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Q96BD5 (PF21A_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 114. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
PHD finger protein 21A
Alternative name(s):
BHC80a
BRAF35-HDAC complex protein BHC80
Gene names
Name:PHF21A
Synonyms:BHC80, KIAA1696
ORF Names:BM-006
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length680 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.10

Subunit structure

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. Ref.1 Ref.8 Ref.9

Subcellular location

Nucleus By similarity.

Tissue specificity

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

Sequence similarities

Contains 1 A.T hook DNA-binding domain.

Contains 1 PHD-type zinc finger.

Sequence caution

The sequence AAF64262.1 differs from that shown. Reason: Frameshift at several positions.

The sequence BAB21787.1 differs from that shown. Reason: Erroneous initiation.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q96BD5-1)

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.
Isoform 2 (identifier: Q96BD5-2)

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
Isoform 3 (identifier: Q96BD5-3)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 680680PHD finger protein 21A
PRO_0000226767

Regions

DNA binding425 – 43713A.T hook
Zinc finger488 – 53548PHD-type
Region486 – 680195Required for transcriptional repression
Coiled coil558 – 60346 Potential
Compositional bias4 – 108105Gln-rich

Amino acid modifications

Modified residue4441Phosphothreonine Ref.13
Modified residue4471Phosphoserine Ref.13

Natural variations

Alternative sequence2041L → LQ in isoform 2 and isoform 3.
VSP_017448
Alternative sequence429 – 48355GRPPK…PTSTD → ANEEHWPK in isoform 2.
VSP_017449
Natural variant3471R → H. Ref.1 Ref.3
Corresponds to variant rs3736508 [ dbSNP | Ensembl ].
VAR_025515

Experimental info

Sequence conflict4471S → P in BAB13839. Ref.3
Sequence conflict662 – 68019PSPSS…GEETK → LCSLPELHSEL Ref.7

Secondary structure

........... 680
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified December 1, 2001. Version 1.
Checksum: C7AF87EB2984A796

FASTA68074,854
        10         20         30         40         50         60 
MELQTLQEAL KVEIQVHQKL VAQMKQDPQN ADLKKQLHEL QAKITALSEK QKRVVEQLRK 

        70         80         90        100        110        120 
NLIVKQEQPD KFQIQPLPQS ENKLQTAQQQ PLQQLQQQQQ YHHHHAQQSA AASPNLTASQ 

       130        140        150        160        170        180 
KTVTTASMIT TKTLPLVLKA ATATMPASVV GQRPTIAMVT AINSQKAVLS TDVQNTPVNL 

       190        200        210        220        230        240 
QTSSKVTGPG AEAVQIVAKN TVTLVQATPP QPIKVPQFIP PPRLTPRPNF LPQVRPKPVA 

       250        260        270        280        290        300 
QNNIPIAPAP PPMLAAPQLI QRPVMLTKFT PTTLPTSQNS IHPVRVVNGQ TATIAKTFPM 

       310        320        330        340        350        360 
AQLTSIVIAT PGTRLAGPQT VQLSKPSLEK QTVKSHTETD EKQTESRTIT PPAAPKPKRE 

       370        380        390        400        410        420 
ENPQKLAFMV SLGLVTHDHL EEIQSKRQER KRRTTANPVY SGAVFEPERK KSAVTYLNST 

       430        440        450        460        470        480 
MHPGTRKRGR PPKYNAVLGF GALTPTSPQS SHPDSPENEK TETTFTFPAP VQPVSLPSPT 

       490        500        510        520        530        540 
STDGDIHEDF CSVCRKSGQL LMCDTCSRVY HLDCLDPPLK TIPKGMWICP RCQDQMLKKE 

       550        560        570        580        590        600 
EAIPWPGTLA IVHSYIAYKA AKEEEKQKLL KWSSDLKQER EQLEQKVKQL SNSISKCMEM 

       610        620        630        640        650        660 
KNTILARQKE MHSSLEKVKQ LIRLIHGIDL SKPVDSEATV GAISNGPDCT PPANAATSTP 

       670        680 
APSPSSQSCT ANCNQGEETK 

« Hide

Isoform 2 (hBHC80-4) [UniParc].

Checksum: B1F247CD92D7D411
Show »

FASTA63470,210
Isoform 3 [UniParc].

Checksum: F95DC57A1D3C0FEC
Show »

FASTA68174,982

References

« Hide 'large scale' references
[1]"A core-BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes."
Hakimi M.-A., Bochar D.A., Chenoweth J., Lane W.S., Mandel G., Shiekhattar R.
Proc. Natl. Acad. Sci. U.S.A. 99:7420-7425(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE BHC COMPLEX WITH HDAC1; HDAC2; HMG20B; KDM1A AND RCOR1, TISSUE SPECIFICITY, VARIANT HIS-347.
[2]"Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
Nagase T., Kikuno R., Hattori A., Kondo Y., Okumura K., Ohara O.
DNA Res. 7:347-355(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Tissue: Brain.
[3]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-456 (ISOFORM 3), VARIANT HIS-347.
Tissue: Embryo and Teratocarcinoma.
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Uterus.
[6]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 121-680 (ISOFORM 1).
Tissue: Fetal kidney.
[7]"A novel gene expressed in human bone marrow."
Zhao M., Song H., Li N., Peng Y., Han Z., Chen Z.
Submitted (NOV-1999) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 284-672 (ISOFORMS 2/3).
Tissue: Bone marrow.
[8]"A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes."
Hakimi M.-A., Dong Y., Lane W.S., Speicher D.W., Shiekhattar R.
J. Biol. Chem. 278:7234-7239(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE BHC COMPLEX WITH HDAC1; HDAC2; HMG20B; KDM1A; RCOR1; ZMYM2; ZNF217; ZMYM3; KIAA0182 AND GTF2I.
[9]"Characterization of BHC80 in BRAF-HDAC complex, involved in neuron-specific gene repression."
Iwase S., Januma A., Miyamoto K., Shono N., Honda A., Yanagisawa J., Baba T.
Biochem. Biophys. Res. Commun. 322:601-608(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH HDAC1; HDAC2; HMG20B; KDM1A AND RCOR1.
[10]"Regulation of LSD1 histone demethylase activity by its associated factors."
Shi Y.-J., Matson C., Lan F., Iwase S., Baba T., Shi Y.
Mol. Cell 19:857-864(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[11]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[12]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-444 AND SER-447, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[14]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[15]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[16]"Solution structure of the PHD domain in PHD finger protein 21A."
RIKEN structural genomics initiative (RSGI)
Submitted (MAR-2008) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 487-535.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS31474.1. [Q96BD5-2]
CCDS44578.1. [Q96BD5-1]
RefSeqNP_001095272.1. NM_001101802.1. [Q96BD5-1]
NP_057705.3. NM_016621.3. [Q96BD5-2]
XP_005253019.1. XM_005252962.2. [Q96BD5-3]
XP_005253020.1. XM_005252963.2. [Q96BD5-3]
XP_005253021.1. XM_005252964.2. [Q96BD5-3]
XP_005253022.1. XM_005252965.2. [Q96BD5-3]
UniGeneHs.502458.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2PUYX-ray1.43A/B486-543[»]
2YQLNMR-A487-535[»]
ProteinModelPortalQ96BD5.
SMRQ96BD5. Positions 486-543.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid119468. 13 interactions.
DIPDIP-60252N.
IntActQ96BD5. 9 interactions.
MINTMINT-1469147.
STRING9606.ENSP00000398824.

PTM databases

PhosphoSiteQ96BD5.

Polymorphism databases

DMDM74731224.

Proteomic databases

MaxQBQ96BD5.
PaxDbQ96BD5.
PRIDEQ96BD5.

Protocols and materials databases

DNASU51317.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000257821; ENSP00000257821; ENSG00000135365. [Q96BD5-3]
ENST00000323180; ENSP00000323152; ENSG00000135365. [Q96BD5-2]
ENST00000418153; ENSP00000398824; ENSG00000135365. [Q96BD5-1]
GeneID51317.
KEGGhsa:51317.
UCSCuc001ncb.4. human. [Q96BD5-2]
uc001ncc.4. human. [Q96BD5-1]
uc001nce.2. human. [Q96BD5-3]

Organism-specific databases

CTD51317.
GeneCardsGC11M045950.
HGNCHGNC:24156. PHF21A.
HPAHPA023580.
MIM608325. gene.
neXtProtNX_Q96BD5.
Orphanet52022. Potocki-Shaffer syndrome.
PharmGKBPA134977844.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG310379.
HOVERGENHBG080293.
InParanoidQ96BD5.
OMAHHHAQSA.
OrthoDBEOG7WMCHZ.
PhylomeDBQ96BD5.
TreeFamTF331518.

Enzyme and pathway databases

ReactomeREACT_604. Hemostasis.

Gene expression databases

ArrayExpressQ96BD5.
BgeeQ96BD5.
CleanExHS_PHF21A.
GenevestigatorQ96BD5.

Family and domain databases

Gene3D3.30.40.10. 1 hit.
InterProIPR017956. 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.
[Graphical view]
PfamPF02178. AT_hook. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]
SMARTSM00384. AT_hook. 1 hit.
SM00249. PHD. 1 hit.
SM00184. RING. 1 hit.
[Graphical view]
SUPFAMSSF57903. SSF57903. 1 hit.
PROSITEPS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ96BD5.
GeneWikiPHF21A.
GenomeRNAi51317.
NextBio54681.
PROQ96BD5.
SOURCESearch...

Entry information

Entry namePF21A_HUMAN
AccessionPrimary (citable) accession number: Q96BD5
Secondary accession number(s): D3DQP5 expand/collapse secondary AC list , Q6AWA2, Q9C0G7, Q9H8V9, Q9HAK6, Q9NZE9
Entry history
Integrated into UniProtKB/Swiss-Prot: March 7, 2006
Last sequence update: December 1, 2001
Last modified: July 9, 2014
This is version 114 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 11

Human chromosome 11: entries, gene names and cross-references to MIM