Human Gene PHF21A (ENST00000676320.1_7) from GENCODE V47lift37
  Description: PHD finger protein 21A, transcript variant 12 (from RefSeq NR_165446.1)
Gencode Transcript: ENST00000676320.1_7
Gencode Gene: ENSG00000135365.17_20
Transcript (Including UTRs)
   Position: hg19 chr11:45,950,870-46,143,005 Size: 192,136 Total Exon Count: 19 Strand: -
Coding Region
   Position: hg19 chr11:45,955,519-46,105,770 Size: 150,252 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:45,950,870-46,143,005)mRNA (may differ from genome)Protein (681 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PF21A_HUMAN
DESCRIPTION: RecName: Full=PHD finger protein 21A; AltName: Full=BHC80a; AltName: Full=BRAF35-HDAC complex protein BHC80;
FUNCTION: 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.
SUBUNIT: 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.
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Highly expressed in brain. Expressed at much lower level in other tissues.
SIMILARITY: Contains 1 A.T hook DNA-binding domain.
SIMILARITY: Contains 1 PHD-type zinc finger.
SEQUENCE CAUTION: Sequence=AAF64262.1; Type=Frameshift; Positions=Several; Sequence=BAB21787.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PHF21A
Diseases sorted by gene-association score: potocki-shaffer syndrome* (22), articulation disorder (6), speech disorder (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -293.30756-0.388 Picture PostScript Text
3' UTR -1754.004649-0.377 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017956 - AT_hook_DNA-bd_motif
IPR019786 - Zinc_finger_PHD-type_CS
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00628 - PHD-finger
PF02178 - AT hook motif

SCOP Domains:
54160 - Chromo domain-like
57850 - RING/U-box
57903 - FYVE/PHD zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2PUY - X-ray MuPIT 2YQL - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q96BD5
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003712 transcription cofactor activity
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0042393 histone binding
GO:0046872 metal ion binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007596 blood coagulation
GO:0016575 histone deacetylation

Cellular Component:
GO:0000118 histone deacetylase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:1990391 DNA repair complex


-  Descriptions from all associated GenBank mRNAs
  AB051483 - Homo sapiens KIAA1696 mRNA for KIAA1696 protein.
AK023258 - Homo sapiens cDNA FLJ13196 fis, clone NT2RP3004428, weakly similar to CHROMODOMAIN HELICASE-DNA-BINDING PROTEIN 4.
BC015714 - Homo sapiens PHD finger protein 21A, mRNA (cDNA clone MGC:16851 IMAGE:3908900), complete cds.
AK021530 - Homo sapiens cDNA FLJ11468 fis, clone HEMBA1001651, weakly similar to CYTADHERENCE HIGH MOLECULAR WEIGHT PROTEIN 1.
AY090777 - Homo sapiens BRAF35/HDAC2 complex 80 kDa protein (BHC80) mRNA, complete cds.
AB384262 - Synthetic construct DNA, clone: pF1KSDA1696, Homo sapiens PHF21A gene for PHD finger protein 21A, complete cds, without stop codon, in Flexi system.
KJ893888 - Synthetic construct Homo sapiens clone ccsbBroadEn_03282 PHF21A gene, encodes complete protein.
EU446805 - Synthetic construct Homo sapiens clone IMAGE:100070167; IMAGE:100012014; FLH257456.01L PHD finger protein 21A (PHF21A) gene, encodes complete protein.
AL359608 - Homo sapiens mRNA; cDNA DKFZp547M146 (from clone DKFZp547M146).
BX648236 - Homo sapiens mRNA; cDNA DKFZp686D02108 (from clone DKFZp686D02108).
JD245316 - Sequence 226340 from Patent EP1572962.
JD493529 - Sequence 474553 from Patent EP1572962.
JD150190 - Sequence 131214 from Patent EP1572962.
JD078551 - Sequence 59575 from Patent EP1572962.
JD207329 - Sequence 188353 from Patent EP1572962.
JD487689 - Sequence 468713 from Patent EP1572962.
JD479765 - Sequence 460789 from Patent EP1572962.
JD474749 - Sequence 455773 from Patent EP1572962.
JD372789 - Sequence 353813 from Patent EP1572962.
JD203954 - Sequence 184978 from Patent EP1572962.
JD395557 - Sequence 376581 from Patent EP1572962.
JD395556 - Sequence 376580 from Patent EP1572962.
JD528469 - Sequence 509493 from Patent EP1572962.
JD479301 - Sequence 460325 from Patent EP1572962.
JD480625 - Sequence 461649 from Patent EP1572962.
JD520309 - Sequence 501333 from Patent EP1572962.
JD056495 - Sequence 37519 from Patent EP1572962.
JD133965 - Sequence 114989 from Patent EP1572962.
JD133965 - Sequence 114989 from Patent EP1572962.
JD456748 - Sequence 437772 from Patent EP1572962.
JD280801 - Sequence 261825 from Patent EP1572962.
JD102191 - Sequence 83215 from Patent EP1572962.
JD132244 - Sequence 113268 from Patent EP1572962.
JD334427 - Sequence 315451 from Patent EP1572962.
JD383299 - Sequence 364323 from Patent EP1572962.
JD134012 - Sequence 115036 from Patent EP1572962.
JD162830 - Sequence 143854 from Patent EP1572962.
JD137498 - Sequence 118522 from Patent EP1572962.
JD274792 - Sequence 255816 from Patent EP1572962.
JD176070 - Sequence 157094 from Patent EP1572962.
JD541123 - Sequence 522147 from Patent EP1572962.
JD429510 - Sequence 410534 from Patent EP1572962.
JD195699 - Sequence 176723 from Patent EP1572962.
JD527141 - Sequence 508165 from Patent EP1572962.
JD444335 - Sequence 425359 from Patent EP1572962.
JD206762 - Sequence 187786 from Patent EP1572962.
JD074063 - Sequence 55087 from Patent EP1572962.
JD357022 - Sequence 338046 from Patent EP1572962.
JD114528 - Sequence 95552 from Patent EP1572962.
JD448004 - Sequence 429028 from Patent EP1572962.
JD210982 - Sequence 192006 from Patent EP1572962.
JD211539 - Sequence 192563 from Patent EP1572962.
JD476060 - Sequence 457084 from Patent EP1572962.
JD096919 - Sequence 77943 from Patent EP1572962.
AL359593 - Homo sapiens mRNA; cDNA DKFZp761M159 (from clone DKFZp761M159).
AF208848 - Homo sapiens BM-006 mRNA, complete cds.
JD241501 - Sequence 222525 from Patent EP1572962.
JD284775 - Sequence 265799 from Patent EP1572962.
JD276349 - Sequence 257373 from Patent EP1572962.
JD367979 - Sequence 349003 from Patent EP1572962.
JD189862 - Sequence 170886 from Patent EP1572962.
JD150066 - Sequence 131090 from Patent EP1572962.
JD290076 - Sequence 271100 from Patent EP1572962.
JD164647 - Sequence 145671 from Patent EP1572962.
JD469184 - Sequence 450208 from Patent EP1572962.
JD469183 - Sequence 450207 from Patent EP1572962.
JD066878 - Sequence 47902 from Patent EP1572962.
JD360824 - Sequence 341848 from Patent EP1572962.
JD299007 - Sequence 280031 from Patent EP1572962.
JD339605 - Sequence 320629 from Patent EP1572962.
JD217600 - Sequence 198624 from Patent EP1572962.
JD189592 - Sequence 170616 from Patent EP1572962.
JD114991 - Sequence 96015 from Patent EP1572962.
JD233024 - Sequence 214048 from Patent EP1572962.
JD496576 - Sequence 477600 from Patent EP1572962.
JD440218 - Sequence 421242 from Patent EP1572962.
JD561880 - Sequence 542904 from Patent EP1572962.
JD410951 - Sequence 391975 from Patent EP1572962.
JD370330 - Sequence 351354 from Patent EP1572962.
JD370392 - Sequence 351416 from Patent EP1572962.
JD200733 - Sequence 181757 from Patent EP1572962.
JD272633 - Sequence 253657 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96BD5 (Reactome details) participates in the following event(s):

R-HSA-996727 REST recruits the BHC complex
R-HSA-3769447 HDAC1/2 containing-complexes deacetylate histones
R-HSA-983231 Factors involved in megakaryocyte development and platelet production
R-HSA-109582 Hemostasis
R-HSA-3214815 HDACs deacetylate histones
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: BHC80, BM-006, D3DQP5, KIAA1696, NR_165446, PF21A_HUMAN, Q6AWA2, Q96BD5, Q9C0G7, Q9H8V9, Q9HAK6, Q9NZE9, uc330azi.1, uc330azi.2
UCSC ID: ENST00000676320.1_7
RefSeq Accession: NM_001352027.3
Protein: Q96BD5 (aka PF21A_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.