Human Gene PCDH9 (ENST00000377865.7_9) from GENCODE V47lift37
  Description: protocadherin 9, transcript variant 1 (from RefSeq NM_203487.3)
Gencode Transcript: ENST00000377865.7_9
Gencode Gene: ENSG00000184226.15_18
Transcript (Including UTRs)
   Position: hg19 chr13:66,876,966-67,804,468 Size: 927,503 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr13:66,878,787-67,802,572 Size: 923,786 Coding Exon Count: 4 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:66,876,966-67,804,468)mRNA (may differ from genome)Protein (1237 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
BioGrid 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


-  MalaCards Disease Associations
  MalaCards Gene Search: PCDH9
Diseases sorted by gene-association score: auditory neuropathy, autosomal dominant, 1 (3), trichorhinophalangeal syndrome, type i (2)

-  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: 14.05 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 147.23 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 -185.70692-0.268 Picture PostScript Text
3' UTR -396.401821-0.218 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.

-  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    
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-  Descriptions from all associated GenBank mRNAs
  AL834258 - Homo sapiens mRNA; cDNA DKFZp761B047 (from clone DKFZp761B047).
AF169692 - Homo sapiens protocadherin-9 (PCDH9) mRNA, complete cds.
BX537422 - Homo sapiens mRNA; cDNA DKFZp686L0546 (from clone DKFZp686L0546); complete cds.
BC136626 - Homo sapiens protocadherin 9, mRNA (cDNA clone MGC:168239 IMAGE:9020616), complete cds.
BC136627 - Homo sapiens protocadherin 9, mRNA (cDNA clone MGC:168240 IMAGE:9020617), complete cds.
BC144321 - Homo sapiens protocadherin 9, mRNA (cDNA clone MGC:177858 IMAGE:9052841), complete cds.
AB384392 - Synthetic construct DNA, clone: pF1KSDB0234, Homo sapiens PCDH9 gene for protocadherin-9 precursor, complete cds, without stop codon, in Flexi system.
KJ897299 - Synthetic construct Homo sapiens clone ccsbBroadEn_06693 PCDH9 gene, encodes complete protein.
KJ534915 - Homo sapiens clone PCDH9_iso-A_fetal-F16 protocadherin 9 isoform A (PCDH9) mRNA, partial cds, alternatively spliced.
AB114416 - Homo sapiens mRNA, HTLV-1-PCDH9 fusion transcripts, isolate: OMT1.
JD432737 - Sequence 413761 from Patent EP1572962.
JD184971 - Sequence 165995 from Patent EP1572962.
JD550768 - Sequence 531792 from Patent EP1572962.
JD112568 - Sequence 93592 from Patent EP1572962.
JD233835 - Sequence 214859 from Patent EP1572962.
JD493097 - Sequence 474121 from Patent EP1572962.
JD312858 - Sequence 293882 from Patent EP1572962.
JD539065 - Sequence 520089 from Patent EP1572962.
JD363518 - Sequence 344542 from Patent EP1572962.
JD146624 - Sequence 127648 from Patent EP1572962.
JD066465 - Sequence 47489 from Patent EP1572962.
BC150296 - Homo sapiens protocadherin 9, mRNA (cDNA clone MGC:167030 IMAGE:8860363), complete cds.
JD191991 - Sequence 173015 from Patent EP1572962.
AK057768 - Homo sapiens cDNA FLJ25039 fis, clone CBL03094, highly similar to Homo sapiens protocadherin-9 (PCDH9) mRNA.
AK054661 - Homo sapiens cDNA FLJ30099 fis, clone BNGH41000098, highly similar to Homo sapiens cadherin superfamily protein VR4-11 mRNA.
JD531214 - Sequence 512238 from Patent EP1572962.
JD035190 - Sequence 16214 from Patent EP1572962.
JD025506 - Sequence 6530 from Patent EP1572962.
JD446081 - Sequence 427105 from Patent EP1572962.
JD122843 - Sequence 103867 from Patent EP1572962.
JD397500 - Sequence 378524 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000377865.1, ENST00000377865.2, ENST00000377865.3, ENST00000377865.4, ENST00000377865.5, ENST00000377865.6, NM_203487, PCDH9 , uc318nxf.1, uc318nxf.2, X5D7N0, X5D7N0_HUMAN
UCSC ID: ENST00000377865.7_9
RefSeq Accession: NM_203487.3

-  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.