Human Gene PRDM5 (uc010inf.3)
  Description: Homo sapiens PR domain containing 5 (PRDM5), mRNA.
RefSeq Summary (NM_018699): The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorigenesis. [provided by RefSeq, Jul 2008]. Sequence Note:.
Transcript (Including UTRs)
   Position: hg19 chr4:121,737,218-121,844,013 Size: 106,796 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr4:121,737,453-121,843,763 Size: 106,311 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:121,737,218-121,844,013)mRNA (may differ from genome)Protein (308 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMalacardsMGIOMIM
PubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: Q0VAI9_HUMAN
DESCRIPTION: SubName: Full=PR domain zinc finger protein 5; SubName: Full=PRDM5 protein;
SIMILARITY: Contains 1 SET domain.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PRDM5
CDC HuGE Published Literature: PRDM5
Positive Disease Associations: Blood Glucose , fasting plasma glucose , Hippocampus , Neuroblastoma
Related Studies:
  1. Blood Glucose
    James B Meigs et al. BMC medical genetics 2007, Genome-wide association with diabetes-related traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903298]
    Framingham 100K SNP data is a resource for association tests of known and novel genes with diabetes and related traits posted at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite. Framingham 100K data replicate the TCF7L2 association with diabetes.
  2. fasting plasma glucose
    Meigs ,et al. 2007, Genome-wide association with diabetes-related traits in the Framingham Heart Study, BMC medical genetics 2007 8 Suppl 1 : S16. [PubMed 17903298]
  3. fasting plasma glucose
    Meigs ,et al. 2007, Genome-wide association with diabetes-related traits in the Framingham Heart Study, BMC medical genetics 2007 8 Suppl 1 : S16. [PubMed 17903298]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PRDM5
Diseases sorted by gene-association score: brittle cornea syndrome 2* (1688), axenfeld-rieger syndrome (10), irregular astigmatism (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 4.20 RPKM in Ovary
Total median expression: 61.21 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 -129.20250-0.517 Picture PostScript Text
3' UTR -42.50235-0.181 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
IPR001214 - SET_dom
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd
IPR022755 - Znf_C2H2_jaz
IPR017125 - Znf_PRDM5

Pfam Domains:
PF00096 - Zinc finger, C2H2 type
PF13894 - C2H2-type zinc finger
PF13912 - C2H2-type zinc finger

SCOP Domains:
82199 - SET domain
57667 - C2H2 and C2HC zinc fingers

ModBase Predicted Comparative 3D Structure on Q0VAI9
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  LF207168 - JP 2014500723-A/14671: Polycomb-Associated Non-Coding RNAs.
AF272897 - Homo sapiens PR-domain zinc finger protein 5 (PRDM5) mRNA, complete cds.
BC121037 - Homo sapiens PR domain containing 5, mRNA (cDNA clone MGC:149729 IMAGE:40117856), complete cds.
BC121038 - Homo sapiens PR domain containing 5, mRNA (cDNA clone MGC:149730 IMAGE:40117857), complete cds.
AK314293 - Homo sapiens cDNA, FLJ95050.
KJ902203 - Synthetic construct Homo sapiens clone ccsbBroadEn_11597 PRDM5 gene, encodes complete protein.
AB464059 - Synthetic construct DNA, clone: pF1KB7860, Homo sapiens PRDM5 gene for PR domain containing 5, without stop codon, in Flexi system.
MA442745 - JP 2018138019-A/14671: Polycomb-Associated Non-Coding RNAs.
AK310958 - Homo sapiens cDNA, FLJ18000.
AK056352 - Homo sapiens cDNA FLJ31790 fis, clone NT2RI2008714, highly similar to PR domain zinc finger protein 5.
BC066942 - Homo sapiens PR domain containing 5, mRNA (cDNA clone IMAGE:4375822), complete cds.
KJ902202 - Synthetic construct Homo sapiens clone ccsbBroadEn_11596 PRDM5 gene, encodes complete protein.
LF362652 - JP 2014500723-A/170155: Polycomb-Associated Non-Coding RNAs.
LF362651 - JP 2014500723-A/170154: Polycomb-Associated Non-Coding RNAs.
MA598229 - JP 2018138019-A/170155: Polycomb-Associated Non-Coding RNAs.
MA598228 - JP 2018138019-A/170154: Polycomb-Associated Non-Coding RNAs.
LF362643 - JP 2014500723-A/170146: Polycomb-Associated Non-Coding RNAs.
LF362642 - JP 2014500723-A/170145: Polycomb-Associated Non-Coding RNAs.
MA598220 - JP 2018138019-A/170146: Polycomb-Associated Non-Coding RNAs.
MA598219 - JP 2018138019-A/170145: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: AK310958, NM_018699, NP_061169, Q0VAI9, Q0VAI9_HUMAN
UCSC ID: uc010inf.3
RefSeq Accession: NM_018699
Protein: Q0VAI9

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK310958.1
exon count: 6CDS single in 3' UTR: no RNA size: 1249
ORF size: 927CDS single in intron: no Alignment % ID: 99.92
txCdsPredict score: 1716.00frame shift in genome: no % Coverage: 100.00
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: 390# 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.