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    PHF5A PHD finger protein 5A [ Homo sapiens (human) ]

    Gene ID: 84844, updated on 27-Nov-2024

    Summary

    Official Symbol
    PHF5Aprovided by HGNC
    Official Full Name
    PHD finger protein 5Aprovided by HGNC
    Primary source
    HGNC:HGNC:18000
    See related
    Ensembl:ENSG00000100410 MIM:617846; AllianceGenome:HGNC:18000
    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
    INI; Rds3; SF3B7; SAP14b; SF3b14b; bK223H9.2
    Summary
    This gene encodes a subunit of the splicing factor 3b protein complex. Splicing factor 3b, together with splicing factor 3a and a 12S RNA unit, forms the U2 small nuclear ribonucleoproteins complex (U2 snRNP). The splicing factor 3b/3a complex binds pre-mRNA upstream of the intron's branch site in a sequence-independent manner and may anchor the U2 snRNP to the pre-mRNA. The protein encoded by this gene contains a PHD-finger-like domain that is flanked by highly basic N- and C-termini. This protein belongs to the PHD-finger superfamily and may act as a chromatin-associated protein. This gene has several pseudogenes on different chromosomes. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in bone marrow (RPKM 19.5), lymph node (RPKM 15.5) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See PHF5A in Genome Data Viewer
    Location:
    22q13.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (41459717..41468692, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (41938569..41947547, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (41855721..41864696, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41832900-41833403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19114 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:41842575-41843270 Neighboring gene uncharacterized LOC105373043 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41843271-41843966 Neighboring gene transducer of ERBB2, 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41864665-41865226 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:41865227-41865788 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13791 Neighboring gene aconitase 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:41906728-41906890 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41908781-41909388 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41909996-41910602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41910603-41911209 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19118 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:41922291-41922505 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41927905-41928713 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41928714-41929522 Neighboring gene Sharpr-MPRA regulatory region 5669 Neighboring gene RNA polymerase III subunit H Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41939835-41940672 Neighboring gene uncharacterized LOC105373044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41951599-41952098 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:41952629-41952876

    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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Clone Names

    • MGC1346

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA binding HDA PubMed 
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in U2-type prespliceosome assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in stem cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of U12-type spliceosomal complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of U2 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of U2 snRNP IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of U2 snRNP NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of U2-type precatalytic spliceosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of U2-type spliceosomal complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of U2-type spliceosomal complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    located_in nuclear matrix IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nuclear speck ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of precatalytic spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of spliceosomal complex NAS
    Non-traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    PHD finger-like domain-containing protein 5A
    Names
    PHD finger-like domain protein 5A
    PHD-finger 5a
    splicing factor 3B associated 14 kDa protein
    splicing factor 3b, subunit 7

    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_032758.4NP_116147.1  PHD finger-like domain-containing protein 5A

      See identical proteins and their annotated locations for NP_116147.1

      Status: REVIEWED

      Source sequence(s)
      AL008582, BC007321, BU584712
      Consensus CDS
      CCDS14016.1
      UniProtKB/Swiss-Prot
      Q7RTV0, Q9UH06
      Related
      ENSP00000216252.3, ENST00000216252.4
      Conserved Domains (1) summary
      pfam03660
      Location:1104
      PHF5; PHF5-like protein

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      41459717..41468692 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      41938569..41947547 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)