Human Gene PAX7 (ENST00000420770.7) from GENCODE V43
  Description: Homo sapiens paired box 7 (PAX7), transcript variant 3, mRNA. (from RefSeq NM_001135254)
RefSeq Summary (NM_001135254): 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. The specific function of the paired box 7 gene is unknown but speculated to involve tumor suppression since fusion of this gene with a forkhead domain family member has been associated with alveolar rhabdomyosarcoma. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008].
Gencode Transcript: ENST00000420770.7
Gencode Gene: ENSG00000009709.12
Transcript (Including UTRs)
   Position: hg38 chr1:18,630,846-18,748,866 Size: 118,021 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg38 chr1:18,631,604-18,744,929 Size: 113,326 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-02-17 22:02:02

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:18,630,846-18,748,866)mRNA (may differ from genome)Protein (505 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGencode

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Paired box protein Pax-7; AltName: Full=HuP1;
FUNCTION: Probable transcription factor. May have a role in myogenesis.
SUBUNIT: Can bind to DNA as a heterodimer with PAX3. Interacts with DAXX.
DISEASE: Defects in PAX7 are a cause of rhabdomyosarcoma type 2 (RMS2) [MIM:268220]. It is a form of rhabdomyosarcoma, a highly malignant tumor of striated muscle derived from primitive mesenchimal cells and exhibiting differentiation along rhabdomyoblastic lines. Rhabdomyosarcoma is one of the most frequently occurring soft tissue sarcomas and the most common in children. It occurs in four forms: alveolar, pleomorphic, embryonal and botryoidal rhabdomyosarcomas. Note=A chromosomal aberration involving PAX7 is found in rhabdomyosarcoma. Translocation t(1;13)(p36;q14) with FOXO1. The resulting protein is a transcriptional activator.
SIMILARITY: Belongs to the paired homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
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: PAX7
Diseases sorted by gene-association score: rhabdomyosarcoma 2, alveolar* (622), embryonal rhabdomyosarcoma (25), rhabdomyosarcoma (23), pleomorphic rhabdomyosarcoma (11), conventional leiomyosarcoma (9), muscle cancer (8), central nervous system mesenchymal non-meningothelial tumor (8), inflammatory leiomyosarcoma (8), skeletal muscle cancer (7), scapuloperoneal myopathy (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.90 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 3.81 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 -343.20758-0.453 Picture PostScript Text
3' UTR -1408.903937-0.358 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
IPR001523 - Paired_dom
IPR022106 - Pax7
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00046 - Homeobox domain
PF00292 - 'Paired box' domain
PF12360 - Paired box protein 7

ModBase Predicted Comparative 3D Structure on P23759
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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0000983 transcription factor activity, RNA polymerase II core promoter sequence-specific
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0007517 muscle organ development
GO:0007519 skeletal muscle tissue development
GO:0009653 anatomical structure morphogenesis
GO:0010453 regulation of cell fate commitment
GO:0010468 regulation of gene expression
GO:0014813 skeletal muscle satellite cell commitment
GO:0021527 spinal cord association neuron differentiation
GO:0021904 dorsal/ventral neural tube patterning
GO:0031062 positive regulation of histone methylation
GO:0043066 negative regulation of apoptotic process
GO:0043393 regulation of protein binding
GO:0043403 skeletal muscle tissue regeneration
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048663 neuron fate commitment
GO:0048706 embryonic skeletal system development
GO:0051216 cartilage development
GO:0060415 muscle tissue morphogenesis
GO:2000288 positive regulation of myoblast proliferation

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  DQ322591 - Homo sapiens PAX7 transcriptional factor isoform B (PAX7B) mRNA, complete cds, alternatively spliced.
X96743 - H.sapiens mRNA for paired box containing transcription factor, PAX7.
JD233150 - Sequence 214174 from Patent EP1572962.
JD328381 - Sequence 309405 from Patent EP1572962.
JD042755 - Sequence 23779 from Patent EP1572962.
JD170415 - Sequence 151439 from Patent EP1572962.
JD341416 - Sequence 322440 from Patent EP1572962.
JD196514 - Sequence 177538 from Patent EP1572962.
JD496572 - Sequence 477596 from Patent EP1572962.
JD204475 - Sequence 185499 from Patent EP1572962.
JD445230 - Sequence 426254 from Patent EP1572962.
JD484826 - Sequence 465850 from Patent EP1572962.
JD142027 - Sequence 123051 from Patent EP1572962.
JD164954 - Sequence 145978 from Patent EP1572962.
JD347635 - Sequence 328659 from Patent EP1572962.
Z35141 - H.sapiens Pax-7 gene for transcription factor.
JD202820 - Sequence 183844 from Patent EP1572962.
BC121165 - Homo sapiens paired box 7, mRNA (cDNA clone MGC:150507 IMAGE:40121582), complete cds.
BC121166 - Homo sapiens paired box 7, mRNA (cDNA clone MGC:150508 IMAGE:40121584), complete cds.
KJ897296 - Synthetic construct Homo sapiens clone ccsbBroadEn_06690 PAX7 gene, encodes complete protein.
JD110775 - Sequence 91799 from Patent EP1572962.
AK094779 - Homo sapiens cDNA FLJ37460 fis, clone BRAWH2011286.
JD280170 - Sequence 261194 from Patent EP1572962.
JD124166 - Sequence 105190 from Patent EP1572962.
JD489406 - Sequence 470430 from Patent EP1572962.
JD533185 - Sequence 514209 from Patent EP1572962.
JD154508 - Sequence 135532 from Patent EP1572962.
JD346136 - Sequence 327160 from Patent EP1572962.
JD422269 - Sequence 403293 from Patent EP1572962.
JD308449 - Sequence 289473 from Patent EP1572962.
JD557807 - Sequence 538831 from Patent EP1572962.
JD530953 - Sequence 511977 from Patent EP1572962.
JD153436 - Sequence 134460 from Patent EP1572962.
JD527838 - Sequence 508862 from Patent EP1572962.
JD385946 - Sequence 366970 from Patent EP1572962.
JD377187 - Sequence 358211 from Patent EP1572962.
JD244357 - Sequence 225381 from Patent EP1572962.
JD218186 - Sequence 199210 from Patent EP1572962.
JD135617 - Sequence 116641 from Patent EP1572962.
JD294943 - Sequence 275967 from Patent EP1572962.
JD559815 - Sequence 540839 from Patent EP1572962.
JD549281 - Sequence 530305 from Patent EP1572962.
JD307800 - Sequence 288824 from Patent EP1572962.
JD206538 - Sequence 187562 from Patent EP1572962.
JD043526 - Sequence 24550 from Patent EP1572962.
JD309819 - Sequence 290843 from Patent EP1572962.
JD036567 - Sequence 17591 from Patent EP1572962.
JD036568 - Sequence 17592 from Patent EP1572962.
JD147638 - Sequence 128662 from Patent EP1572962.
JD253783 - Sequence 234807 from Patent EP1572962.
JD078847 - Sequence 59871 from Patent EP1572962.
JD150377 - Sequence 131401 from Patent EP1572962.
JD245287 - Sequence 226311 from Patent EP1572962.
JD163908 - Sequence 144932 from Patent EP1572962.
JD345054 - Sequence 326078 from Patent EP1572962.
AY578141 - Homo sapiens PAX7 isoform B (PAX7) mRNA, 3' UTR.
JD426914 - Sequence 407938 from Patent EP1572962.
JD164059 - Sequence 145083 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000420770.1, ENST00000420770.2, ENST00000420770.3, ENST00000420770.4, ENST00000420770.5, ENST00000420770.6, HUP1, NM_001135254, P23759, PAX7_HUMAN, Q0VA99, uc010oct.1, uc010oct.2, uc010oct.3, uc010oct.4
UCSC ID: ENST00000420770.7
RefSeq Accession: NM_001135254
Protein: P23759 (aka PAX7_HUMAN)
CCDS: CCDS44074.1

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