Human Gene PAX1 (ENST00000613128.5) from GENCODE V43
  Description: Homo sapiens paired box 1 (PAX1), transcript variant 2, mRNA. (from RefSeq NM_001257096)
RefSeq Summary (NM_001257096): This gene is a member of the paired box (PAX) family of transcription factors. Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. These genes play critical roles during fetal development. This gene plays a role in pattern formation during embryogenesis and may be essential for development of the vertebral column. This gene is silenced by methylation in ovarian and cervical cancers and may be a tumor suppressor gene. Mutations in this gene are also associated with vertebral malformations. [provided by RefSeq, Mar 2012].
Gencode Transcript: ENST00000613128.5
Gencode Gene: ENSG00000125813.15
Transcript (Including UTRs)
   Position: hg38 chr20:21,705,664-21,718,481 Size: 12,818 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg38 chr20:21,705,713-21,714,562 Size: 8,850 Coding Exon Count: 5 

Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-02-17 22:02:02

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr20:21,705,664-21,718,481)mRNA (may differ from genome)Protein (457 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  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: PAX1
Diseases sorted by gene-association score: otofaciocervical syndrome 2* (1279), otofaciocervical syndrome* (274), spondylocostal dysostosis 1, autosomal recessive (14), klippel-feil syndrome (13), diaphanospondylodysostosis (9), scheuermann disease (8), neural tube defects (3)
* = 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: 0.37 RPKM in Thyroid
Total median expression: 1.18 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 -5.6049-0.114 Picture PostScript Text
3' UTR -1235.303919-0.315 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
Genome BrowserNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGI Ensembl   
Protein Sequence Protein Sequence   
Alignment Alignment   

-  Descriptions from all associated GenBank mRNAs
  BC143791 - Homo sapiens cDNA clone IMAGE:9052305.
BC143793 - Homo sapiens cDNA clone IMAGE:9052307.
AK303335 - Homo sapiens cDNA FLJ60204 complete cds, highly similar to Paired box protein Pax-1.
BC069134 - Homo sapiens paired box 1, mRNA (cDNA clone MGC:95415 IMAGE:7216990), complete cds.

-  Other Names for This Gene
  Alternate Gene Symbols: A0A087WXV5, ENST00000613128.1, ENST00000613128.2, ENST00000613128.3, ENST00000613128.4, NM_001257096, uc010zsl.1, uc010zsl.2, uc010zsl.3, uc010zsl.4
UCSC ID: ENST00000613128.5
RefSeq Accession: NM_001257096

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