 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:170067058-170067246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170067590-170068090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170068091-170068591 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170092723-170093223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17797 Neighboring gene chromosome 6 open reading frame 120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17798 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:170124719-170125261 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17799 Neighboring gene MPRA-validated peak6328 silencer Neighboring gene dynein light chain Tctex-type 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170171824-170172324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170172325-170172825 Neighboring gene ER membrane associated RNA degradation Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:170183046-170183546 Neighboring gene long intergenic non-protein coding RNA 242 Neighboring gene long intergenic non-protein coding RNA 574

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide meta-analysis of six type 1 diabetes cohorts identifies multiple associated loci.
    EBI GWAS Catalog
    Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ10975, MGC111009

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone acetyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    part_of RSC-type complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of SWI/SNF complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in chromatin NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in kinetochore NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of npBAF complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of npBAF complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in nuclear matrix NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    PHD finger protein 10
    Names
    BRG1-associated factor 45a
    BRG1-associated factor, 45-KD, A
    PHD zinc finger protein XAP135

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_018288.4NP_060758.2  PHD finger protein 10 isoform a

      See identical proteins and their annotated locations for NP_060758.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform.
      Source sequence(s)
      AL513547, BC110323, DB460742
      Consensus CDS
      CCDS5308.2
      UniProtKB/Swiss-Prot
      Q2YDA3, Q53HG8, Q8WUB8, Q9BXD2, Q9NV26
      UniProtKB/TrEMBL
      S5FMB0
      Related
      ENSP00000341805.4, ENST00000339209.9
      Conserved Domains (3) summary
      cd15528
      Location:379433
      PHD1_PHF10; PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins
      cd15529
      Location:435478
      PHD2_PHF10; PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins
      cd21085
      Location:73161
      WH_NTD_PHF10; N-terminal winged helix DNA-binding domain found in PHD finger protein 10 (PHF10) and similar proteins
    2. NM_133325.3NP_579866.2  PHD finger protein 10 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice junction which results in 6 fewer nt when compared to variant 1. It encodes an isoform (b) that lacks 2 internal amino acids compared to isoform a.
      Source sequence(s)
      AL513547
      Consensus CDS
      CCDS5309.2
      UniProtKB/TrEMBL
      S5FMB0
      Related
      ENSP00000355743.4, ENST00000366780.8
      Conserved Domains (2) summary
      cd15528
      Location:377431
      PHD1_PHF10; PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins
      cd15529
      Location:433476
      PHD2_PHF10; PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      169703902..169724500 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      171057816..171078422 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355780.1XP_054211755.1  PHD finger protein 10 isoform X1