Phf5a

Functionⁱ

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. 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 (By similarity). Acts as a transcriptional regulator by binding to the GJA1/Cx43 promoter and enhancing its up-regulation by ESR1/ER-alpha (PubMed:12810571).By similarity1 Publication

Sites

Feature key	Position(s)	DescriptionActions	Length
Metal bindingⁱ	11	Zinc 1By similarity	1
Metal bindingⁱ	23	Zinc 2By similarity	1
Metal bindingⁱ	26	Zinc 2By similarity	1
Metal bindingⁱ	30	Zinc 3By similarity	1
Metal bindingⁱ	33	Zinc 3By similarity	1
Metal bindingⁱ	46	Zinc 1By similarity	1
Metal bindingⁱ	49	Zinc 1By similarity	1
Metal bindingⁱ	58	Zinc 2By similarity	1
Metal bindingⁱ	61	Zinc 2By similarity	1
Metal bindingⁱ	72	Zinc 3By similarity	1
Metal bindingⁱ	75	Zinc 3By similarity	1
Metal bindingⁱ	85	Zinc 1By similarity	1

GO - Molecular functionⁱ

DNA binding Source: UniProtKB-KW
DNA-binding transcription factor activity
Source: UniProtKB
Inferred from direct assayⁱ
- 12810571
metal ion binding Source: UniProtKB-KW
RNA binding Source: UniProtKB-KW

View the complete GO annotation on QuickGO ...

GO - Biological processⁱ

mRNA splicing, via spliceosome Source: UniProtKB
positive regulation of transcription, DNA-templated
Source: UniProtKB
Inferred from direct assayⁱ
- 12810571
transcription, DNA-templated Source: UniProtKB-KW

View the complete GO annotation on QuickGO ...

Keywordsⁱ

Molecular function	DNA-binding, RNA-binding
Biological process	mRNA processing, mRNA splicing, Transcription, Transcription regulation
Ligand	Metal-binding, Zinc

Enzyme and pathway databases

Reactomeⁱ	R-RNO-72163 mRNA Splicing - Major Pathway

Reactomeⁱ

R-RNO-72163 mRNA Splicing - Major Pathway

Names & Taxonomyⁱ

Protein namesⁱ	Recommended name: PHD finger-like domain-containing protein 5A Short name: PHD finger-like domain protein 5A Alternative name(s): Splicing factor 3B-associated 14 kDa protein Short name: SF3b14b
Gene namesⁱ	Name:Phf5a Synonyms:Ini
Organismⁱ	Rattus norvegicus (Rat)
Taxonomic identifierⁱ	10116 [NCBI]
Taxonomic lineageⁱ	cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Dipnotetrapodomorpha › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Boreoeutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Rattus
Proteomesⁱ	UP000002494 Componentⁱ: Chromosome 7

Organism-specific databases

Rat genome database More...RGDⁱ	621555 Phf5a

RGDⁱ

621555 Phf5a

Subcellular locationⁱ

Keywords - Cellular componentⁱ

Nucleus, Spliceosome

PTM / Processingⁱ

Molecule processing

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Initiator methionineⁱ		RemovedBy similarity
ChainⁱPRO_0000218718	2 – 110	PHD finger-like domain-containing protein 5AAdd BLAST		109

Amino acid modifications

Feature key	Position(s)	DescriptionActions	Length
Modified residueⁱ	2	N-acetylalanineBy similarity	1
Modified residueⁱ	3	N6-acetyllysineBy similarity	1
Modified residueⁱ	94	PhosphoserineBy similarity	1

Keywords - PTMⁱ

Acetylation, Phosphoprotein

Proteomic databases

PaxDbⁱ	P83871
PRIDEⁱ	P83871

PTM databases

iPTMnetⁱ	P83871
PhosphoSitePlusⁱ	P83871

Expressionⁱ

Tissue specificityⁱ

Expressed in all tissues tested including brain, heart, ovary, uterus, skeletal muscle and testis.1 Publication

Inductionⁱ

By estrogen.1 Publication

Gene expression databases

Bgeeⁱ	ENSRNOG00000024170 Expressed in 10 organ(s), highest expression level in colon
ExpressionAtlasⁱ	P83871 baseline and differential
Genevisibleⁱ	P83871 RN

Interactionⁱ

Subunit structureⁱ

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. Within the SF3B complex interacts directly with SF3B1 and SF3B3. The SF3B complex composed of SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6 and PHF5A interacts with U2AF2. SF3B associates with the splicing factor SF3A and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (By similarity). 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).By similarity

Sites

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Siteⁱ	17	Interaction with SF3B3By similarity		1
Siteⁱ	100	Interaction with RNABy similarity		1

Protein-protein interaction databases

STRINGⁱ	10116.ENSRNOP00000005837

STRINGⁱ

10116.ENSRNOP00000005837

Structureⁱ

3D structure databases

ProteinModelPortalⁱ	P83871
SMRⁱ	P83871
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Family & Domainsⁱ

Region

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Regionⁱ	35 – 51	Interaction with SF3B1 AND SF3B3By similarityAdd BLAST		17
Regionⁱ	79 – 82	Interaction with SF3B3By similarity		4

Sequence similaritiesⁱ

Belongs to the PHF5 family.Curated

Phylogenomic databases

eggNOGⁱ	KOG1705 Eukaryota ENOG4111JIM LUCA
Ensembl GeneTree More...GeneTreeⁱ	ENSGT00390000018518
HOGENOMⁱ	HOG000168285
HOVERGENⁱ	HBG053587
InParanoidⁱ	P83871
KEGG Orthology (KO) More...KOⁱ	K12834
OMAⁱ	YCKECTV
Database of Orthologous Groups More...OrthoDBⁱ	EOG091G0W8V
PhylomeDBⁱ	P83871
TreeFamⁱ	TF105627

Family and domain databases

InterProⁱ	View protein in InterPro IPR005345 PHF5
PANTHERⁱ	PTHR13120 PTHR13120, 1 hit
Pfam protein domain database More...Pfamⁱ	View protein in Pfam PF03660 PHF5, 1 hit
PIRSFⁱ	PIRSF016468 PHF5, 1 hit

Sequence (1+)ⁱ

Sequence statusⁱ: Complete.

Sequence processingⁱ: The displayed sequence is further processed into a mature form.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show all Align All

P83871-1 [UniParc]FASTA Add to basket

« Hide

        10         20         30         40         50
MAKHHPDLIF CRKQAGVAIG RLCEKCDGKC VICDSYVRPC TLVRICDECN 
        60         70         80         90        100
YGSYQGRCVI CGGPGVSDAY YCKECTIQEK DRDGCPKIVN LGSSKTDLFY 
       110
ERKKYGFKKR

Length:110

Mass (Da):12,405

Last modified:April 26, 2004 - v1

Checksum:ⁱ90F7469DE7292BF7

GO

Computationally mapped potential isoform sequencesⁱ

There is 1 potential isoform mapped to this entry.BLAST Align Show all Add to basket

	Entry	Entry name		Protein names	Gene names	Length	Annotation

	Q7TPJ6	Q7TPJ6_RAT		Ac2-246 Ac2-246 (PHD finger-like domain-containing protein 5A)	Phf5a	102	Annotation score:

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	AF495522 mRNA Translation: AAM14623.1
NCBI Reference Sequences More...RefSeqⁱ	NP_620243.1, NM_138888.1
UniGeneⁱ	Rn.9116

Genome annotation databases

Ensemblⁱ	ENSRNOT00000005837; ENSRNOP00000005837; ENSRNOG00000024170
GeneIDⁱ	192246
KEGGⁱ	rno:192246
UCSC genome browser More...UCSCⁱ	RGD:621555 rat

Protein	Similar proteins		Species	Score	Length	Source
P83871	PHD finger-like domain-containing protein 5A	)	HUMAN		110	UniRef100_Q7RTV0
PHD finger-like domain-containing protein 5A		MOUSE		110
Uncharacterized protein		ORNAN		93
PHD finger protein 5A		TAEGU		93
PHD finger-like domain-containing protein 5A (Fragment)		APTFO		93
+115

Protein	Similar proteins		Species	Score	Length	Source
P83871	PHD finger-like domain-containing protein 5A	)	HUMAN		110	UniRef90_Q7RTV0
PHD finger-like domain-containing protein 5A		MOUSE		110
Uncharacterized protein		ORNAN		93
PHD finger protein 5A		TAEGU		93
PHD finger-like domain-containing protein 5A (Fragment)		APTFO		93
+118

Protein	Similar proteins		Species	Score	Length	Source
P83871	PHD finger-like domain-containing protein 5A	)	HUMAN		110	UniRef50_Q7RTV0
PHD finger-like domain-containing protein 5A		MOUSE		110
Uncharacterized protein		ORNAN		93
PHD finger protein 5A		TAEGU		93
PHD finger-like domain-containing protein 5A (Fragment)		APTFO		93
+133

Cross-referencesⁱ

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	AF495522 mRNA Translation: AAM14623.1
RefSeqⁱ	NP_620243.1, NM_138888.1
UniGeneⁱ	Rn.9116

3D structure databases

ProteinModelPortalⁱ	P83871
SMRⁱ	P83871
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Protein-protein interaction databases

STRINGⁱ	10116.ENSRNOP00000005837

STRINGⁱ

10116.ENSRNOP00000005837

PTM databases

iPTMnetⁱ	P83871
PhosphoSitePlusⁱ	P83871

Proteomic databases

PaxDbⁱ	P83871
PRIDEⁱ	P83871

Protocols and materials databases

Structural Biology Knowledgebase	Search...

Structural Biology Knowledgebase

Search...

Genome annotation databases

Ensemblⁱ	ENSRNOT00000005837; ENSRNOP00000005837; ENSRNOG00000024170
GeneIDⁱ	192246
KEGGⁱ	rno:192246
UCSCⁱ	RGD:621555 rat

Organism-specific databases

CTDⁱ	84844
RGDⁱ	621555 Phf5a

Phylogenomic databases

eggNOGⁱ	KOG1705 Eukaryota ENOG4111JIM LUCA
GeneTreeⁱ	ENSGT00390000018518
HOGENOMⁱ	HOG000168285
HOVERGENⁱ	HBG053587
InParanoidⁱ	P83871
KOⁱ	K12834
OMAⁱ	YCKECTV
OrthoDBⁱ	EOG091G0W8V
PhylomeDBⁱ	P83871
TreeFamⁱ	TF105627

Enzyme and pathway databases

Reactomeⁱ	R-RNO-72163 mRNA Splicing - Major Pathway

Reactomeⁱ

R-RNO-72163 mRNA Splicing - Major Pathway

Miscellaneous databases

Protein Ontology More...PROⁱ	PR:P83871

PROⁱ

PR:P83871

Gene expression databases

Bgeeⁱ	ENSRNOG00000024170 Expressed in 10 organ(s), highest expression level in colon
ExpressionAtlasⁱ	P83871 baseline and differential
Genevisibleⁱ	P83871 RN

Family and domain databases

InterProⁱ	View protein in InterPro IPR005345 PHF5
PANTHERⁱ	PTHR13120 PTHR13120, 1 hit
Pfamⁱ	View protein in Pfam PF03660 PHF5, 1 hit
PIRSFⁱ	PIRSF016468 PHF5, 1 hit
ProtoNetⁱ	Search...

Entry informationⁱ

Entry nameⁱ	PHF5A_RAT
Accessionⁱ	P83871Primary (citable) accession number: P83871
Entry historyⁱ	Integrated into UniProtKB/Swiss-Prot:	April 26, 2004
	Last sequence update:	April 26, 2004
	Last modified:	September 12, 2018
	This is version 110 of the entry and version 1 of the sequence. See complete history.
Entry statusⁱ	Reviewed (UniProtKB/Swiss-Prot)
Annotation program	Chordata Protein Annotation Program

UniProtKB

UniParc

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UniProtKB - P83871 (PHF5A_RAT)

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PHD finger-like domain-containing protein 5A

Select a section on the left to see content.

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Sites

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

Enzyme and pathway databases

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

Organism-specific databases

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Nucleus

Nucleus

Keywords - Cellular componenti

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Amino acid modifications

Keywords - PTMi

Proteomic databases

PTM databases

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Sites

Protein-protein interaction databases

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

Family and domain databases

Sequence databases

Genome annotation databases

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Miscellaneous databases

Gene expression databases

Family and domain databases

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

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Functionⁱ

GO - Molecular functionⁱ

GO - Biological processⁱ

Names & Taxonomyⁱ

Subcellular locationⁱ

Keywords - Cellular componentⁱ

PTM / Processingⁱ

Keywords - PTMⁱ

Expressionⁱ

Interactionⁱ

Structureⁱ

Family & Domainsⁱ

Sequence similaritiesⁱ

Cross-referencesⁱ

Entry informationⁱ

Miscellaneousⁱ

Keywords - Technical termⁱ