Human Gene THAP4 (uc002wbt.3) Description and Page Index
  Description: Homo sapiens THAP domain containing 4 (THAP4), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr2:242,523,820-242,576,725 Size: 52,906 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr2:242,524,021-242,576,432 Size: 52,412 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:242,523,820-242,576,725)mRNA (may differ from genome)Protein (577 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: THAP4_HUMAN
DESCRIPTION: RecName: Full=THAP domain-containing protein 4;
SUBUNIT: Homodimer (Probable).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Contains 1 THAP-type zinc finger.
SEQUENCE CAUTION: Sequence=AAH00247.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAH09439.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAA91560.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): THAP4
CDC HuGE Published Literature: THAP4
Positive Disease Associations: Brain structure
Related Studies:
  1. Brain structure
    Stein ,et al. Neuroimage 2010, Voxelwise Genome-Wide Association Study , NeuroImage 2010 . [PubMed 20171287]

-  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: 28.21 RPKM in Kidney - Cortex
Total median expression: 920.80 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -202.60293-0.691 Picture PostScript Text
3' UTR -61.30201-0.305 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
IPR011038 - Calycin-like
IPR014878 - DUF1794
IPR006612 - Znf_C2CH

Pfam Domains:
PF05485 - THAP domain
PF08768 - Domain of unknown function (DUF1794)

Protein Data Bank (PDB) 3-D Structure
MuPIT help

3IA8
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q8WY91
FrontTopSide
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 orthologGenome BrowserGenome BrowserNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGDEnsembl WormBase 
 Protein SequenceProtein Sequence Protein Sequence 
 AlignmentAlignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0020037 heme binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding

Biological Process:
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0008150 biological_process

Cellular Component:
GO:0005575 cellular_component


-  Descriptions from all associated GenBank mRNAs
  AK225608 - Homo sapiens mRNA for THAP domain containing 4 variant, clone: REC02241.
LF383626 - JP 2014500723-A/191129: Polycomb-Associated Non-Coding RNAs.
BC071896 - Homo sapiens THAP domain containing 4, mRNA (cDNA clone IMAGE:6088454), partial cds.
BC094822 - Homo sapiens THAP domain containing 4, mRNA (cDNA clone IMAGE:6214144), partial cds.
AF258556 - Homo sapiens PP238 mRNA, complete cds.
BC069235 - Homo sapiens THAP domain containing 4, mRNA (cDNA clone MGC:78456 IMAGE:6645198), complete cds.
AK001216 - Homo sapiens cDNA FLJ10354 fis, clone NT2RM2001194.
AF132970 - Homo sapiens CGI-36 protein mRNA, complete cds.
BC000767 - Homo sapiens THAP domain containing 4, mRNA (cDNA clone IMAGE:2961488), complete cds.
BC001842 - Homo sapiens THAP domain containing 4, mRNA (cDNA clone IMAGE:2961488), complete cds.
BC000247 - Homo sapiens THAP domain containing 4, mRNA (cDNA clone IMAGE:3356125), complete cds.
BC009439 - Homo sapiens THAP domain containing 4, mRNA (cDNA clone IMAGE:3508461), complete cds.
GQ901007 - Homo sapiens clone HEL-T-119 epididymis secretory sperm binding protein mRNA, complete cds.
JD224753 - Sequence 205777 from Patent EP1572962.
JD246396 - Sequence 227420 from Patent EP1572962.
KJ902548 - Synthetic construct Homo sapiens clone ccsbBroadEn_11942 THAP4 gene, encodes complete protein.
KJ902549 - Synthetic construct Homo sapiens clone ccsbBroadEn_11943 THAP4 gene, encodes complete protein.
LF319115 - JP 2014500723-A/126618: Polycomb-Associated Non-Coding RNAs.
LF319116 - JP 2014500723-A/126619: Polycomb-Associated Non-Coding RNAs.
JD382496 - Sequence 363520 from Patent EP1572962.
JD310857 - Sequence 291881 from Patent EP1572962.
JD040724 - Sequence 21748 from Patent EP1572962.
LF319117 - JP 2014500723-A/126620: Polycomb-Associated Non-Coding RNAs.
JD044878 - Sequence 25902 from Patent EP1572962.
JD315490 - Sequence 296514 from Patent EP1572962.
JD404565 - Sequence 385589 from Patent EP1572962.
JD492686 - Sequence 473710 from Patent EP1572962.
JD128615 - Sequence 109639 from Patent EP1572962.
LF319118 - JP 2014500723-A/126621: Polycomb-Associated Non-Coding RNAs.
JD404803 - Sequence 385827 from Patent EP1572962.
JD302135 - Sequence 283159 from Patent EP1572962.
JD454726 - Sequence 435750 from Patent EP1572962.
MA619203 - JP 2018138019-A/191129: Polycomb-Associated Non-Coding RNAs.
MA554692 - JP 2018138019-A/126618: Polycomb-Associated Non-Coding RNAs.
MA554693 - JP 2018138019-A/126619: Polycomb-Associated Non-Coding RNAs.
MA554694 - JP 2018138019-A/126620: Polycomb-Associated Non-Coding RNAs.
MA554695 - JP 2018138019-A/126621: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: CGI-36, NM_015963, NP_057047, PP238, Q53NU7, Q6GRN0, Q6IPJ3, Q8WY91, Q9NW26, Q9Y325, THAP4_HUMAN
UCSC ID: uc002wbt.3
RefSeq Accession: NM_015963
Protein: Q8WY91 (aka THAP4_HUMAN or THA4_HUMAN)
CCDS: CCDS2551.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015963.5
exon count: 6CDS single in 3' UTR: no RNA size: 2245
ORF size: 1734CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3263.00frame shift in genome: no % Coverage: 99.24
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.