UniProtKB - Q96BD5 (PF21A_HUMAN)
PHD finger protein 21A
PHF21A
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 PublicationRegions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
DNA bindingi | 425 – 437 | A.T hookAdd BLAST | 13 | |
Zinc fingeri | 488 – 535 | PHD-typePROSITE-ProRule annotationAdd BLAST | 48 |
GO - Molecular functioni
- chromatin binding Source: GO_Central
- DNA binding Source: UniProtKB-KW
- metal ion binding Source: UniProtKB-KW
GO - Biological processi
- chromatin organization Source: UniProtKB-KW
- negative regulation of transcription by RNA polymerase II Source: MGI
Keywordsi
Molecular function | Chromatin regulator, DNA-binding, Repressor |
Biological process | Transcription, Transcription regulation |
Ligand | Metal-binding, Zinc |
Enzyme and pathway databases
PathwayCommonsi | Q96BD5 |
Reactomei | R-HSA-3214815, HDACs deacetylate histones R-HSA-9679191, Potential therapeutics for SARS R-HSA-983231, Factors involved in megakaryocyte development and platelet production |
SignaLinki | Q96BD5 |
SIGNORi | Q96BD5 |
Names & Taxonomyi
Protein namesi | Recommended name: PHD finger protein 21AAlternative name(s): BHC80a BRAF35-HDAC complex protein BHC80 |
Gene namesi | Name:PHF21A Synonyms:BHC80, KIAA1696 ORF Names:BM-006 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
HGNCi | HGNC:24156, PHF21A |
MIMi | 608325, gene |
neXtProti | NX_Q96BD5 |
VEuPathDBi | HostDB:ENSG00000135365 |
Subcellular locationi
Nucleus
- Nucleus By similarity
Nucleus
- histone deacetylase complex Source: MGI
- nucleoplasm Source: Reactome
Other locations
- DNA repair complex Source: MGI
Keywords - Cellular componenti
NucleusPathology & Biotechi
Involvement in diseasei
Intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures (IDDBCS)2 Publications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_083199 | 429 | G → S in IDDBCS; unknown pathological significance. 1 Publication | 1 | |
Natural variantiVAR_083200 | 580 – 680 | Missing in IDDBCS. 2 PublicationsAdd BLAST | 101 |
Keywords - Diseasei
Disease variant, Epilepsy, Mental retardationOrganism-specific databases
DisGeNETi | 51317 |
MalaCardsi | PHF21A |
MIMi | 618725, phenotype |
OpenTargetsi | ENSG00000135365 |
Orphaneti | 52022, Potocki-Shaffer syndrome |
PharmGKBi | PA134977844 |
Miscellaneous databases
Pharosi | Q96BD5, Tbio |
Genetic variation databases
BioMutai | PHF21A |
DMDMi | 74731224 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000226767 | 1 – 680 | PHD finger protein 21AAdd BLAST | 680 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Cross-linki | 65 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Modified residuei | 350 | PhosphothreonineCombined sources | 1 | |
Modified residuei | 444 | PhosphothreonineCombined sources | 1 | |
Modified residuei | 447 | PhosphoserineCombined sources | 1 |
Keywords - PTMi
Isopeptide bond, Phosphoprotein, Ubl conjugationProteomic databases
EPDi | Q96BD5 |
jPOSTi | Q96BD5 |
MassIVEi | Q96BD5 |
MaxQBi | Q96BD5 |
PaxDbi | Q96BD5 |
PeptideAtlasi | Q96BD5 |
PRIDEi | Q96BD5 |
ProteomicsDBi | 76065 [Q96BD5-1] 76066 [Q96BD5-2] 76067 [Q96BD5-3] |
PTM databases
GlyGeni | Q96BD5, 8 sites, 2 O-linked glycans (8 sites) |
iPTMneti | Q96BD5 |
PhosphoSitePlusi | Q96BD5 |
Expressioni
Tissue specificityi
Gene expression databases
Bgeei | ENSG00000135365, Expressed in corpus callosum and 233 other tissues |
ExpressionAtlasi | Q96BD5, baseline and differential |
Genevisiblei | Q96BD5, HS |
Organism-specific databases
HPAi | ENSG00000135365, Low tissue specificity |
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 PublicationsBinary interactionsi
Q96BD5
Protein-protein interaction databases
BioGRIDi | 119468, 76 interactors |
CORUMi | Q96BD5 |
DIPi | DIP-60252N |
IntActi | Q96BD5, 45 interactors |
MINTi | Q96BD5 |
STRINGi | 9606.ENSP00000398824 |
Miscellaneous databases
RNActi | Q96BD5, protein |
Structurei
Secondary structure
3D structure databases
AlphaFoldDBi | Q96BD5 |
BMRBi | Q96BD5 |
SMRi | Q96BD5 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q96BD5 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 82 – 118 | DisorderedSequence analysisAdd BLAST | 37 | |
Regioni | 318 – 363 | DisorderedSequence analysisAdd BLAST | 46 | |
Regioni | 440 – 463 | DisorderedSequence analysisAdd BLAST | 24 | |
Regioni | 486 – 680 | Required for transcriptional repressionAdd BLAST | 195 | |
Regioni | 639 – 680 | DisorderedSequence analysisAdd BLAST | 42 |
Coiled coil
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Coiled coili | 558 – 603 | Sequence analysisAdd BLAST | 46 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 331 – 345 | Basic and acidic residuesSequence analysisAdd BLAST | 15 | |
Compositional biasi | 442 – 463 | Polar residuesSequence analysisAdd BLAST | 22 | |
Compositional biasi | 650 – 680 | Polar residuesSequence analysisAdd BLAST | 31 |
Zinc finger
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Zinc fingeri | 488 – 535 | PHD-typePROSITE-ProRule annotationAdd BLAST | 48 |
Keywords - Domaini
Coiled coil, Zinc-fingerPhylogenomic databases
eggNOGi | KOG0383, Eukaryota |
GeneTreei | ENSGT00940000156124 |
HOGENOMi | CLU_020260_1_0_1 |
InParanoidi | Q96BD5 |
OMAi | QKEMHGS |
OrthoDBi | 1185408at2759 |
PhylomeDBi | Q96BD5 |
TreeFami | TF331518 |
Family and domain databases
Gene3Di | 3.30.40.10, 1 hit |
InterProi | View 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 |
Pfami | View protein in Pfam PF00628, PHD, 1 hit |
SMARTi | View protein in SMART SM00249, PHD, 1 hit |
SUPFAMi | SSF57903, SSF57903, 1 hit |
PROSITEi | View protein in PROSITE PS01359, ZF_PHD_1, 1 hit PS50016, ZF_PHD_2, 1 hit |
s (3+)i Sequence
Sequence statusi: Complete.
This entry describes 3 produced by isoformsialternative splicing. AlignAdd to basketThis entry has 3 described isoforms and 12 potential isoforms that are computationally mapped.Show allAlign All
This isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
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
Computationally mapped potential isoform sequencesi
There are 12 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basketH0YCI1 | H0YCI1_HUMAN | PHD finger protein 21A | PHF21A | 150 | Annotation score: | ||
A0A1B0GX09 | A0A1B0GX09_HUMAN | PHD finger protein 21A | PHF21A | 133 | Annotation score: | ||
E9PQM3 | E9PQM3_HUMAN | PHD finger protein 21A | PHF21A | 101 | Annotation score: | ||
E9PLU5 | E9PLU5_HUMAN | PHD finger protein 21A | PHF21A | 134 | Annotation score: | ||
E9PLV4 | E9PLV4_HUMAN | PHD finger protein 21A | PHF21A | 62 | Annotation score: | ||
E9PR02 | E9PR02_HUMAN | PHD finger protein 21A | PHF21A | 51 | Annotation score: | ||
E9PS51 | E9PS51_HUMAN | PHD finger protein 21A | PHF21A | 82 | Annotation score: | ||
H0YEK2 | H0YEK2_HUMAN | PHD finger protein 21A | PHF21A | 569 | Annotation score: | ||
E9PNN4 | E9PNN4_HUMAN | PHD finger protein 21A | PHF21A | 11 | Annotation score: | ||
E9PNW9 | E9PNW9_HUMAN | PHD finger protein 21A | PHF21A | 26 | Annotation score: | ||
There are more potential isoformsShow all |
Sequence cautioni
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 447 | S → P in BAB13839 (PubMed:14702039).Curated | 1 | |
Sequence conflicti | 662 – 680 | PSPSS…GEETK → LCSLPELHSEL (Ref. 7) CuratedAdd BLAST | 19 |
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_025515 | 347 | R → H2 PublicationsCorresponds to variant dbSNP:rs3736508Ensembl. | 1 | |
Natural variantiVAR_083199 | 429 | G → S in IDDBCS; unknown pathological significance. 1 Publication | 1 | |
Natural variantiVAR_083200 | 580 – 680 | Missing in IDDBCS. 2 PublicationsAdd BLAST | 101 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_017448 | 204 | L → LQ in isoform 2 and isoform 3. 3 Publications | 1 | |
Alternative sequenceiVSP_017449 | 429 – 483 | GRPPK…PTSTD → ANEEHWPK in isoform 2. 3 PublicationsAdd BLAST | 55 |
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. |
CCDSi | CCDS31474.1 [Q96BD5-2] CCDS44578.1 [Q96BD5-1] |
RefSeqi | NP_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] |
Genome annotation databases
Ensembli | ENST00000323180.10; ENSP00000323152.6; ENSG00000135365.17 [Q96BD5-2] ENST00000418153.6; ENSP00000398824.2; ENSG00000135365.17 ENST00000676320.1; ENSP00000502222.1; ENSG00000135365.17 [Q96BD5-3] ENST00000690620.1; ENSP00000508589.1; ENSG00000135365.17 [Q96BD5-2] |
GeneIDi | 51317 |
KEGGi | hsa:51317 |
MANE-Selecti | ENST00000676320.1; ENSP00000502222.1; NM_001352027.3; NP_001338956.1 [Q96BD5-3] |
UCSCi | uc001ncb.5, human [Q96BD5-1] |
Keywords - Coding sequence diversityi
Alternative splicingSimilar 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. |
CCDSi | CCDS31474.1 [Q96BD5-2] CCDS44578.1 [Q96BD5-1] |
RefSeqi | NP_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] |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2PUY | X-ray | 1.43 | A/B | 486-543 | [»] | |
2YQL | NMR | - | A | 487-535 | [»] | |
AlphaFoldDBi | Q96BD5 | |||||
BMRBi | Q96BD5 | |||||
SMRi | Q96BD5 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 119468, 76 interactors |
CORUMi | Q96BD5 |
DIPi | DIP-60252N |
IntActi | Q96BD5, 45 interactors |
MINTi | Q96BD5 |
STRINGi | 9606.ENSP00000398824 |
PTM databases
GlyGeni | Q96BD5, 8 sites, 2 O-linked glycans (8 sites) |
iPTMneti | Q96BD5 |
PhosphoSitePlusi | Q96BD5 |
Genetic variation databases
BioMutai | PHF21A |
DMDMi | 74731224 |
Proteomic databases
EPDi | Q96BD5 |
jPOSTi | Q96BD5 |
MassIVEi | Q96BD5 |
MaxQBi | Q96BD5 |
PaxDbi | Q96BD5 |
PeptideAtlasi | Q96BD5 |
PRIDEi | Q96BD5 |
ProteomicsDBi | 76065 [Q96BD5-1] 76066 [Q96BD5-2] 76067 [Q96BD5-3] |
Protocols and materials databases
Antibodypediai | 26236, 230 antibodies from 29 providers |
DNASUi | 51317 |
Genome annotation databases
Ensembli | ENST00000323180.10; ENSP00000323152.6; ENSG00000135365.17 [Q96BD5-2] ENST00000418153.6; ENSP00000398824.2; ENSG00000135365.17 ENST00000676320.1; ENSP00000502222.1; ENSG00000135365.17 [Q96BD5-3] ENST00000690620.1; ENSP00000508589.1; ENSG00000135365.17 [Q96BD5-2] |
GeneIDi | 51317 |
KEGGi | hsa:51317 |
MANE-Selecti | ENST00000676320.1; ENSP00000502222.1; NM_001352027.3; NP_001338956.1 [Q96BD5-3] |
UCSCi | uc001ncb.5, human [Q96BD5-1] |
Organism-specific databases
CTDi | 51317 |
DisGeNETi | 51317 |
GeneCardsi | PHF21A |
HGNCi | HGNC:24156, PHF21A |
HPAi | ENSG00000135365, Low tissue specificity |
MalaCardsi | PHF21A |
MIMi | 608325, gene 618725, phenotype |
neXtProti | NX_Q96BD5 |
OpenTargetsi | ENSG00000135365 |
Orphaneti | 52022, Potocki-Shaffer syndrome |
PharmGKBi | PA134977844 |
VEuPathDBi | HostDB:ENSG00000135365 |
HUGEi | Search... |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG0383, Eukaryota |
GeneTreei | ENSGT00940000156124 |
HOGENOMi | CLU_020260_1_0_1 |
InParanoidi | Q96BD5 |
OMAi | QKEMHGS |
OrthoDBi | 1185408at2759 |
PhylomeDBi | Q96BD5 |
TreeFami | TF331518 |
Enzyme and pathway databases
PathwayCommonsi | Q96BD5 |
Reactomei | R-HSA-3214815, HDACs deacetylate histones R-HSA-9679191, Potential therapeutics for SARS R-HSA-983231, Factors involved in megakaryocyte development and platelet production |
SignaLinki | Q96BD5 |
SIGNORi | Q96BD5 |
Miscellaneous databases
BioGRID-ORCSi | 51317, 21 hits in 1087 CRISPR screens |
ChiTaRSi | PHF21A, human |
EvolutionaryTracei | Q96BD5 |
GeneWikii | PHF21A |
GenomeRNAii | 51317 |
Pharosi | Q96BD5, Tbio |
PROi | PR:Q96BD5 |
RNActi | Q96BD5, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000135365, Expressed in corpus callosum and 233 other tissues |
ExpressionAtlasi | Q96BD5, baseline and differential |
Genevisiblei | Q96BD5, HS |
Family and domain databases
Gene3Di | 3.30.40.10, 1 hit |
InterProi | View 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 |
Pfami | View protein in Pfam PF00628, PHD, 1 hit |
SMARTi | View protein in SMART SM00249, PHD, 1 hit |
SUPFAMi | SSF57903, SSF57903, 1 hit |
PROSITEi | View protein in PROSITE PS01359, ZF_PHD_1, 1 hit PS50016, ZF_PHD_2, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | PF21A_HUMAN | |
Accessioni | Q96BD5Primary (citable) accession number: Q96BD5 Secondary accession number(s): D3DQP5 Q9NZE9 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | March 7, 2006 |
Last sequence update: | December 1, 2001 | |
Last modified: | May 25, 2022 | |
This is version 176 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any 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, Reference proteomeDocuments
- Human chromosome 11
Human chromosome 11: entries, gene names and cross-references to MIM - Human entries with genetic variants
List of human entries with genetic variants - Human variants curated from literature reports
Index of human variants curated from literature reports - MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references