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Protein

PHD finger protein 12

Gene

PHF12

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

Functioni

Acts as a transcriptional repressor. Involved in recruitment of functional SIN3A complexes to DNA. Represses transcription at least in part through the activity of an associated histone deacetylase (HDAC). May also repress transcription in a SIN3A-independent manner through recruitment of functional AES complexes to DNA.1 Publication1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri56 – 105PHD-type 1PROSITE-ProRule annotationAdd BLAST50
Zinc fingeri271 – 321PHD-type 2; atypicalPROSITE-ProRule annotationAdd BLAST51

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000109118-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
PHD finger protein 12
Alternative name(s):
PHD factor 1
Short name:
Pf1
Gene namesi
Name:PHF12Imported
Synonyms:KIAA1523Imported
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

HGNCiHGNC:20816. PHF12.

Subcellular locationi

  • Nucleus 1 Publication

GO - Cellular componenti

  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
  • Sin3 complex Source: MGI
  • transcriptional repressor complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi57649.
OpenTargetsiENSG00000109118.
PharmGKBiPA134954478.

Polymorphism and mutation databases

BioMutaiPHF12.
DMDMi71153050.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000593021 – 1004PHD finger protein 12Add BLAST1004

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei131PhosphoserineCombined sources1
Modified residuei134PhosphoserineCombined sources1
Cross-linki467Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei555PhosphoserineCombined sources1
Modified residuei557PhosphothreonineCombined sources1
Modified residuei570PhosphothreonineCombined sources1
Modified residuei671PhosphothreonineCombined sources1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ96QT6.
MaxQBiQ96QT6.
PaxDbiQ96QT6.
PeptideAtlasiQ96QT6.
PRIDEiQ96QT6.

PTM databases

iPTMnetiQ96QT6.
PhosphoSitePlusiQ96QT6.

Expressioni

Gene expression databases

BgeeiENSG00000109118.
CleanExiHS_PHF12.
ExpressionAtlasiQ96QT6. baseline and differential.
GenevisibleiQ96QT6. HS.

Organism-specific databases

HPAiHPA021410.
HPA021452.

Interactioni

Subunit structurei

Isoform 2 interacts with SIN3A in a complex composed of HDAC1, SAP30 and SIN3A. Interacts with AES.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
MORF4L1Q9UBU8-23EBI-10293106,EBI-10288852

GO - Molecular functioni

Protein-protein interaction databases

BioGridi121686. 16 interactors.
DIPiDIP-59632N.
IntActiQ96QT6. 13 interactors.
STRINGi9606.ENSP00000329933.

Structurei

Secondary structure

11004
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi209 – 219Combined sources11
Turni229 – 231Combined sources3
Beta strandi233 – 235Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2L9SNMR-A200-241[»]
2LKMNMR-A200-241[»]
ProteinModelPortaliQ96QT6.
SMRiQ96QT6.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ96QT6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini815 – 869FHAPROSITE-ProRule annotationAdd BLAST55

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni102 – 273Interaction with SIN3A1 PublicationAdd BLAST172
Regioni105 – 128PBRAdd BLAST24
Regioni300 – 704Interaction with SIN3A1 PublicationAdd BLAST405

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi894 – 897Poly-ArgSequence analysis4
Compositional biasi929 – 932Poly-SerSequence analysis4

Domaini

The polybasic region (PBR) is responsive to the binding to phosphoinositides (PtdInsPs).

Sequence similaritiesi

Contains 1 FHA domain.PROSITE-ProRule annotation
Contains 2 PHD-type zinc fingers.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri56 – 105PHD-type 1PROSITE-ProRule annotationAdd BLAST50
Zinc fingeri271 – 321PHD-type 2; atypicalPROSITE-ProRule annotationAdd BLAST51

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG4299. Eukaryota.
ENOG410XQQA. LUCA.
GeneTreeiENSGT00440000033777.
HOGENOMiHOG000220810.
HOVERGENiHBG057884.
InParanoidiQ96QT6.
OMAiRPCNCKA.
OrthoDBiEOG091G055U.
PhylomeDBiQ96QT6.
TreeFamiTF336193.

Family and domain databases

Gene3Di2.60.200.20. 1 hit.
3.30.40.10. 2 hits.
InterProiIPR000253. FHA_dom.
IPR031966. PHF12_MRG-bd.
IPR008984. SMAD_FHA_domain.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF00628. PHD. 2 hits.
PF16737. PHF12_MRG_bd. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 2 hits.
[Graphical view]
SUPFAMiSSF49879. SSF49879. 1 hit.
SSF57903. SSF57903. 2 hits.
PROSITEiPS50006. FHA_DOMAIN. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 2 hits.
[Graphical view]

Sequences (5)i

Sequence statusi: Complete.

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

Isoform 1Curated (identifier: Q96QT6-1) [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
MWEKMETKTI VYDLDTSGGL MEQIQALLAP PKTDEAEKRS RKPEKEPRRS
60 70 80 90 100
GRATNHDSCD SCKEGGDLLC CDHCPAAFHL QCCNPPLSEE MLPPGEWMCH
110 120 130 140 150
RCTVRRKKRE QKKELGHVNG LVDKSGKRTT SPSSDTDLLD RSASKTELKA
160 170 180 190 200
IAHARILERR ASRPGTPTSS ASTETPTSEQ NDVDEDIIDV DEEPVAAEPD
210 220 230 240 250
YVQPQLRRPF ELLIAAAMER NPTQFQLPNE LTCTTALPGS SKRRRKEETT
260 270 280 290 300
GKNVKKTQHE LDHNGLVPLP VKVCFTCNRS CRVAPLIQCD YCPLLFHMDC
310 320 330 340 350
LEPPLTAMPL GRWMCPNHIE HVVLNQKNMT LSNRCQVFDR FQDTVSQHVV
360 370 380 390 400
KVDFLNRIHK KHPPNRRVLQ SVKRRSLKVP DAIKSQYQFP PPLIAPAAIR
410 420 430 440 450
DGELICNGIP EESQMHLLNS EHLATQAEQQ EWLCSVVALQ CSILKHLSAK
460 470 480 490 500
QMPSHWDSEQ TEKADIKPVI VTDSSVTTSL QTADKTPTPS HYPLSCPSGI
510 520 530 540 550
STQNSLSCSP PHQSPALEDI GCSSCAEKSK KTPCGTANGP VNTEVKANGP
560 570 580 590 600
HLYSSPTDST DPRRLPGANT PLPGLSHRQG WPRPLTPPAA GGLQNHTVGI
610 620 630 640 650
IVKTENATGP SSCPQRSLVP VPSLPPSIPS SCASIENTST LQRKTVQSQI
660 670 680 690 700
GPPLTDSRPL GSPPNATRVL TPPQAAGDGI LATTANQRFS SPAPSSDGKV
710 720 730 740 750
SPGTLSIGSA LTVPSFPANS TAMVDLTNSL RAFMDVNGEI EINMLDEKLI
760 770 780 790 800
KFLALQRIHQ LFPSRVQPSP GSVGTHQLAS GGHHIEVQRK EVQARAVFYP
810 820 830 840 850
LLGLGGAVNM CYRTLYIGTG ADMDVCLTNY GHCNYVSGKH ACIFYDENTK
860 870 880 890 900
HYELLNYSEH GTTVDNVLYS CDFSEKTPPT PPSSIVAKVQ SVIRRRRHQK
910 920 930 940 950
QDEEPSEEAA MMSSQAQGPQ RRPCNCKASS SSLIGGSGAG WEGTALLHHG
960 970 980 990 1000
SYIKLGCLQF VFSITEFATK QPKGDASLLQ DGVLAEKLSL KPHQGPVLRS

NSVP
Note: No experimental confirmation available.Curated
Length:1,004
Mass (Da):109,698
Last modified:July 19, 2005 - v2
Checksum:i239223BE9EAF619B
GO
Isoform 21 Publication (identifier: Q96QT6-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     697-704: DGKVSPGT → GECCSALG
     705-1004: Missing.

Show »
Length:704
Mass (Da):76,988
Checksum:iD7175FC65EB0B42E
GO
Isoform 3Curated (identifier: Q96QT6-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     80-107: LQCCNPPLSEEMLPPGEWMCHRCTVRRK → LVVYQDFVAPISLFHGTFHDGPTCSFAQ
     787-849: VQRKEVQARA...HACIFYDENT → GAHVHTCHHI...SRNKMATTAF
     850-1004: Missing.

Note: Incomplete sequence. No experimental confirmation available.Curated
Show »
Length:849
Mass (Da):92,707
Checksum:iBF045D3AE4254F02
GO
Isoform 4Curated (identifier: Q96QT6-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-414: Missing.

Note: No experimental confirmation available.Curated
Show »
Length:590
Mass (Da):62,943
Checksum:iA258D4B3544FC1F9
GO
Isoform 5 (identifier: Q96QT6-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     787-849: VQRKEVQARA...HACIFYDENT → GAHVHTCHHI...SRNKMATTAF
     850-1004: Missing.

Note: No experimental confirmation available.
Show »
Length:849
Mass (Da):92,924
Checksum:i9BAC91901BA5DB22
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti762F → Y in BAB14875 (PubMed:14702039).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0517671 – 414Missing in isoform 4. 1 PublicationAdd BLAST414
Alternative sequenceiVSP_05176880 – 107LQCCN…TVRRK → LVVYQDFVAPISLFHGTFHD GPTCSFAQ in isoform 3. 1 PublicationAdd BLAST28
Alternative sequenceiVSP_051769697 – 704DGKVSPGT → GECCSALG in isoform 2. 2 Publications8
Alternative sequenceiVSP_051770705 – 1004Missing in isoform 2. 2 PublicationsAdd BLAST300
Alternative sequenceiVSP_051771787 – 849VQRKE…YDENT → GAHVHTCHHIIRSPLYVCEW SPCLHGESELPVSQTSLCAF HGLNKAPWFFSEESRNKMAT TAF in isoform 3 and isoform 5. 2 PublicationsAdd BLAST63
Alternative sequenceiVSP_051772850 – 1004Missing in isoform 3 and isoform 5. 2 PublicationsAdd BLAST155

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY030283 mRNA. Translation: AAK38349.1.
AK024290 mRNA. Translation: BAB14875.1.
AK160370 mRNA. Translation: BAD18713.1.
AC024267 Genomic DNA. No translation available.
CH471159 Genomic DNA. Translation: EAW51166.1.
BC001657 mRNA. Translation: AAH01657.1. Sequence problems.
BC110882 mRNA. Translation: AAI10883.1.
BC121044 mRNA. Translation: AAI21045.1.
AB040956 mRNA. Translation: BAA96047.1.
CCDSiCCDS11247.1. [Q96QT6-2]
CCDS32598.1. [Q96QT6-1]
CCDS76981.1. [Q96QT6-5]
RefSeqiNP_001028733.1. NM_001033561.1. [Q96QT6-1]
NP_001277060.1. NM_001290131.1. [Q96QT6-5]
NP_065940.1. NM_020889.2. [Q96QT6-2]
UniGeneiHs.444173.

Genome annotation databases

EnsembliENST00000268756; ENSP00000268756; ENSG00000109118. [Q96QT6-2]
ENST00000332830; ENSP00000329933; ENSG00000109118. [Q96QT6-1]
ENST00000577226; ENSP00000465161; ENSG00000109118. [Q96QT6-5]
GeneIDi57649.
KEGGihsa:57649.
UCSCiuc002hdg.2. human. [Q96QT6-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY030283 mRNA. Translation: AAK38349.1.
AK024290 mRNA. Translation: BAB14875.1.
AK160370 mRNA. Translation: BAD18713.1.
AC024267 Genomic DNA. No translation available.
CH471159 Genomic DNA. Translation: EAW51166.1.
BC001657 mRNA. Translation: AAH01657.1. Sequence problems.
BC110882 mRNA. Translation: AAI10883.1.
BC121044 mRNA. Translation: AAI21045.1.
AB040956 mRNA. Translation: BAA96047.1.
CCDSiCCDS11247.1. [Q96QT6-2]
CCDS32598.1. [Q96QT6-1]
CCDS76981.1. [Q96QT6-5]
RefSeqiNP_001028733.1. NM_001033561.1. [Q96QT6-1]
NP_001277060.1. NM_001290131.1. [Q96QT6-5]
NP_065940.1. NM_020889.2. [Q96QT6-2]
UniGeneiHs.444173.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2L9SNMR-A200-241[»]
2LKMNMR-A200-241[»]
ProteinModelPortaliQ96QT6.
SMRiQ96QT6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121686. 16 interactors.
DIPiDIP-59632N.
IntActiQ96QT6. 13 interactors.
STRINGi9606.ENSP00000329933.

PTM databases

iPTMnetiQ96QT6.
PhosphoSitePlusiQ96QT6.

Polymorphism and mutation databases

BioMutaiPHF12.
DMDMi71153050.

Proteomic databases

EPDiQ96QT6.
MaxQBiQ96QT6.
PaxDbiQ96QT6.
PeptideAtlasiQ96QT6.
PRIDEiQ96QT6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000268756; ENSP00000268756; ENSG00000109118. [Q96QT6-2]
ENST00000332830; ENSP00000329933; ENSG00000109118. [Q96QT6-1]
ENST00000577226; ENSP00000465161; ENSG00000109118. [Q96QT6-5]
GeneIDi57649.
KEGGihsa:57649.
UCSCiuc002hdg.2. human. [Q96QT6-1]

Organism-specific databases

CTDi57649.
DisGeNETi57649.
GeneCardsiPHF12.
H-InvDBHIX0202392.
HGNCiHGNC:20816. PHF12.
HPAiHPA021410.
HPA021452.
neXtProtiNX_Q96QT6.
OpenTargetsiENSG00000109118.
PharmGKBiPA134954478.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4299. Eukaryota.
ENOG410XQQA. LUCA.
GeneTreeiENSGT00440000033777.
HOGENOMiHOG000220810.
HOVERGENiHBG057884.
InParanoidiQ96QT6.
OMAiRPCNCKA.
OrthoDBiEOG091G055U.
PhylomeDBiQ96QT6.
TreeFamiTF336193.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000109118-MONOMER.

Miscellaneous databases

ChiTaRSiPHF12. human.
EvolutionaryTraceiQ96QT6.
GeneWikiiPHF12.
GenomeRNAii57649.
PROiQ96QT6.

Gene expression databases

BgeeiENSG00000109118.
CleanExiHS_PHF12.
ExpressionAtlasiQ96QT6. baseline and differential.
GenevisibleiQ96QT6. HS.

Family and domain databases

Gene3Di2.60.200.20. 1 hit.
3.30.40.10. 2 hits.
InterProiIPR000253. FHA_dom.
IPR031966. PHF12_MRG-bd.
IPR008984. SMAD_FHA_domain.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF00628. PHD. 2 hits.
PF16737. PHF12_MRG_bd. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 2 hits.
[Graphical view]
SUPFAMiSSF49879. SSF49879. 1 hit.
SSF57903. SSF57903. 2 hits.
PROSITEiPS50006. FHA_DOMAIN. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPHF12_HUMAN
AccessioniPrimary (citable) accession number: Q96QT6
Secondary accession number(s): Q0VAI5
, Q2TAK2, Q6ZML2, Q9BV34, Q9H7U9, Q9P205
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: July 19, 2005
Last modified: November 2, 2016
This is version 137 of the entry and version 2 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 17
    Human chromosome 17: entries, gene names and cross-references to MIM
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.