Human Gene PAX9 (ENST00000361487.7) from GENCODE V44
  Description: Homo sapiens paired box 9 (PAX9), transcript variant 1, mRNA. (from RefSeq NM_001372076)
RefSeq Summary (NM_001372076): This gene is a member of the paired box (PAX) family of transcription factors. Members of this gene family typically contain a paired box domain, an octapeptide, and a paired-type homeodomain. These genes play critical roles during fetal development and cancer growth. Mice lacking this gene exhibit impaired development of organs, musculature and the skeleton, including absent and abnormally developed teeth, and neonatal lethality. Mutations in the human gene are associated with selective tooth agenesis-3. [provided by RefSeq, Sep 2015]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.
Gencode Transcript: ENST00000361487.7
Gencode Gene: ENSG00000198807.13
Transcript (Including UTRs)
   Position: hg38 chr14:36,661,860-36,679,362 Size: 17,503 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg38 chr14:36,662,090-36,676,452 Size: 14,363 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 09:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr14:36,661,860-36,679,362)mRNA (may differ from genome)Protein (341 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGencode

-  Comments and Description Text from UniProtKB
DESCRIPTION: SubName: Full=Paired box gene 9; SubName: Full=Paired box protein 9;
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Contains 1 paired 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

-  MalaCards Disease Associations
  MalaCards Gene Search: PAX9
Diseases sorted by gene-association score: tooth agenesis, selective, 3* (1329), tooth agenesis* (307), anodontia (25), chromosome 14q11-q22 deletion syndrome (8), holoprosencephaly 8 (6), ectodermal dysplasia 10b, hypohidrotic/hair/tooth type, autosomal recessive (5), cleft lip (5), mouth disease (4), cleft palate, isolated (2)
* = Manually curated disease association

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.46 RPKM in Esophagus - Mucosa
Total median expression: 29.78 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 -85.20230-0.370 Picture PostScript Text
3' UTR -620.002910-0.213 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
IPR009057 - Homeodomain-like
IPR001523 - Paired_dom
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00292 - 'Paired box' domain

ModBase Predicted Comparative 3D Structure on Q2L4T1
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
Genome BrowserGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007492 endoderm development
GO:0009887 animal organ morphogenesis
GO:0042476 odontogenesis
GO:0042481 regulation of odontogenesis
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0060325 face morphogenesis
GO:0071363 cellular response to growth factor stimulus

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  LF213290 - JP 2014500723-A/20793: Polycomb-Associated Non-Coding RNAs.
MA448867 - JP 2018138019-A/20793: Polycomb-Associated Non-Coding RNAs.
JD271475 - Sequence 252499 from Patent EP1572962.
BC001159 - Homo sapiens paired box 9, mRNA (cDNA clone MGC:1535 IMAGE:3534582), complete cds.
JD351928 - Sequence 332952 from Patent EP1572962.
AK313627 - Homo sapiens cDNA, FLJ94197, highly similar to Homo sapiens paired box gene 9 (PAX9), mRNA.
AB248958 - Homo sapiens Pax9 mRNA for paired box protein 9, complete cds.
JD565076 - Sequence 546100 from Patent EP1572962.
JD182082 - Sequence 163106 from Patent EP1572962.
AB463995 - Synthetic construct DNA, clone: pF1KB7675, Homo sapiens PAX9 gene for paired box 9, without stop codon, in Flexi system.
EU176374 - Synthetic construct Homo sapiens clone IMAGE:100006595; FLH263926.01X; RZPDo839E12246D paired box 9 (PAX9) gene, encodes complete protein.
EU176711 - Synthetic construct Homo sapiens clone IMAGE:100011621; FLH263909.01L; RZPDo839E04246D paired box 9 (PAX9) gene, encodes complete protein.
X92850 - H.sapiens mRNA for Pax9 protein.
U59628 - Human PAX-9 mRNA, partial cds.
AK310339 - Homo sapiens cDNA, FLJ17381.
JD287336 - Sequence 268360 from Patent EP1572962.
JD398432 - Sequence 379456 from Patent EP1572962.
JD150365 - Sequence 131389 from Patent EP1572962.
JD524412 - Sequence 505436 from Patent EP1572962.
JD432875 - Sequence 413899 from Patent EP1572962.
JD455837 - Sequence 436861 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000361487.1, ENST00000361487.2, ENST00000361487.3, ENST00000361487.4, ENST00000361487.5, ENST00000361487.6, hCG_20991, NM_001372076, Q2L4T1, Q2L4T1_HUMAN, uc059axm.1, uc059axm.2
UCSC ID: ENST00000361487.7
RefSeq Accession: NM_001372076
Protein: Q2L4T1 CCDS: CCDS9662.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.