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Protein

PHD finger protein 6

Gene

PHF6

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Transcriptional regulator that associates with ribosomal RNA promoters and suppresses ribosomal RNA (rRNA) transcription.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri14 – 52C2HC pre-PHD-type 1PROSITE-ProRule annotationAdd BLAST39
Zinc fingeri80 – 132PHD-type 1PROSITE-ProRule annotationAdd BLAST53
Zinc fingeri209 – 249C2HC pre-PHD-type 2PROSITE-ProRule annotationAdd BLAST41
Zinc fingeri278 – 330PHD-type 2PROSITE-ProRule annotationAdd BLAST53

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • enzyme binding Source: UniProtKB
  • histone binding Source: UniProtKB
  • histone deacetylase binding Source: UniProtKB
  • phosphoprotein binding Source: UniProtKB
  • poly(A) RNA binding Source: UniProtKB
  • ribonucleoprotein complex binding Source: UniProtKB
  • scaffold protein binding Source: UniProtKB
  • tubulin binding Source: UniProtKB
  • zinc ion binding Source: InterPro

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

SIGNORiQ8IWS0.

Names & Taxonomyi

Protein namesi
Recommended name:
PHD finger protein 6
Alternative name(s):
PHD-like zinc finger protein
Gene namesi
Name:PHF6
Synonyms:CENP-31, KIAA1823
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

HGNCiHGNC:18145. PHF6.

Subcellular locationi

GO - Cellular componenti

  • condensed chromosome kinetochore Source: UniProtKB-SubCell
  • nucleolus Source: UniProtKB
  • nucleoplasm Source: UniProtKB
  • nucleus Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Centromere, Chromosome, Kinetochore, Nucleus

Pathology & Biotechi

Involvement in diseasei

Boerjeson-Forssman-Lehmann syndrome (BFLS)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA X-linked recessive disorder characterized by moderate to severe mental retardation, epilepsy, hypogonadism, hypometabolism, obesity with marked gynecomastia, swelling of subcutaneous tissue of the face, narrow palpebral fissure and large but not deformed ears.
See also OMIM:301900
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01763345C → Y in BFLS; Loss of interaction with UBTF. 2 PublicationsCorresponds to variant rs28935179dbSNPEnsembl.1
Natural variantiVAR_01763499C → F in BFLS; Loss of interaction with UBTF. 2 PublicationsCorresponds to variant rs132630298dbSNPEnsembl.1
Natural variantiVAR_017635229H → R in BFLS. 1 PublicationCorresponds to variant rs104894918dbSNPEnsembl.1
Natural variantiVAR_017636234K → E in BFLS. 1 PublicationCorresponds to variant rs104894917dbSNPEnsembl.1
Natural variantiVAR_017637257R → G in BFLS. 1 PublicationCorresponds to variant rs104894919dbSNPEnsembl.1
Natural variantiVAR_076933305C → F in BFLS. 1 Publication1

Keywords - Diseasei

Disease mutation, Epilepsy, Hypotrichosis, Mental retardation

Organism-specific databases

DisGeNETi84295.
MalaCardsiPHF6.
MIMi301900. phenotype.
OpenTargetsiENSG00000156531.
Orphaneti127. Borjeson-Forssman-Lehmann syndrome.
PharmGKBiPA33263.

Polymorphism and mutation databases

BioMutaiPHF6.
DMDMi42559482.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00000592932 – 365PHD finger protein 6Add BLAST364

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Modified residuei138PhosphoserineCombined sources1
Modified residuei145PhosphoserineCombined sources1
Modified residuei155PhosphoserineCombined sources1
Cross-linki173Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei183PhosphoserineBy similarity1
Modified residuei199PhosphoserineCombined sources1
Cross-linki227Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei358PhosphothreonineCombined sources1
Isoform 2 (identifier: Q8IWS0-2)
Modified residuei146PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ8IWS0.
MaxQBiQ8IWS0.
PaxDbiQ8IWS0.
PeptideAtlasiQ8IWS0.
PRIDEiQ8IWS0.

PTM databases

iPTMnetiQ8IWS0.
PhosphoSitePlusiQ8IWS0.

Expressioni

Tissue specificityi

Ubiquitously expressed.1 Publication

Gene expression databases

BgeeiENSG00000156531.
CleanExiHS_PHF6.
ExpressionAtlasiQ8IWS0. baseline and differential.
GenevisibleiQ8IWS0. HS.

Organism-specific databases

HPAiHPA001023.

Interactioni

Subunit structurei

Interacts with UBTF. Interacts with the NuRD complex component RBBP4 (via the nucleolar localization motif), the interaction mediates transcriptional repression activity.2 Publications

GO - Molecular functioni

  • enzyme binding Source: UniProtKB
  • histone binding Source: UniProtKB
  • histone deacetylase binding Source: UniProtKB
  • phosphoprotein binding Source: UniProtKB
  • scaffold protein binding Source: UniProtKB
  • tubulin binding Source: UniProtKB

Protein-protein interaction databases

BioGridi124022. 43 interactors.
IntActiQ8IWS0. 7 interactors.
MINTiMINT-4534083.
STRINGi9606.ENSP00000329097.

Structurei

Secondary structure

1365
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni213 – 215Combined sources3
Helixi219 – 221Combined sources3
Helixi222 – 225Combined sources4
Beta strandi228 – 230Combined sources3
Beta strandi237 – 239Combined sources3
Helixi240 – 244Combined sources5
Beta strandi257 – 259Combined sources3
Helixi265 – 275Combined sources11
Turni281 – 283Combined sources3
Beta strandi290 – 294Combined sources5
Helixi303 – 308Combined sources6
Beta strandi312 – 316Combined sources5
Turni317 – 320Combined sources4
Beta strandi321 – 325Combined sources5
Helixi327 – 329Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4NN2X-ray1.47A/B208-333[»]
4R7AX-ray1.85A157-171[»]
ProteinModelPortaliQ8IWS0.
SMRiQ8IWS0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni14 – 132Extended PHD1 domain (ePHD1)PROSITE-ProRule annotationAdd BLAST119
Regioni209 – 330Extended PHD2 domain (ePHD2)PROSITE-ProRule annotationAdd BLAST122

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi13 – 16Nuclear localization signalSequence analysis4
Motifi129 – 133Nuclear localization signalSequence analysis5
Motifi157 – 169Nucleolar localization signalSequence analysisAdd BLAST13

Domaini

The PHD-type zinc finger 1 mediates both nucleolar localization and interaction with UBTF.
The ePHD2 domain folds as an integrated structural module comprizing the C2HC pre-PHD-type 2 zinc finger and the PHD-type 2 zinc finger. It mediates non-specific binding to dsDNA, but doesn't bind histones in contrast to many PHD-type zinc fingers.

Sequence similaritiesi

Contains 2 C2HC pre-PHD-type zinc fingers.PROSITE-ProRule annotation
Contains 2 PHD-type zinc fingers.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri14 – 52C2HC pre-PHD-type 1PROSITE-ProRule annotationAdd BLAST39
Zinc fingeri80 – 132PHD-type 1PROSITE-ProRule annotationAdd BLAST53
Zinc fingeri209 – 249C2HC pre-PHD-type 2PROSITE-ProRule annotationAdd BLAST41
Zinc fingeri278 – 330PHD-type 2PROSITE-ProRule annotationAdd BLAST53

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiENOG410IPTE. Eukaryota.
ENOG410XS42. LUCA.
GeneTreeiENSGT00530000063780.
HOGENOMiHOG000026798.
HOVERGENiHBG049389.
InParanoidiQ8IWS0.
PhylomeDBiQ8IWS0.
TreeFamiTF325426.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
SMARTiSM00249. PHD. 2 hits.
[Graphical view]
PROSITEiPS51805. EPHD. 2 hits.
[Graphical view]

Sequences (5)i

Sequence statusi: Complete.

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

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8IWS0-1) [UniParc]FASTAAdd to basket
Also known as: PHF6a, PHF6b

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSSSVEQKKG PTRQRKCGFC KSNRDKECGQ LLISENQKVA AHHKCMLFSS
60 70 80 90 100
ALVSSHSDNE SLGGFSIEDV QKEIKRGTKL MCSLCHCPGA TIGCDVKTCH
110 120 130 140 150
RTYHYHCALH DKAQIREKPS QGIYMVYCRK HKKTAHNSEA DLEESFNEHE
160 170 180 190 200
LEPSSPKSKK KSRKGRPRKT NFKGLSEDTR STSSHGTDEM ESSSYRDRSP
210 220 230 240 250
HRSSPSDTRP KCGFCHVGEE ENEARGKLHI FNAKKAAAHY KCMLFSSGTV
260 270 280 290 300
QLTTTSRAEF GDFDIKTVLQ EIKRGKRMKC TLCSQPGATI GCEIKACVKT
310 320 330 340 350
YHYHCGVQDK AKYIENMSRG IYKLYCKNHS GNDERDEEDE ERESKSRGKV
360
EIDQQQLTQQ QLNGN
Length:365
Mass (Da):41,290
Last modified:March 1, 2003 - v1
Checksum:iE8E587909EF9701D
GO
Isoform 2 (identifier: Q8IWS0-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     140-140: A → AA
     279-311: KCTLCSQPGATIGCEIKACVKTYHYHCGVQDKA → VCSFYICYATLHLICCFKFRVHPKFIQSSENLK
     312-365: Missing.

Note: No experimental confirmation available.Combined sources
Show »
Length:312
Mass (Da):35,329
Checksum:i107F45F45063D7A0
GO
Isoform 3 (identifier: Q8IWS0-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     140-140: Missing.

Note: No experimental confirmation available.
Show »
Length:364
Mass (Da):41,219
Checksum:i2BEB117AF92F7ECC
GO
Isoform 4 (identifier: Q8IWS0-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     140-140: Missing.
     279-311: KCTLCSQPGATIGCEIKACVKTYHYHCGVQDKA → VCSFYICYATLHLICCFKFRVHPKFIQSSENLK
     312-365: Missing.

Note: No experimental confirmation available.
Show »
Length:310
Mass (Da):35,187
Checksum:iB6091E6AC014F78A
GO
Isoform 5 (identifier: Q8IWS0-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     47-80: Missing.

Note: No experimental confirmation available.
Show »
Length:331
Mass (Da):37,628
Checksum:iCA296A2F39167444
GO

Sequence cautioni

The sequence BAB47452 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti126V → A in AAH05994 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01763345C → Y in BFLS; Loss of interaction with UBTF. 2 PublicationsCorresponds to variant rs28935179dbSNPEnsembl.1
Natural variantiVAR_01763499C → F in BFLS; Loss of interaction with UBTF. 2 PublicationsCorresponds to variant rs132630298dbSNPEnsembl.1
Natural variantiVAR_017635229H → R in BFLS. 1 PublicationCorresponds to variant rs104894918dbSNPEnsembl.1
Natural variantiVAR_017636234K → E in BFLS. 1 PublicationCorresponds to variant rs104894917dbSNPEnsembl.1
Natural variantiVAR_017637257R → G in BFLS. 1 PublicationCorresponds to variant rs104894919dbSNPEnsembl.1
Natural variantiVAR_076933305C → F in BFLS. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_05493747 – 80Missing in isoform 5. 1 PublicationAdd BLAST34
Alternative sequenceiVSP_009372140A → AA in isoform 2. 1 Publication1
Alternative sequenceiVSP_053441140Missing in isoform 3 and isoform 4. 1 Publication1
Alternative sequenceiVSP_009373279 – 311KCTLC…VQDKA → VCSFYICYATLHLICCFKFR VHPKFIQSSENLK in isoform 2 and isoform 4. 2 PublicationsAdd BLAST33
Alternative sequenceiVSP_009374312 – 365Missing in isoform 2 and isoform 4. 2 PublicationsAdd BLAST54

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY157622 mRNA. Translation: AAO13214.1.
AB058726 mRNA. Translation: BAB47452.1. Different initiation.
AK290095 mRNA. Translation: BAF82784.1.
AK303369 mRNA. Translation: BAG64426.1.
AL591668, AC004383 Genomic DNA. Translation: CAI41600.1.
AL591668 Genomic DNA. Translation: CAI41601.1.
CH471107 Genomic DNA. Translation: EAX11762.1.
CH471107 Genomic DNA. Translation: EAX11763.1.
CH471107 Genomic DNA. Translation: EAX11766.1.
BC005994 mRNA. Translation: AAH05994.1.
CCDSiCCDS14639.1. [Q8IWS0-1]
CCDS14640.1. [Q8IWS0-2]
RefSeqiNP_001015877.1. NM_001015877.1. [Q8IWS0-1]
NP_115711.2. NM_032335.3. [Q8IWS0-2]
NP_115834.1. NM_032458.2. [Q8IWS0-1]
UniGeneiHs.356501.

Genome annotation databases

EnsembliENST00000332070; ENSP00000329097; ENSG00000156531. [Q8IWS0-1]
ENST00000370800; ENSP00000359836; ENSG00000156531. [Q8IWS0-2]
ENST00000370803; ENSP00000359839; ENSG00000156531. [Q8IWS0-1]
GeneIDi84295.
KEGGihsa:84295.
UCSCiuc004exh.4. human. [Q8IWS0-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY157622 mRNA. Translation: AAO13214.1.
AB058726 mRNA. Translation: BAB47452.1. Different initiation.
AK290095 mRNA. Translation: BAF82784.1.
AK303369 mRNA. Translation: BAG64426.1.
AL591668, AC004383 Genomic DNA. Translation: CAI41600.1.
AL591668 Genomic DNA. Translation: CAI41601.1.
CH471107 Genomic DNA. Translation: EAX11762.1.
CH471107 Genomic DNA. Translation: EAX11763.1.
CH471107 Genomic DNA. Translation: EAX11766.1.
BC005994 mRNA. Translation: AAH05994.1.
CCDSiCCDS14639.1. [Q8IWS0-1]
CCDS14640.1. [Q8IWS0-2]
RefSeqiNP_001015877.1. NM_001015877.1. [Q8IWS0-1]
NP_115711.2. NM_032335.3. [Q8IWS0-2]
NP_115834.1. NM_032458.2. [Q8IWS0-1]
UniGeneiHs.356501.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4NN2X-ray1.47A/B208-333[»]
4R7AX-ray1.85A157-171[»]
ProteinModelPortaliQ8IWS0.
SMRiQ8IWS0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi124022. 43 interactors.
IntActiQ8IWS0. 7 interactors.
MINTiMINT-4534083.
STRINGi9606.ENSP00000329097.

PTM databases

iPTMnetiQ8IWS0.
PhosphoSitePlusiQ8IWS0.

Polymorphism and mutation databases

BioMutaiPHF6.
DMDMi42559482.

Proteomic databases

EPDiQ8IWS0.
MaxQBiQ8IWS0.
PaxDbiQ8IWS0.
PeptideAtlasiQ8IWS0.
PRIDEiQ8IWS0.

Protocols and materials databases

DNASUi84295.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000332070; ENSP00000329097; ENSG00000156531. [Q8IWS0-1]
ENST00000370800; ENSP00000359836; ENSG00000156531. [Q8IWS0-2]
ENST00000370803; ENSP00000359839; ENSG00000156531. [Q8IWS0-1]
GeneIDi84295.
KEGGihsa:84295.
UCSCiuc004exh.4. human. [Q8IWS0-1]

Organism-specific databases

CTDi84295.
DisGeNETi84295.
GeneCardsiPHF6.
HGNCiHGNC:18145. PHF6.
HPAiHPA001023.
MalaCardsiPHF6.
MIMi300414. gene.
301900. phenotype.
neXtProtiNX_Q8IWS0.
OpenTargetsiENSG00000156531.
Orphaneti127. Borjeson-Forssman-Lehmann syndrome.
PharmGKBiPA33263.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IPTE. Eukaryota.
ENOG410XS42. LUCA.
GeneTreeiENSGT00530000063780.
HOGENOMiHOG000026798.
HOVERGENiHBG049389.
InParanoidiQ8IWS0.
PhylomeDBiQ8IWS0.
TreeFamiTF325426.

Enzyme and pathway databases

SIGNORiQ8IWS0.

Miscellaneous databases

ChiTaRSiPHF6. human.
GeneWikiiPHF6.
GenomeRNAii84295.
PROiQ8IWS0.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000156531.
CleanExiHS_PHF6.
ExpressionAtlasiQ8IWS0. baseline and differential.
GenevisibleiQ8IWS0. HS.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
SMARTiSM00249. PHD. 2 hits.
[Graphical view]
PROSITEiPS51805. EPHD. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPHF6_HUMAN
AccessioniPrimary (citable) accession number: Q8IWS0
Secondary accession number(s): A8K230
, B4E0G4, D3DTG3, E9PC97, Q5JRC7, Q5JRC8, Q96JK3, Q9BRU0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: March 1, 2003
Last modified: November 30, 2016
This is version 133 of the entry and version 1 of the sequence. [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 X
    Human chromosome X: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.