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Protein

PHD finger protein 21A

Gene

PHF21A

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

Functioni

Component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it may act as a scaffold. Inhibits KDM1A-mediated demethylation of 'Lys-4' of histone H3 in vitro, suggesting a role in demethylation regulation.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi425 – 437A.T hookAdd BLAST13
Zinc fingeri488 – 535PHD-typePROSITE-ProRule annotationAdd BLAST48

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionChromatin regulator, DNA-binding, Repressor
Biological processTranscription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-3214815 HDACs deacetylate histones
R-HSA-983231 Factors involved in megakaryocyte development and platelet production

Names & Taxonomyi

Protein namesi
Recommended name:
PHD finger protein 21A
Alternative name(s):
BHC80a
BRAF35-HDAC complex protein BHC80
Gene namesi
Name:PHF21A
Synonyms:BHC80, KIAA1696
ORF Names:BM-006
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

EuPathDBiHostDB:ENSG00000135365.15
HGNCiHGNC:24156 PHF21A
MIMi608325 gene
neXtProtiNX_Q96BD5

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

Pathology & Biotechi

Organism-specific databases

DisGeNETi51317
MalaCardsiPHF21A
OpenTargetsiENSG00000135365
Orphaneti52022 Potocki-Shaffer syndrome
PharmGKBiPA134977844

Polymorphism and mutation databases

BioMutaiPHF21A
DMDMi74731224

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002267671 – 680PHD finger protein 21AAdd BLAST680

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki65Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei350PhosphothreonineCombined sources1
Modified residuei444PhosphothreonineCombined sources1
Modified residuei447PhosphoserineCombined sources1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ96BD5
MaxQBiQ96BD5
PaxDbiQ96BD5
PeptideAtlasiQ96BD5
PRIDEiQ96BD5
ProteomicsDBi76065
76066 [Q96BD5-2]
76067 [Q96BD5-3]

PTM databases

iPTMnetiQ96BD5
PhosphoSitePlusiQ96BD5

Expressioni

Tissue specificityi

Highly expressed in brain. Expressed at much lower level in other tissues.1 Publication

Gene expression databases

BgeeiENSG00000135365 Expressed in 220 organ(s), highest expression level in corpus callosum
CleanExiHS_PHF21A
ExpressionAtlasiQ96BD5 baseline and differential
GenevisibleiQ96BD5 HS

Organism-specific databases

HPAiHPA023580

Interactioni

Subunit structurei

Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST and PHF21A/BHC80. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. In the complex, it interacts directly with HDAC1, HDAC2, HMG20B/BRAF35, KDM1A and RCOR1/CoREST.3 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi119468, 62 interactors
CORUMiQ96BD5
DIPiDIP-60252N
IntActiQ96BD5, 35 interactors
MINTiQ96BD5
STRINGi9606.ENSP00000398824

Structurei

Secondary structure

1680
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ96BD5
SMRiQ96BD5
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ96BD5

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni486 – 680Required for transcriptional repressionAdd BLAST195

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili558 – 603Sequence analysisAdd BLAST46

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi4 – 108Gln-richAdd BLAST105

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri488 – 535PHD-typePROSITE-ProRule annotationAdd BLAST48

Keywords - Domaini

Coiled coil, Zinc-finger

Phylogenomic databases

eggNOGiENOG410IREA Eukaryota
ENOG41112YM LUCA
GeneTreeiENSGT00530000063984
HOVERGENiHBG080293
InParanoidiQ96BD5
OMAiHHHAQSA
OrthoDBiEOG091G03CB
PhylomeDBiQ96BD5
TreeFamiTF331518

Family and domain databases

Gene3Di3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR019786 Zinc_finger_PHD-type_CS
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR019787 Znf_PHD-finger
IPR013083 Znf_RING/FYVE/PHD
PfamiView protein in Pfam
PF00628 PHD, 1 hit
SMARTiView protein in SMART
SM00249 PHD, 1 hit
SUPFAMiSSF57903 SSF57903, 1 hit
PROSITEiView protein in PROSITE
PS01359 ZF_PHD_1, 1 hit
PS50016 ZF_PHD_2, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 3 described isoforms and 12 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q96BD5-1) [UniParc]FASTAAdd to basket

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
MELQTLQEAL KVEIQVHQKL VAQMKQDPQN ADLKKQLHEL QAKITALSEK
60 70 80 90 100
QKRVVEQLRK NLIVKQEQPD KFQIQPLPQS ENKLQTAQQQ PLQQLQQQQQ
110 120 130 140 150
YHHHHAQQSA AASPNLTASQ KTVTTASMIT TKTLPLVLKA ATATMPASVV
160 170 180 190 200
GQRPTIAMVT AINSQKAVLS TDVQNTPVNL QTSSKVTGPG AEAVQIVAKN
210 220 230 240 250
TVTLVQATPP QPIKVPQFIP PPRLTPRPNF LPQVRPKPVA QNNIPIAPAP
260 270 280 290 300
PPMLAAPQLI QRPVMLTKFT PTTLPTSQNS IHPVRVVNGQ TATIAKTFPM
310 320 330 340 350
AQLTSIVIAT PGTRLAGPQT VQLSKPSLEK QTVKSHTETD EKQTESRTIT
360 370 380 390 400
PPAAPKPKRE ENPQKLAFMV SLGLVTHDHL EEIQSKRQER KRRTTANPVY
410 420 430 440 450
SGAVFEPERK KSAVTYLNST MHPGTRKRGR PPKYNAVLGF GALTPTSPQS
460 470 480 490 500
SHPDSPENEK TETTFTFPAP VQPVSLPSPT STDGDIHEDF CSVCRKSGQL
510 520 530 540 550
LMCDTCSRVY HLDCLDPPLK TIPKGMWICP RCQDQMLKKE EAIPWPGTLA
560 570 580 590 600
IVHSYIAYKA AKEEEKQKLL KWSSDLKQER EQLEQKVKQL SNSISKCMEM
610 620 630 640 650
KNTILARQKE MHSSLEKVKQ LIRLIHGIDL SKPVDSEATV GAISNGPDCT
660 670 680
PPANAATSTP APSPSSQSCT ANCNQGEETK
Length:680
Mass (Da):74,854
Last modified:December 1, 2001 - v1
Checksum:iC7AF87EB2984A796
GO
Isoform 2 (identifier: Q96BD5-2) [UniParc]FASTAAdd to basket
Also known as: hBHC80-4

The sequence of this isoform differs from the canonical sequence as follows:
     204-204: L → LQ
     429-483: GRPPKYNAVLGFGALTPTSPQSSHPDSPENEKTETTFTFPAPVQPVSLPSPTSTD → ANEEHWPK

Show »
Length:634
Mass (Da):70,210
Checksum:iB1F247CD92D7D411
GO
Isoform 3 (identifier: Q96BD5-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     204-204: L → LQ

Show »
Length:681
Mass (Da):74,982
Checksum:iF95DC57A1D3C0FEC
GO

Computationally mapped potential isoform sequencesi

There are 12 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H0YEK2H0YEK2_HUMAN
PHD finger protein 21A
PHF21A
116Annotation score:
E9PQM3E9PQM3_HUMAN
PHD finger protein 21A
PHF21A
101Annotation score:
H0YCI1H0YCI1_HUMAN
PHD finger protein 21A
PHF21A
150Annotation score:
E9PLU5E9PLU5_HUMAN
PHD finger protein 21A
PHF21A
134Annotation score:
E9PR02E9PR02_HUMAN
PHD finger protein 21A
PHF21A
51Annotation score:
E9PS51E9PS51_HUMAN
PHD finger protein 21A
PHF21A
82Annotation score:
E9PLV4E9PLV4_HUMAN
PHD finger protein 21A
PHF21A
62Annotation score:
H0YCM5H0YCM5_HUMAN
PHD finger protein 21A
PHF21A
93Annotation score:
A0A1B0GX09A0A1B0GX09_HUMAN
PHD finger protein 21A
PHF21A
133Annotation score:
E9PNW9E9PNW9_HUMAN
PHD finger protein 21A
PHF21A
26Annotation score:
There are more potential isoformsShow all

Sequence cautioni

The sequence AAF64262 differs from that shown. Reason: Frameshift at several positions.Curated
The sequence BAB21787 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti447S → P in BAB13839 (PubMed:14702039).Curated1
Sequence conflicti662 – 680PSPSS…GEETK → LCSLPELHSEL (Ref. 7) CuratedAdd BLAST19

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_025515347R → H2 PublicationsCorresponds to variant dbSNP:rs3736508Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_017448204L → LQ in isoform 2 and isoform 3. 3 Publications1
Alternative sequenceiVSP_017449429 – 483GRPPK…PTSTD → ANEEHWPK in isoform 2. 3 PublicationsAdd BLAST55

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY090777 mRNA Translation: AAM09095.1
AB051483 mRNA Translation: BAB21787.1 Different initiation.
AK021530 mRNA Translation: BAB13839.1
AK023258 mRNA Translation: BAB14492.1
CH471064 Genomic DNA Translation: EAW68012.1
CH471064 Genomic DNA Translation: EAW68013.1
CH471064 Genomic DNA Translation: EAW68015.1
CH471064 Genomic DNA Translation: EAW68017.1
BC015714 mRNA Translation: AAH15714.1
BX648236 mRNA Translation: CAH10542.1
AF208848 mRNA Translation: AAF64262.1 Frameshift.
CCDSiCCDS31474.1 [Q96BD5-2]
CCDS44578.1 [Q96BD5-1]
RefSeqiNP_001095272.1, NM_001101802.1 [Q96BD5-1]
NP_057705.3, NM_016621.3 [Q96BD5-2]
XP_005253022.1, XM_005252965.4 [Q96BD5-3]
XP_011518475.1, XM_011520173.2
XP_011518476.1, XM_011520174.2 [Q96BD5-3]
XP_011518481.1, XM_011520179.2 [Q96BD5-2]
XP_016873380.1, XM_017017891.1 [Q96BD5-1]
UniGeneiHs.502458

Genome annotation databases

EnsembliENST00000323180; ENSP00000323152; ENSG00000135365 [Q96BD5-2]
ENST00000418153; ENSP00000398824; ENSG00000135365 [Q96BD5-1]
GeneIDi51317
KEGGihsa:51317
UCSCiuc001ncb.5 human [Q96BD5-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY090777 mRNA Translation: AAM09095.1
AB051483 mRNA Translation: BAB21787.1 Different initiation.
AK021530 mRNA Translation: BAB13839.1
AK023258 mRNA Translation: BAB14492.1
CH471064 Genomic DNA Translation: EAW68012.1
CH471064 Genomic DNA Translation: EAW68013.1
CH471064 Genomic DNA Translation: EAW68015.1
CH471064 Genomic DNA Translation: EAW68017.1
BC015714 mRNA Translation: AAH15714.1
BX648236 mRNA Translation: CAH10542.1
AF208848 mRNA Translation: AAF64262.1 Frameshift.
CCDSiCCDS31474.1 [Q96BD5-2]
CCDS44578.1 [Q96BD5-1]
RefSeqiNP_001095272.1, NM_001101802.1 [Q96BD5-1]
NP_057705.3, NM_016621.3 [Q96BD5-2]
XP_005253022.1, XM_005252965.4 [Q96BD5-3]
XP_011518475.1, XM_011520173.2
XP_011518476.1, XM_011520174.2 [Q96BD5-3]
XP_011518481.1, XM_011520179.2 [Q96BD5-2]
XP_016873380.1, XM_017017891.1 [Q96BD5-1]
UniGeneiHs.502458

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2PUYX-ray1.43A/B486-543[»]
2YQLNMR-A487-535[»]
ProteinModelPortaliQ96BD5
SMRiQ96BD5
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119468, 62 interactors
CORUMiQ96BD5
DIPiDIP-60252N
IntActiQ96BD5, 35 interactors
MINTiQ96BD5
STRINGi9606.ENSP00000398824

PTM databases

iPTMnetiQ96BD5
PhosphoSitePlusiQ96BD5

Polymorphism and mutation databases

BioMutaiPHF21A
DMDMi74731224

Proteomic databases

EPDiQ96BD5
MaxQBiQ96BD5
PaxDbiQ96BD5
PeptideAtlasiQ96BD5
PRIDEiQ96BD5
ProteomicsDBi76065
76066 [Q96BD5-2]
76067 [Q96BD5-3]

Protocols and materials databases

DNASUi51317
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000323180; ENSP00000323152; ENSG00000135365 [Q96BD5-2]
ENST00000418153; ENSP00000398824; ENSG00000135365 [Q96BD5-1]
GeneIDi51317
KEGGihsa:51317
UCSCiuc001ncb.5 human [Q96BD5-1]

Organism-specific databases

CTDi51317
DisGeNETi51317
EuPathDBiHostDB:ENSG00000135365.15
GeneCardsiPHF21A
HGNCiHGNC:24156 PHF21A
HPAiHPA023580
MalaCardsiPHF21A
MIMi608325 gene
neXtProtiNX_Q96BD5
OpenTargetsiENSG00000135365
Orphaneti52022 Potocki-Shaffer syndrome
PharmGKBiPA134977844
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IREA Eukaryota
ENOG41112YM LUCA
GeneTreeiENSGT00530000063984
HOVERGENiHBG080293
InParanoidiQ96BD5
OMAiHHHAQSA
OrthoDBiEOG091G03CB
PhylomeDBiQ96BD5
TreeFamiTF331518

Enzyme and pathway databases

ReactomeiR-HSA-3214815 HDACs deacetylate histones
R-HSA-983231 Factors involved in megakaryocyte development and platelet production

Miscellaneous databases

ChiTaRSiPHF21A human
EvolutionaryTraceiQ96BD5
GeneWikiiPHF21A
GenomeRNAii51317
PROiPR:Q96BD5
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000135365 Expressed in 220 organ(s), highest expression level in corpus callosum
CleanExiHS_PHF21A
ExpressionAtlasiQ96BD5 baseline and differential
GenevisibleiQ96BD5 HS

Family and domain databases

Gene3Di3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR019786 Zinc_finger_PHD-type_CS
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR019787 Znf_PHD-finger
IPR013083 Znf_RING/FYVE/PHD
PfamiView protein in Pfam
PF00628 PHD, 1 hit
SMARTiView protein in SMART
SM00249 PHD, 1 hit
SUPFAMiSSF57903 SSF57903, 1 hit
PROSITEiView protein in PROSITE
PS01359 ZF_PHD_1, 1 hit
PS50016 ZF_PHD_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPF21A_HUMAN
AccessioniPrimary (citable) accession number: Q96BD5
Secondary accession number(s): D3DQP5
, Q6AWA2, Q9C0G7, Q9H8V9, Q9HAK6, Q9NZE9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 7, 2006
Last sequence update: December 1, 2001
Last modified: November 7, 2018
This is version 154 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 entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  2. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. Human chromosome 11
    Human chromosome 11: entries, gene names and cross-references to MIM
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Main funding by: National Institutes of Health

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