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Protein

PHD finger-like domain-containing protein 5A

Gene

PHF5A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

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 (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).By similarity3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi11Zinc 1Combined sources1 Publication1
Metal bindingi23Zinc 2Combined sources1 Publication1
Metal bindingi26Zinc 2Combined sources1 Publication1
Metal bindingi30Zinc 3Combined sources1 Publication1
Metal bindingi33Zinc 3Combined sources1 Publication1
Metal bindingi46Zinc 1Combined sources1 Publication1
Metal bindingi49Zinc 1Combined sources1 Publication1
Metal bindingi58Zinc 2Combined sources1 Publication1
Metal bindingi61Zinc 2Combined sources1 Publication1
Metal bindingi72Zinc 3Combined sources1 Publication1
Metal bindingi75Zinc 3Combined sources1 Publication1
Metal bindingi85Zinc 1Combined sources1 Publication1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionActivator, DNA-binding, RNA-binding
Biological processmRNA processing, mRNA splicing, Transcription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 22

Organism-specific databases

EuPathDBiHostDB:ENSG00000100410.7
HGNCiHGNC:18000 PHF5A
MIMi617846 gene
neXtProtiNX_Q7RTV0

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi36Y → C: No apparent effect on cell growth, localization of SF3B1 protein or formation of nuclear speckles. Alters the structure of the presumed branchpoint (BP) adenosine binding pocket within the splicing factor SF3B complex which may lead to decreased binding affinity and thus affect pre-mRNA splicing. 1 Publication1
Mutagenesisi36Y → E, S or A: Alters the structure of the presumed branchpoint (BP) adenosine binding pocket within the splicing factor SF3B complex which may lead to decreased binding affinity and thus affect pre-mRNA splicing. 1 Publication1

Organism-specific databases

DisGeNETi84844
OpenTargetsiENSG00000100410
PharmGKBiPA134876104

Polymorphism and mutation databases

BioMutaiPHF5A
DMDMi46577625

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00002187162 – 110PHD finger-like domain-containing protein 5AAdd BLAST109

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineBy similarity1
Modified residuei3N6-acetyllysineCombined sources1
Modified residuei94PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ7RTV0
MaxQBiQ7RTV0
PaxDbiQ7RTV0
PeptideAtlasiQ7RTV0
PRIDEiQ7RTV0
TopDownProteomicsiQ7RTV0

PTM databases

iPTMnetiQ7RTV0
PhosphoSitePlusiQ7RTV0

Expressioni

Gene expression databases

BgeeiENSG00000100410
CleanExiHS_PHF5A
ExpressionAtlasiQ7RTV0 baseline and differential
GenevisibleiQ7RTV0 HS

Organism-specific databases

HPAiHPA028885

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 (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).By similarity5 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei17Interaction with SF3B31 Publication1
Sitei100Interaction with RNA1 Publication1

Protein-protein interaction databases

BioGridi124296, 37 interactors
CORUMiQ7RTV0
IntActiQ7RTV0, 17 interactors
MINTiQ7RTV0
STRINGi9606.ENSP00000216252

Structurei

Secondary structure

1110
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 10Combined sources6
Beta strandi17 – 19Combined sources3
Turni24 – 28Combined sources5
Turni31 – 33Combined sources3
Beta strandi39 – 42Combined sources4
Helixi47 – 50Combined sources4
Turni53 – 56Combined sources4
Turni59 – 61Combined sources3
Beta strandi70 – 72Combined sources3
Helixi73 – 77Combined sources5
Helixi80 – 83Combined sources4
Beta strandi88 – 90Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5IFEX-ray3.10D1-110[»]
5O9Zelectron microscopy4.50y1-110[»]
5SYBX-ray1.82A/B1-110[»]
5ZD5electron microscopy3.95D7-91[»]
ProteinModelPortaliQ7RTV0
SMRiQ7RTV0
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni35 – 51Interaction with SF3B1 AND SF3B31 PublicationAdd BLAST17
Regioni79 – 82Interaction with SF3B31 Publication4

Sequence similaritiesi

Belongs to the PHF5 family.Curated

Phylogenomic databases

eggNOGiKOG1705 Eukaryota
ENOG4111JIM LUCA
GeneTreeiENSGT00390000018518
HOGENOMiHOG000168285
HOVERGENiHBG053587
InParanoidiQ7RTV0
KOiK12834
OMAiYCKECTV
OrthoDBiEOG091G0W8V
PhylomeDBiQ7RTV0
TreeFamiTF105627

Family and domain databases

InterProiView protein in InterPro
IPR005345 PHF5
PANTHERiPTHR13120 PTHR13120, 1 hit
PfamiView protein in Pfam
PF03660 PHF5, 1 hit
PIRSFiPIRSF016468 PHF5, 1 hit

Sequencei

Sequence statusi: Complete.

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

Q7RTV0-1 [UniParc]FASTAAdd 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:December 15, 2003 - v1
Checksum:i90F7469DE7292BF7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR456398 mRNA Translation: CAG30284.1
AL008582 Genomic DNA No translation available.
BC007321 mRNA Translation: AAH07321.1
BC075808 mRNA Translation: AAH75808.1
BK000563 mRNA Translation: DAA00074.1
CCDSiCCDS14016.1
RefSeqiNP_116147.1, NM_032758.3
UniGeneiHs.474980
Hs.707800

Genome annotation databases

EnsembliENST00000216252; ENSP00000216252; ENSG00000100410
GeneIDi84844
KEGGihsa:84844
UCSCiuc003bab.4 human

Similar proteinsi

Entry informationi

Entry nameiPHF5A_HUMAN
AccessioniPrimary (citable) accession number: Q7RTV0
Secondary accession number(s): Q9UH06
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 26, 2004
Last sequence update: December 15, 2003
Last modified: May 23, 2018
This is version 134 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 22
    Human chromosome 22: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families
  5. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

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