Human Gene PHF12 (ENST00000332830.9_8) from GENCODE V47lift37
  Description: PHD finger protein 12, transcript variant 1 (from RefSeq NM_001033561.2)
Gencode Transcript: ENST00000332830.9_8
Gencode Gene: ENSG00000109118.14_14
Transcript (Including UTRs)
   Position: hg19 chr17:27,232,268-27,278,536 Size: 46,269 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr17:27,233,201-27,277,978 Size: 44,778 Coding Exon Count: 15 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:27,232,268-27,278,536)mRNA (may differ from genome)Protein (1004 aa)
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-  Comments and Description Text from UniProtKB
  ID: PHF12_HUMAN
DESCRIPTION: RecName: Full=PHD finger protein 12; AltName: Full=PHD factor 1; Short=Pf1;
FUNCTION: 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.
SUBUNIT: Isoform 2 interacts with SIN3A in a complex composed of HDAC1, SAP30 and SIN3A. Interacts with AES.
SUBCELLULAR LOCATION: Nucleus.
DOMAIN: The polybasic region (PBR) is responsive to the binding to phosphoinositides (PtdInsPs).
SIMILARITY: Contains 1 FHA domain.
SIMILARITY: Contains 2 PHD-type zinc fingers.

-  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: PHF12
Diseases sorted by gene-association score: spastic paraplegia 23 (4), chromosome 17q11.2 deletion syndrome, 1.4-mb (1)

-  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.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.16 RPKM in Whole Blood
Total median expression: 348.31 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -316.00558-0.566 Picture PostScript Text
3' UTR -191.20933-0.205 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
IPR000253 - FHA_dom
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

Pfam Domains:
PF00628 - PHD-finger
PF16737 - PHD finger protein 12 MRG binding domain

SCOP Domains:
49879 - SMAD/FHA domain
57889 - Cysteine-rich domain
57903 - FYVE/PHD zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2L9S - NMR MuPIT 2LKM - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q96QT6
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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 Details  
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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:0001106 RNA polymerase II transcription corepressor activity
GO:0001222 transcription corepressor binding
GO:0003682 chromatin binding
GO:0005515 protein binding
GO:0035091 phosphatidylinositol binding
GO:0042393 histone binding
GO:0046872 metal ion binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0045892 negative regulation of transcription, DNA-templated

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016580 Sin3 complex
GO:0017053 transcriptional repressor complex


-  Descriptions from all associated GenBank mRNAs
  AK294056 - Homo sapiens cDNA FLJ58454 complete cds, highly similar to PHD finger protein 12.
AK291420 - Homo sapiens cDNA FLJ78652 complete cds, highly similar to Homo sapiens PHD finger protein 12 (PHF12), transcript variant 1, mRNA.
BC110882 - Homo sapiens PHD finger protein 12, mRNA (cDNA clone MGC:131914 IMAGE:6157238), complete cds.
AK160370 - Homo sapiens mRNA for FLJ00295 protein.
AY030283 - Homo sapiens PHD zinc finger transcription factor mRNA, complete cds.
BC121043 - Homo sapiens PHD finger protein 12, mRNA (cDNA clone MGC:149738 IMAGE:40117907), complete cds.
BC121044 - Homo sapiens PHD finger protein 12, mRNA (cDNA clone MGC:149739 IMAGE:40117911), complete cds.
AL161953 - Homo sapiens mRNA; cDNA DKFZp434A1716 (from clone DKFZp434A1716).
LF209206 - JP 2014500723-A/16709: Polycomb-Associated Non-Coding RNAs.
AK091441 - Homo sapiens cDNA FLJ34122 fis, clone FCBBF3009949.
AX746984 - Sequence 509 from Patent EP1308459.
AK024290 - Homo sapiens cDNA FLJ14228 fis, clone NT2RP3004148.
AB040956 - Homo sapiens mRNA for KIAA1523 protein, partial cds.
JD121231 - Sequence 102255 from Patent EP1572962.
JD164742 - Sequence 145766 from Patent EP1572962.
JD368574 - Sequence 349598 from Patent EP1572962.
JD292971 - Sequence 273995 from Patent EP1572962.
LF326801 - JP 2014500723-A/134304: Polycomb-Associated Non-Coding RNAs.
JD112546 - Sequence 93570 from Patent EP1572962.
JD121962 - Sequence 102986 from Patent EP1572962.
JD398894 - Sequence 379918 from Patent EP1572962.
JD136007 - Sequence 117031 from Patent EP1572962.
JD239792 - Sequence 220816 from Patent EP1572962.
JD555982 - Sequence 537006 from Patent EP1572962.
JD193862 - Sequence 174886 from Patent EP1572962.
BC001657 - Homo sapiens PHD finger protein 12, mRNA (cDNA clone IMAGE:3356959), partial cds.
MA562378 - JP 2018138019-A/134304: Polycomb-Associated Non-Coding RNAs.
MA444783 - JP 2018138019-A/16709: Polycomb-Associated Non-Coding RNAs.
JD104660 - Sequence 85684 from Patent EP1572962.
JD320893 - Sequence 301917 from Patent EP1572962.
JD205467 - Sequence 186491 from Patent EP1572962.
JD216878 - Sequence 197902 from Patent EP1572962.
JD443913 - Sequence 424937 from Patent EP1572962.
JD215432 - Sequence 196456 from Patent EP1572962.
JD408165 - Sequence 389189 from Patent EP1572962.
JD395325 - Sequence 376349 from Patent EP1572962.
JD439610 - Sequence 420634 from Patent EP1572962.
JD461536 - Sequence 442560 from Patent EP1572962.
JD365925 - Sequence 346949 from Patent EP1572962.
JD124101 - Sequence 105125 from Patent EP1572962.
DL492604 - Novel nucleic acids.
JD406428 - Sequence 387452 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000332830.1, ENST00000332830.2, ENST00000332830.3, ENST00000332830.4, ENST00000332830.5, ENST00000332830.6, ENST00000332830.7, ENST00000332830.8, KIAA1523 , NM_001033561, PHF12 , PHF12_HUMAN, Q0VAI5, Q2TAK2, Q6ZML2, Q96QT6, Q9BV34, Q9H7U9, Q9P205, uc317tnk.1, uc317tnk.2
UCSC ID: ENST00000332830.9_8
RefSeq Accession: NM_001033561.2
Protein: Q96QT6 (aka PHF12_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.