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Aliases for PHF5A Gene

Aliases for PHF5A Gene

  • PHD Finger Protein 5A 2 3 5
  • PHD Finger-Like Domain Protein 5A 3 4
  • Splicing Factor 3b, Subunit 7 2 3
  • SF3b14b 3 4
  • PHD Finger-Like Domain-Containing Protein 5A 3
  • Splicing Factor 3B Associated 14 KDa Protein 3
  • Splicing Factor 3B-Associated 14 KDa Protein 4
  • PHD-Finger 5a 3
  • BK223H9.2 3
  • SAP14b 3
  • SF3B7 3
  • Rds3 3
  • INI 3

External Ids for PHF5A Gene

Previous GeneCards Identifiers for PHF5A Gene

  • GC22M038470
  • GC22M040098
  • GC22M040180
  • GC22M041855
  • GC22M024821

Summaries for PHF5A Gene

Entrez Gene Summary for PHF5A Gene

  • 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]

GeneCards Summary for PHF5A Gene

PHF5A (PHD Finger Protein 5A) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity.

UniProtKB/Swiss-Prot for PHF5A Gene

  • Involved with the PAF1 complex (PAF1C) in transcriptional elongation by RNA polymerase II, and in regulation of development and maintenance of embryonic stem cell (ESC) pluripotency. Required for maintenance of ESCs self-renewal and cellular reprogramming of stem cells. Maintains pluripotency by recruiting and stabilizing PAF1C on pluripotency genes loci, and by regulating the expression of the pluripotency genes. Regulates the deposition of elongation-associated histone modifications, including dimethylated histone H3 Lys-79 (H3K79me2) and trimethylated histone H3 Lys-36 (H3K36me3), on PAF1C targets, self-renewal and pluripotency genes. Regulates RNA polymerase II promoter-proximal pause release of the PAF1C targets and self-renewal genes, and the levels of elongating (Ser-2 phosphorylated) RNA polymerase II in their gene bodies. Regulates muscle specification in adult stem cells by stabilizing PAF1C in chromatin to promote myogenic differentiation (By similarity). Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex (PubMed:27720643, PubMed:28541300). SF3B complex is required for A complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA (PubMed:12234937). Acts as a transcriptional regulator by binding to the GJA1/Cx43 promoter and enhancing its up-regulation by ESR1/ER-alpha (By similarity).

Additional gene information for PHF5A Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHF5A Gene

Genomics for PHF5A Gene

GeneHancer (GH) Regulatory Elements for PHF5A Gene

Promoters and enhancers for PHF5A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22I041467 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 563.5 -2.1 -2105 7 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 PHF5A ACO2 POLR3H MEI1 TOB2 EP300 NAGA CSDC2 L3MBTL2 FAM109B
GH22I041444 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 46 +22.0 22009 5.9 MLX ZFP64 FEZF1 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 ZNF143 TOB2 LOC105373043 L3MBTL2 ZC3H7B PHF5A EP300 SLC25A17 POLR3H NDUFA6-AS1 XRCC6
GH22I040634 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 35.8 +832.4 832398 4.4 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B ZNF213 MKL1 EP300 XRCC6 PHF5A EP300-AS1 ENSG00000272834 RPL4P6 ENSG00000232754 DNAJB7 TNRC6B
GH22I041961 Enhancer 0.9 ENCODE 80.7 -492.4 -492367 0.2 ZNF493 ZNF529 ZFP64 ZEB1 ZNF213 ZNF302 ZNF138 SCRT2 ZNF214 ZNF654 RN7SKP80 EP300 PHF5A POLDIP3 RPL5P34 RRP7BP ENSG00000232754 NDUFA6 L3MBTL2 ZC3H7B
GH22I041090 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 34.1 +375.9 375859 4.7 HDGF FOXA2 SMAD1 MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 EP300 MIR1281 PHF5A ENSG00000272834 L3MBTL2 XRCC6 LOC100506544 EP300-AS1 ENSG00000232754 ENSG00000227413
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PHF5A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PHF5A gene promoter:

Genomic Locations for PHF5A Gene

Genomic Locations for PHF5A Gene
chr22:41,459,717-41,468,725
(GRCh38/hg38)
Size:
9,009 bases
Orientation:
Minus strand
chr22:41,855,721-41,864,729
(GRCh37/hg19)

Genomic View for PHF5A Gene

Genes around PHF5A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF5A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHF5A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHF5A Gene

Proteins for PHF5A Gene

  • Protein details for PHF5A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7RTV0-PHF5A_HUMAN
    Recommended name:
    PHD finger-like domain-containing protein 5A
    Protein Accession:
    Q7RTV0
    Secondary Accessions:
    • Q9UH06

    Protein attributes for PHF5A Gene

    Size:
    110 amino acids
    Molecular mass:
    12405 Da
    Quaternary structure:
    • Interacts (via N-terminus) with U2AF1 and SRSF5; acts to bridge the two. Interacts (via C-terminus) with EP400 and DDX1; acts to bridge the two (By similarity). Component of splicing factor SF3B complex which is composed of at least eight subunits; SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6, PHF5A and DDX42 (PubMed:12234937, PubMed:12738865, PubMed:27720643, PubMed:28541300). Within the SF3B complex interacts directly with SF3B1 and SF3B3 (PubMed:27720643). The SF3B complex composed of SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6 and PHF5A interacts with U2AF2 (PubMed:27720643). SF3B associates with the splicing factor SF3A and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP) (PubMed:12234937). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (PubMed:15146077). Interacts with the PAF1 complex (PAF1C) composed of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61. Within the PAF1C interacts directly with CDC73 and WDR61. Interacts with RNA polymerase II (By similarity).

    Three dimensional structures from OCA and Proteopedia for PHF5A Gene

neXtProt entry for PHF5A Gene

Post-translational modifications for PHF5A Gene

  • Ubiquitination at isoforms=95
  • Modification sites at PhosphoSitePlus

Other Protein References for PHF5A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PHF5A Gene

Domains & Families for PHF5A Gene

Gene Families for PHF5A Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for PHF5A Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for PHF5A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q7RTV0

UniProtKB/Swiss-Prot:

PHF5A_HUMAN :
  • Belongs to the PHF5 family.
Family:
  • Belongs to the PHF5 family.
genes like me logo Genes that share domains with PHF5A: view

Function for PHF5A Gene

Molecular function for PHF5A Gene

UniProtKB/Swiss-Prot Function:
Involved with the PAF1 complex (PAF1C) in transcriptional elongation by RNA polymerase II, and in regulation of development and maintenance of embryonic stem cell (ESC) pluripotency. Required for maintenance of ESCs self-renewal and cellular reprogramming of stem cells. Maintains pluripotency by recruiting and stabilizing PAF1C on pluripotency genes loci, and by regulating the expression of the pluripotency genes. Regulates the deposition of elongation-associated histone modifications, including dimethylated histone H3 Lys-79 (H3K79me2) and trimethylated histone H3 Lys-36 (H3K36me3), on PAF1C targets, self-renewal and pluripotency genes. Regulates RNA polymerase II promoter-proximal pause release of the PAF1C targets and self-renewal genes, and the levels of elongating (Ser-2 phosphorylated) RNA polymerase II in their gene bodies. Regulates muscle specification in adult stem cells by stabilizing PAF1C in chromatin to promote myogenic differentiation (By similarity). Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex (PubMed:27720643, PubMed:28541300). SF3B complex is required for A complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA (PubMed:12234937). Acts as a transcriptional regulator by binding to the GJA1/Cx43 promoter and enhancing its up-regulation by ESR1/ER-alpha (By similarity).

Phenotypes From GWAS Catalog for PHF5A Gene

Gene Ontology (GO) - Molecular Function for PHF5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity ISS,IEA --
GO:0003723 RNA binding IEA,HDA 22658674
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PHF5A: view
genes like me logo Genes that share phenotypes with PHF5A: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PHF5A Gene

Localization for PHF5A Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF5A Gene

Nucleus. Nucleus speckle.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PHF5A gene
Compartment Confidence
nucleus 5
extracellular 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PHF5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005686 U2 snRNP IDA 12234937
GO:0005689 U12-type spliceosomal complex IDA 15146077
genes like me logo Genes that share ontologies with PHF5A: view

Pathways & Interactions for PHF5A Gene

genes like me logo Genes that share pathways with PHF5A: view

Pathways by source for PHF5A Gene

1 KEGG pathway for PHF5A Gene

Gene Ontology (GO) - Biological Process for PHF5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with PHF5A: view

No data available for SIGNOR curated interactions for PHF5A Gene

Drugs & Compounds for PHF5A Gene

No Compound Related Data Available

Transcripts for PHF5A Gene

mRNA/cDNA for PHF5A Gene

Unigene Clusters for PHF5A Gene

PHD finger protein 5A:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PHF5A Gene

No ASD Table

Relevant External Links for PHF5A Gene

GeneLoc Exon Structure for
PHF5A
ECgene alternative splicing isoforms for
PHF5A

Expression for PHF5A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PHF5A Gene

Protein differential expression in normal tissues from HIPED for PHF5A Gene

This gene is overexpressed in Bone (7.9) and Breast (7.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PHF5A Gene



Protein tissue co-expression partners for PHF5A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PHF5A Gene:

PHF5A

SOURCE GeneReport for Unigene cluster for PHF5A Gene:

Hs.474980

Evidence on tissue expression from TISSUES for PHF5A Gene

  • Intestine(4.2)
genes like me logo Genes that share expression patterns with PHF5A: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PHF5A Gene

Orthologs for PHF5A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PHF5A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PHF5A 33 34
  • 100 (n)
oppossum
(Monodelphis domestica)
Mammalia PHF5A 34
  • 100 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHF5A 34
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PHF5A 33 34
  • 94.85 (n)
cow
(Bos Taurus)
Mammalia PHF5A 33 34
  • 92.42 (n)
mouse
(Mus musculus)
Mammalia Phf5a 33 16 34
  • 91.52 (n)
rat
(Rattus norvegicus)
Mammalia Phf5a 33
  • 91.52 (n)
chicken
(Gallus gallus)
Aves PHF5A 33 34
  • 84.55 (n)
lizard
(Anolis carolinensis)
Reptilia PHF5A 34
  • 100 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phf5a 33
  • 83.03 (n)
Str.6129 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.7202 33
zebrafish
(Danio rerio)
Actinopterygii phf5a 33 34
  • 84.85 (n)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta CG9548 35 33 34
  • 81.35 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009905 33
  • 77.68 (n)
worm
(Caenorhabditis elegans)
Secernentea phf-5 33 34
  • 76.76 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ABR103C 33
  • 58.9 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RDS3 33 34 36
  • 57.37 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C15675g 33
  • 56.63 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G30000 33
  • 77.27 (n)
rice
(Oryza sativa)
Liliopsida Os04g0663300 33
  • 78.48 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 97 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU00348 33
  • 65.7 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes ini1 33
  • 62.86 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13935 33
Species where no ortholog for PHF5A was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PHF5A Gene

ENSEMBL:
Gene Tree for PHF5A (if available)
TreeFam:
Gene Tree for PHF5A (if available)

Paralogs for PHF5A Gene

genes like me logo Genes that share paralogs with PHF5A: view

No data available for Paralogs for PHF5A Gene

Variants for PHF5A Gene

Sequence variations from dbSNP and Humsavar for PHF5A Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs1000007362 -- 41,465,916(-) A/G intron_variant
rs1000121371 -- 41,459,283(-) A/G downstream_transcript_variant
rs1000123302 -- 41,465,706(-) C/T intron_variant
rs1000464580 -- 41,459,472(-) C/A downstream_transcript_variant
rs1001000809 -- 41,463,547(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PHF5A Gene

Variant ID Type Subtype PubMed ID
nsv516925 CNV loss 19592680
nsv524585 CNV loss 19592680
nsv834207 CNV loss 17160897
nsv834208 CNV loss 17160897
nsv962799 CNV duplication 23825009

Variation tolerance for PHF5A Gene

Residual Variation Intolerance Score: 53.6% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PHF5A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHF5A

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF5A Gene

Disorders for PHF5A Gene

Additional Disease Information for PHF5A

No disorders were found for PHF5A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PHF5A Gene

Publications for PHF5A Gene

  1. Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein. (PMID: 12234937) Will CL … Lührmann R (The EMBO journal 2002) 2 3 4 58
  2. Complex assembly mechanism and an RNA-binding mode of the human p14-SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analyses. (PMID: 18076038) Kuwasako K … Yokoyama S (Proteins 2008) 2 3 58
  3. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins JE … Dunham I (Genome biology 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome. (PMID: 15146077) Will CL … Lührmann R (RNA (New York, N.Y.) 2004) 3 4 58

Products for PHF5A Gene

Sources for PHF5A Gene

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