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

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: mouse all
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Genomic context

Location:: 22q13.2

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (41459717..41468692, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (41938569..41947547, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (41855721..41864696, complement)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PHF5A promotes esophageal squamous cell carcinoma progression via stabilizing VEGFA.
Title: PHF5A promotes esophageal squamous cell carcinoma progression via stabilizing VEGFA.
De novo PHF5A variants are associated with craniofacial abnormalities, developmental delay, and hypospadias.
Title: De novo PHF5A variants are associated with craniofacial abnormalities, developmental delay, and hypospadias.
PHF5A is a potential diagnostic, prognostic, and immunological biomarker in pan-cancer.
Title: PHF5A is a potential diagnostic, prognostic, and immunological biomarker in pan-cancer.
PHF5A regulates the expression of the DOCK5 variant to promote HNSCC progression through p38 MAPK activation.
Title: PHF5A regulates the expression of the DOCK5 variant to promote HNSCC progression through p38 MAPK activation.
[PHF5A Promotes Proliferation and Migration of Non-Small Cell Lung Cancer by Regulating of PI3K/AKT Pathway].
Title: [PHF5A Promotes Proliferation and Migration of Non-Small Cell Lung Cancer  by Regulating of PI3K/AKT Pathway].
Research progress and therapeutic prospect of PHF5A acting as a new target for malignant tumors.
Title: Research progress and therapeutic prospect of PHF5A acting as a new target for malignant tumors.
PHF5A Contributes to the Maintenance of the Cancer Stem-like Phenotype in Non-Small Cell Lung Cancer by Regulating Histone Deacetylase 8.
Title: PHF5A Contributes to the Maintenance of the Cancer Stem-like Phenotype in Non-Small Cell Lung Cancer by Regulating Histone Deacetylase 8.
Phf5a regulates DNA repair in class switch recombination via p400 and histone H2A variant deposition.
Title: Phf5a regulates DNA repair in class switch recombination via p400 and histone H2A variant deposition.
we validated that PHF5A played an oncogenic role via AS in LUAD and suggested that PHF5A might serve as a potential drug target with a promising anticancer therapeutic effect.
Title: PHD finger protein 5A promoted lung adenocarcinoma progression via alternative splicing.
Acetylation of PHF5A modulates stress responses and colorectal carcinogenesis through alternative splicing-mediated upregulation of KDM3A.
Title: Acetylation of PHF5A Modulates Stress Responses and Colorectal Carcinogenesis through Alternative Splicing-Mediated Upregulation of KDM3A.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	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	IBA Inferred from Biological aspect of Ancestor more info
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

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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)

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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.