Human Gene PRRX1 (ENST00000239461.11_4) from GENCODE V47lift37
  Description: paired related homeobox 1, transcript variant pmx-1b (from RefSeq NM_022716.4)
Gencode Transcript: ENST00000239461.11_4
Gencode Gene: ENSG00000116132.12_8
Transcript (Including UTRs)
   Position: hg19 chr1:170,633,272-170,708,562 Size: 75,291 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr1:170,633,360-170,705,327 Size: 71,968 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:170,633,272-170,708,562)mRNA (may differ from genome)Protein (245 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PRRX1_HUMAN
DESCRIPTION: RecName: Full=Paired mesoderm homeobox protein 1; AltName: Full=Homeobox protein PHOX1; AltName: Full=Paired-related homeobox protein 1; Short=PRX-1;
FUNCTION: Acts as a transcriptional regulator of muscle creatine kinase (MCK) and so has a role in the establishment of diverse mesodermal muscle types. The protein binds to an A/T-rich element in the muscle creatine enhancer (By similarity).
SUBCELLULAR LOCATION: Nucleus.
DISEASE: Defects in PRRX1 are the cause of agnathia-otocephaly complex (AGOTC) [MIM:202650]. AGOTC is a rare condition characterized by mandibular hypoplasia or agnathia, ventromedial auricular malposition (melotia) and/or auricular fusion (synotia), and microstomia with oroglossal hypoplasia or aglossia. Holoprosencephaly is the most commonly identified association, but skeletal, genitourinary, and cardiovascular anomalies, and situs inversus have been reported. The disorder is almost always lethal.
SIMILARITY: Belongs to the paired homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding 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: PRRX1
Diseases sorted by gene-association score: agnathia-otocephaly complex* (1698), auriculo-condylar syndrome* (400), dysgnathia complex* (400), auriculocondylar syndrome 1* (283)
* = Manually curated disease association

-  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: 35.74 RPKM in Cervix - Endocervix
Total median expression: 434.68 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 -39.0088-0.443 Picture PostScript Text
3' UTR -768.503235-0.238 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
IPR017970 - Homeobox_CS
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like
IPR003654 - OAR_dom

Pfam Domains:
PF00046 - Homeodomain
PF03826 - OAR motif

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on P54821
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 DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001105 RNA polymerase II transcription coactivator activity
GO:0003677 DNA binding
GO:0003713 transcription coactivator activity
GO:0043565 sequence-specific DNA binding
GO:0071837 HMG box domain binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0002053 positive regulation of mesenchymal cell proliferation
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0030326 embryonic limb morphogenesis
GO:0042472 inner ear morphogenesis
GO:0042474 middle ear morphogenesis
GO:0045880 positive regulation of smoothened signaling pathway
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048664 neuron fate determination
GO:0048701 embryonic cranial skeleton morphogenesis
GO:0048704 embryonic skeletal system morphogenesis
GO:0048844 artery morphogenesis
GO:0051216 cartilage development
GO:0060021 palate development
GO:0070570 regulation of neuron projection regeneration
GO:0097150 neuronal stem cell population maintenance

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK225968 - Homo sapiens mRNA for paired mesoderm homeobox 1 isoform pmx-1b variant, clone: FCC113D08.
BC074993 - Homo sapiens paired related homeobox 1, mRNA (cDNA clone MGC:103918 IMAGE:30915308), complete cds.
EU446648 - Synthetic construct Homo sapiens clone IMAGE:100070209; IMAGE:100011857; FLH258737.01L paired related homeobox 1 (PRRX1) gene, encodes complete protein.
AB527492 - Synthetic construct DNA, clone: pF1KB7942, Homo sapiens PRRX1 gene for paired related homeobox 1, without stop codon, in Flexi system.
AB451463 - Homo sapiens PRRX1 mRNA for paired mesoderm homeobox 1 isoform pmx-1b, partial cds, clone: FLJ09016AAAF.
M95929 - Human homeobox protein (PHOX1) mRNA, 3' end.
JD485752 - Sequence 466776 from Patent EP1572962.
JD040548 - Sequence 21572 from Patent EP1572962.
JD041019 - Sequence 22043 from Patent EP1572962.
JD215060 - Sequence 196084 from Patent EP1572962.
JD470431 - Sequence 451455 from Patent EP1572962.
JD320403 - Sequence 301427 from Patent EP1572962.
JD503315 - Sequence 484339 from Patent EP1572962.
JD378480 - Sequence 359504 from Patent EP1572962.
JD489357 - Sequence 470381 from Patent EP1572962.
JD113730 - Sequence 94754 from Patent EP1572962.
JD562371 - Sequence 543395 from Patent EP1572962.
JD429609 - Sequence 410633 from Patent EP1572962.
JD153902 - Sequence 134926 from Patent EP1572962.
JD433947 - Sequence 414971 from Patent EP1572962.
JD040477 - Sequence 21501 from Patent EP1572962.
JD224057 - Sequence 205081 from Patent EP1572962.
JD512179 - Sequence 493203 from Patent EP1572962.
JD038194 - Sequence 19218 from Patent EP1572962.
JD266279 - Sequence 247303 from Patent EP1572962.
JD038442 - Sequence 19466 from Patent EP1572962.
JD168822 - Sequence 149846 from Patent EP1572962.
JD509055 - Sequence 490079 from Patent EP1572962.
JD042428 - Sequence 23452 from Patent EP1572962.
JD563958 - Sequence 544982 from Patent EP1572962.
JD239310 - Sequence 220334 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B5BUM7, ENST00000239461.1, ENST00000239461.10, ENST00000239461.2, ENST00000239461.3, ENST00000239461.4, ENST00000239461.5, ENST00000239461.6, ENST00000239461.7, ENST00000239461.8, ENST00000239461.9, NM_022716, O60807, P54821, PMX1, PRRX1_HUMAN, uc317efu.1, uc317efu.2
UCSC ID: ENST00000239461.11_4
RefSeq Accession: NM_022716.4
Protein: P54821 (aka PRRX1_HUMAN)

-  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.