Human Gene PARD3B (uc002vap.2)
  Description: Homo sapiens par-3 partitioning defective 3 homolog B (C. elegans) (PARD3B), transcript variant b, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr2:205,410,516-206,484,886 Size: 1,074,371 Total Exon Count: 22 Strand: +
Coding Region
   Position: hg19 chr2:205,410,723-206,480,537 Size: 1,069,815 Coding Exon Count: 22 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:205,410,516-206,484,886)mRNA (may differ from genome)Protein (1143 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMalacardsMGI
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  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): PARD3B
CDC HuGE Published Literature: PARD3B
Positive Disease Associations: Acquired Immunodeficiency Syndrome , Body Height , C-Reactive Protein , Cholesterol, HDL , E-Selectin , Knee osteoarthritis , Osteoarthritis, Knee , Platelet Count , Tuberculosis
Related Studies:
  1. Acquired Immunodeficiency Syndrome
    Jennifer L Troyer et al. The Journal of infectious diseases 2011, Genome-wide association study implicates PARD3B-based AIDS restriction., The Journal of infectious diseases. [PubMed 21502085]
    These observations suggest a potential unsuspected pathway of host genetic influence on the dynamics of AIDS progression.
  2. Body Height
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  3. C-Reactive Protein
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PARD3B
Diseases sorted by gene-association score: amyotrophic lateral sclerosis 2, juvenile (8)

-  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: 8.78 RPKM in Nerve - Tibial
Total median expression: 131.00 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 -124.50207-0.601 Picture PostScript Text
3' UTR -1269.224349-0.292 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
  Pfam Domains:
PF00595 - PDZ domain (Also known as DHR or GLGF)
PF12053 - N-terminal of Par3 and HAL proteins
PF13180 - PDZ domain

SCOP Domains:
50156 - PDZ domain-like

ModBase Predicted Comparative 3D Structure on Q8TEW8-2
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
  AB053321 - Homo sapiens ALS2CR19 mRNA, complete cds.
AX765741 - Sequence 57 from Patent WO02055706.
AX765687 - Sequence 3 from Patent WO02055706.
AK056157 - Homo sapiens cDNA FLJ31595 fis, clone NT2RI2002517, weakly similar to Homo sapiens PAR3 mRNA.
BC156252 - Synthetic construct Homo sapiens clone IMAGE:100061657, MGC:190065 par-3 partitioning defective 3 homolog B (C. elegans) (PARD3B) mRNA, encodes complete protein.
BC172499 - Synthetic construct Homo sapiens clone IMAGE:100069193, MGC:199204 par-3 partitioning defective 3 homolog B (C. elegans) (PARD3B) mRNA, encodes complete protein.
AB073472 - Homo sapiens mRNA for PAR3 beta, complete cds.
AB092439 - Homo sapiens mRNA for PAR3 beta alternatively spliced form, complete cds.
AF428250 - Homo sapiens partitioning-defective 3-like protein splice variant a (PAR3L) mRNA, complete cds; alternatively spliced.
AF428251 - Homo sapiens partitioning-defective 3-like protein splice variant b (PAR3L) mRNA, complete cds; alternatively spliced.
AF466152 - Homo sapiens partitioning-defective 3-like protein splice variant c (PAR3L) mRNA, complete cds; alternatively spliced.
AK057965 - Homo sapiens cDNA FLJ25236 fis, clone STM02096.
JD216992 - Sequence 198016 from Patent EP1572962.
JD474340 - Sequence 455364 from Patent EP1572962.
AX765692 - Sequence 8 from Patent WO02055706.
AX765688 - Sequence 4 from Patent WO02055706.
AX765742 - Sequence 58 from Patent WO02055706.
AL832951 - Homo sapiens mRNA; cDNA DKFZp666K2410 (from clone DKFZp666K2410).
AK312083 - Homo sapiens cDNA, FLJ92364.
BC012984 - Homo sapiens par-3 partitioning defective 3 homolog B (C. elegans), mRNA (cDNA clone IMAGE:3628944).
LF205218 - JP 2014500723-A/12721: Polycomb-Associated Non-Coding RNAs.
BC068029 - Homo sapiens cDNA clone IMAGE:30394954, partial cds.
JD104395 - Sequence 85419 from Patent EP1572962.
JD446577 - Sequence 427601 from Patent EP1572962.
LF317866 - JP 2014500723-A/125369: Polycomb-Associated Non-Coding RNAs.
LF317867 - JP 2014500723-A/125370: Polycomb-Associated Non-Coding RNAs.
JD376872 - Sequence 357896 from Patent EP1572962.
JD396367 - Sequence 377391 from Patent EP1572962.
JD207517 - Sequence 188541 from Patent EP1572962.
JD312952 - Sequence 293976 from Patent EP1572962.
JD424998 - Sequence 406022 from Patent EP1572962.
JD444976 - Sequence 426000 from Patent EP1572962.
JD561224 - Sequence 542248 from Patent EP1572962.
JD300363 - Sequence 281387 from Patent EP1572962.
JD555953 - Sequence 536977 from Patent EP1572962.
MA440795 - JP 2018138019-A/12721: Polycomb-Associated Non-Coding RNAs.
MA553443 - JP 2018138019-A/125369: Polycomb-Associated Non-Coding RNAs.
MA553444 - JP 2018138019-A/125370: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: ALS2CR19, NM_152526, NP_689739, PAR3B, PAR3L, Q8TEW8-2
UCSC ID: uc002vap.2
RefSeq Accession: NM_152526
Protein: Q8TEW8-2, splice isoform of Q8TEW8 CCDS: CCDS42806.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_152526.5
exon count: 22CDS single in 3' UTR: no RNA size: 7988
ORF size: 3432CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 7061.00frame 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: 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.