Pax9 paired box 9 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pax9provided by RGD
Official Full Name: paired box 9provided by RGD
Primary source: RGD:1560838
See related: EnsemblRapid:ENSRNOG00000065348 AllianceGenome:RGD:1560838
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of DNA-templated transcription and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including face morphogenesis; positive regulation of transcription by RNA polymerase II; and regulation of odontogenesis. Predicted to be located in nucleolus and nucleoplasm. Human ortholog(s) of this gene implicated in tooth agenesis. Orthologous to human PAX9 (paired box 9). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 35.1), Adrenal (RPKM 13.6) and 5 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 6q23

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (79917466..79938551)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (74186749..74203508)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (77607705..77624453)

Chromosome 6 - NC_086024.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

calcitonin gene expression could be directly activated by Nkx2.1, whereas Pax9 is not involved in transcription from the 2kbp calcitonin promoter
Title: Functional analysis of Nkx2.1 and Pax9 for calcitonin gene transcription.

Submit: New GeneRIF Correction

General gene information

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Markers

BM390839 (e-PCR)
- UniSTS:260902

RH141318 (e-PCR)
- UniSTS:223314

D10Bir5 (e-PCR), detects polymorphism
- UniSTS:141485

PMC317134P1 (e-PCR)
- UniSTS:273075

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
involved_in cellular response to growth factor stimulus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to growth factor stimulus	ISO Inferred from Sequence Orthology more info
involved_in endoderm development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within endoderm development	ISO Inferred from Sequence Orthology more info
involved_in face morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within face morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in odontogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within odontogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of odontogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of odontogenesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: paired box protein Pax-9

Names: paired box gene 9

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.