Tbio PHF5A PHD finger-like domain-containing protein 5A

Protein Summary

Description

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). 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]

Uniprot Accession IDs

• Q7RTV0
• Q9UH06
• PHD finger-like domain protein 5A

Gene Name

• PHF5A

Ensembl ID

• ENST00000216252
• ENSP00000216252
• ENSG00000100410

Symbol

• INI
• Rds3
• SF3B7
• SAP14b
• SF3b14b
• bK223H9.2

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
interacting protein	0.94
transcription factor binding site profile	0.88
histone modification site profile	0.86
disease perturbation	0.68
small molecule perturbation	0.68

Protein Classes

No PANTHER Classes or DTO Classes found

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 42.05   (req: < 5)

Gene RIFs: 4   (req: <= 3)

Antibodies: 184   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 42.05   (req: >= 5)

Gene RIFs: 4   (req: > 3)

Antibodies: 184   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 6

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Expression Data (0 Tissues)

tutorial

No expression data found

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Related Tools (4)

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (313)

Explore Interacting Targets

1 – 10 of 313

• See Interactions on String-DB

ZRSR2

Tbio

Novelty:  0.03449891

p_int:  0.999999935

p_ni:  6.4e-8

p_wrong:  1e-9

Score:  0.919

Data Source:  BioPlex,STRINGDB

ZMAT5

Tdark

Novelty:  0.97115324

p_int:  0.999999929

p_ni:  5.6e-8

p_wrong:  1.5e-8

Score:  0.775

Data Source:  BioPlex,STRINGDB

TTC33

Tdark

Novelty:  0.31237949

p_int:  0.999999853

p_ni:  1.26e-7

p_wrong:  2.1e-8

Data Source:  BioPlex

SNRNP48

Tbio

Novelty:  0.16395917

p_int:  0.999999819

p_ni:  1.62e-7

p_wrong:  1.8e-8

Score:  0.72

Data Source:  BioPlex,STRINGDB

PDCD7

Tbio

Novelty:  0.15531712

p_int:  0.99999971

p_ni:  2.9e-7

Score:  0.72

Data Source:  BioPlex,STRINGDB

SLC4A1AP

Tdark

Family:  Transporter

Novelty:  0.41125302

p_int:  0.999999467

p_ni:  5.32e-7

Data Source:  BioPlex

SNRNP35

Tdark

Novelty:  1.00002211

p_int:  0.999999443

p_ni:  2.38e-7

p_wrong:  3.19e-7

Score:  0.89

Data Source:  BioPlex,STRINGDB

RNPC3

Tbio

Novelty:  0.07154673

p_int:  0.999999161

p_ni:  8.31e-7

p_wrong:  8e-9

Score:  0.973

Data Source:  BioPlex,STRINGDB

CCDC97

Tdark

Novelty:  2.36351796

p_int:  0.999996428

p_ni:  0.000003571

p_wrong:  1e-9

Score:  0.54

Data Source:  BioPlex,STRINGDB

SF3A2

Tbio

Novelty:  0.03658692

p_int:  0.999994768

p_ni:  0.000005232

Score:  0.999

Data Source:  BioPlex,STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (6)

Reactome (4)

KEGG (1)

WikiPathways (1)

Metabolism of RNA (R-HSA-8953854)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Metabolism of RNA	686 targets	R-HSA-8953854
Reactome	Processing of Capped Intron-Containing Pre-mRNA	241 targets	R-HSA-72203
Reactome	mRNA Splicing	188 targets	R-HSA-72172
Reactome	mRNA Splicing - Major Pathway	180 targets	R-HSA-72163

Name	Explore in Pharos	Explore in Source
Metabolism of RNA	686 targets	R-HSA-8953854
Processing of Capped Intron-Containing Pre-mRNA	241 targets	R-HSA-72203
mRNA Splicing	188 targets	R-HSA-72172
mRNA Splicing - Major Pathway	180 targets	R-HSA-72163

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (11)

Functions (4)

Components (5)

Processes (2)

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1 – 4 of 4

GO Term	Evidence	Assigned by
RNA binding	Inferred from High Throughput Direct Assay (HDA)	UniProtKB
DNA-binding transcription factor activity	Inferred from Sequence or structural Similarity (ISS)	UniProtKB
DNA binding	Inferred from Electronic Annotation (IEA)	UniProtKB-KW
metal ion binding	Inferred from Electronic Annotation (IEA)	UniProtKB-KW

Disease Associations (null)

No disease associations found

GWAS Traits (26)

• Explore on Target Illumination GWAS Analytics (TIGA)

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1 – 5 of 26

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
mathematical ability	EFO_0004875	2	2	2		84.1
lymphocyte percentage of leukocytes	EFO_0007993	2	2	2		81.7
IGF-1 measurement	EFO_0004627	1	1	1		73.9
asthma	EFO_0000270	3	3	0	1.1	68.5
Vitiligo	EFO_0004208	2	2	0	1.3	68.2

• Explore on Target Illumination GWAS Analytics (TIGA)

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GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
mathematical ability	EFO_0004875	2		84.1
lymphocyte percentage of leukocytes	EFO_0007993	2		81.7
IGF-1 measurement	EFO_0004627	1		73.9
asthma	EFO_0000270	0	1.1	68.5
Vitiligo	EFO_0004208	0	1.3	68.2

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UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Acetylation
Activator
Complete proteome
DNA-binding
Metal-binding
mRNA processing
mRNA splicing
Nucleus
Phosphoprotein

GWAS Trait Find Similar Targets

No Header	No Header
alcohol consumption measurement
alcohol use disorder measurement
allergic rhinitis
allergy
asthma
bitter alcoholic beverage consumption measurement
bitter non-alcoholic beverage consumption measurement
body height
Crohn's disease
diet measurement

MGI Phenotype Find Similar Targets

No Header	No Header
mortality/aging

IDG Resources

No IDG generated resources found

Orthologs (15)

1 – 5 of 15

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	PHD finger protein 5A	VGNC:5294	745456
Macaque	PHD finger protein 5A		711683
Mouse	PHD finger protein 5A	MGI:2156864	68479
Rat	PHD finger protein 5A	RGD:621555	192246
Dog	PHD finger protein 5A	VGNC:44491	474489

Species	Name	OMA	EggNOG	Inparanoid
Chimp	PHD finger protein 5A
Macaque	PHD finger protein 5A
Mouse	PHD finger protein 5A
Rat	PHD finger protein 5A
Dog	PHD finger protein 5A

Publication Statistics

PubMed Score 42.05

PubMed score by year

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PubTator Score 75.19

PubTator score by year

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Related Publications

Text Mined References (16)

GeneRif Annotations (4)

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PMID	Year	Title