Human Gene PCDH11X (uc004efh.2)
  Description: Homo sapiens protocadherin 11 X-linked (PCDH11X), transcript variant b, mRNA.
Transcript (Including UTRs)
   Position: hg19 chrX:91,034,260-91,139,006 Size: 104,747 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chrX:91,090,504-91,137,950 Size: 47,447 Coding Exon Count: 3 

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 (chrX:91,034,260-91,139,006)mRNA (may differ from genome)Protein (1025 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMalacardsMGIPubMed
TreefamUniProtKBWikipedia

-  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): PCDH11X
CDC HuGE Published Literature: PCDH11X
Positive Disease Associations: Alzheimer's disease
Related Studies:
  1. Alzheimer's disease
    Minerva M Carrasquillo , et al. Nature genetics 2009 41(2):192-8, Genetic variation in PCDH11X is associated with susceptibility to late-onset Alzheimer's disease., Nature genetics 2009 41(2):192-8. [PubMed 19136949]
  2. Alzheimer's disease
    Carrasquillo ,et al. 2009, Genetic variation in PCDH11X is associated with susceptibility to late-onset Alzheimer's disease, Nature genetics 2009 41- 2 : 192-8. [PubMed 19136949]

-  MalaCards Disease Associations
  MalaCards Gene Search: PCDH11X
Diseases sorted by gene-association score: dyslexia (14), schizoaffective disorder (8), spherocytosis, type 5 (5), usher syndrome, type 1b (1)

-  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: 1.80 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 8.76 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 -243.53633-0.385 Picture PostScript Text
3' UTR -320.211056-0.303 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:
PF00028 - Cadherin domain
PF08266 - Cadherin-like
PF08374 - Protocadherin

SCOP Domains:
49313 - Cadherin-like

ModBase Predicted Comparative 3D Structure on Q9BZA7-2
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
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  LP896569 - Sequence 1433 from Patent EP3253886.
AF332218 - Homo sapiens chromosome X protocadherin 11 (PCDH11) mRNA, complete cds, alternatively spliced.
AF332219 - Homo sapiens chromosome X protocadherin 11 (PCDH11) mRNA, complete cds, alternatively spliced.
BC167817 - Synthetic construct Homo sapiens clone IMAGE:100068207, MGC:195824 protocadherin 11 X-linked (PCDH11X) mRNA, encodes complete protein.
AF206516 - Homo sapiens protocadherin-S mRNA, complete cds.
AF217288 - Homo sapiens protocadherin-S mRNA, complete cds, alternatively spliced.
AY861432 - Homo sapiens protocadherin 11X isoform 8 (PCDH11X) mRNA, complete cds, alternatively spliced.
AY861433 - Homo sapiens protocadherin 11X isoform 7 (PCDH11X) mRNA, complete cds, alternatively spliced.
AY861434 - Homo sapiens protocadherin 11X isoform 6 (PCDH11X) mRNA, complete cds, alternatively spliced.
AY861435 - Homo sapiens protocadherin 11X isoform 5 (PCDH11X) mRNA, partial cds, alternatively spliced.
AB037747 - Homo sapiens mRNA for KIAA1326 protein, partial cds.
AJ276804 - Homo sapiens mRNA for protocadherin (PCDHX gene).
AK299813 - Homo sapiens cDNA FLJ56943 partial cds, highly similar to Protocadherin-11 X-linked precursor.
AK316263 - Homo sapiens cDNA, FLJ79162 partial cds, highly similar to Protocadherin-11 X-linked precursor.
AK299638 - Homo sapiens cDNA FLJ61367 complete cds, highly similar to Protocadherin-11 X-linked precursor.
AB026187 - Homo sapiens PCDH-X mRNA for protocadherin-Xa, complete cds.
JD391464 - Sequence 372488 from Patent EP1572962.
AJ564847 - Homo sapiens 5'UTR for PCDHX gene, exon 1.
JD245626 - Sequence 226650 from Patent EP1572962.
JD453783 - Sequence 434807 from Patent EP1572962.
JD369948 - Sequence 350972 from Patent EP1572962.
JD306766 - Sequence 287790 from Patent EP1572962.
JD479931 - Sequence 460955 from Patent EP1572962.
AJ564855 - Homo sapiens 5'UTR for PCDHX gene, exon 2.
JD056317 - Sequence 37341 from Patent EP1572962.
JD479589 - Sequence 460613 from Patent EP1572962.
AJ564856 - Homo sapiens 5'UTR for PCDHX gene, exon 3.
AJ564932 - Homo sapiens mRNA for protocadherin (PCDHX gene), exon 4.1.
AJ564931 - Homo sapiens mRNA for protocadherin (PCDHX gene), exon 4.
AJ564935 - Homo sapiens mRNA for protocadherin (PCDHX gene), exon 5.2.
AJ564936 - Homo sapiens mRNA for protocadherin (PCDHX gene), exon 5.3.
AJ564933 - Homo sapiens mRNA for protocadherin (PCDHX gene), exon 5.
AJ564934 - Homo sapiens mRNA for protocadherin (PCDHX gene), exon 5.1.
U79247 - Human clone 23599 mRNA sequence.
AB026188 - Homo sapiens PCDH-X mRNA for protocadherin-Xb, partial cds.
AJ564937 - Homo sapiens mRNA for protocadherin (PCDHX gene), exon 6.
JD146027 - Sequence 127051 from Patent EP1572962.
JD088788 - Sequence 69812 from Patent EP1572962.
JD148401 - Sequence 129425 from Patent EP1572962.
JD153732 - Sequence 134756 from Patent EP1572962.
JD498965 - Sequence 479989 from Patent EP1572962.
JD357242 - Sequence 338266 from Patent EP1572962.
JD551287 - Sequence 532311 from Patent EP1572962.
JD240955 - Sequence 221979 from Patent EP1572962.
JD257009 - Sequence 238033 from Patent EP1572962.
JD421450 - Sequence 402474 from Patent EP1572962.
JD179068 - Sequence 160092 from Patent EP1572962.
JD440718 - Sequence 421742 from Patent EP1572962.
JD063001 - Sequence 44025 from Patent EP1572962.
JD444809 - Sequence 425833 from Patent EP1572962.
JD073076 - Sequence 54100 from Patent EP1572962.
JD073075 - Sequence 54099 from Patent EP1572962.
JD344711 - Sequence 325735 from Patent EP1572962.
JD443412 - Sequence 424436 from Patent EP1572962.
JD138361 - Sequence 119385 from Patent EP1572962.
JD138362 - Sequence 119386 from Patent EP1572962.
JD176190 - Sequence 157214 from Patent EP1572962.
JD176191 - Sequence 157215 from Patent EP1572962.
JD531720 - Sequence 512744 from Patent EP1572962.
JD176192 - Sequence 157216 from Patent EP1572962.
JD499575 - Sequence 480599 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA1326, NM_032967, NP_116749, PCDH11, PCDHX, Q9BZA7-2
UCSC ID: uc004efh.2
RefSeq Accession: NM_032967
Protein: Q9BZA7-2, splice isoform of Q9BZA7

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_032967.2
exon count: 6CDS single in 3' UTR: no RNA size: 4767
ORF size: 3078CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6530.00frame 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.