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A chicken embryo gene expression database

	Anatomical Location
	Stage
	Gene Name
	GEISHA ID
	Multiple Parameters

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PAX9
paired box 9

The human orthologue of this gene is associated
with the following human disease:

Tooth agenesis, selective, 3

Gene

Official Symbol	PAX9
Official Full Name	paired box 9
CGNC ID	49451
also known as	ChPax9, PAX-9, paired box protein Pax-9\|paired box gene 9, Paired box protein Pax-9
gene type	protein-coding

Genomic Map

	Ensembl
	NCBI
	UCSC
	Gallus-Browse

Sequence Information

Genomic
RNA	NM_204912
Polypeptide	NP_990243

Gene Expression

In Situ Hybridization

GEISHA

Orthology

	Entrez Gene	Ensembl Gene	Genetic Phenotypes	MOD
Fruit Fly
Human	5083	ENSG00000198807	MIM:106600	MIM:167416
Mouse	18511	ENSMUSG00000001497	All phenotypic alleles (7):Targeted, knock-out(2) Targeted, other(5)	MGI:97493
Xenopus	100485934, 378646, 100270674, 398655			482237, 5934626
Zebrafish	30558	ENSDARG00000053829	ZDB-GENE-980526-399	ZFIN:ZDB-GENE-980526-399

Gene Ontology

Molecular Function	DNA binding
Biological Process	multicellular organismal development, regulation of transcription, DNA-templated, more...transcription, DNA-templated
Cellular Component	nucleus

Links to other databases

Entrez Gene	395740
Ensembl Gene	ENSGALG00000010114
KEGG	gga:395740

Entry 1

GEISHA Id	PAX9.UApcr	Data Source	GEISHA ISH Analysis
Forward cDNA Template Primer	5’-AACCACATCTACTCCTACCC-3’
Reverse cDNA Template Primer	5’-AATTAACCCTCACTAAAGGACGTGATCTCAATAGCAGTG-3’	cDNA Template Length	1000
Complete cDNA Template Probe	show AACCACATCTACTCCTACCCCAGCCCCATCGCTGCCGCGGGAGCCAAGGTGCCCACGCCTCCGGGAGTGCCTGCCATCC CTGGTACCATGGCCATGCCTCGCACCTGGCCTTCGTCCCACTCGGTGACGGACATCCTGGGCATCCGCTCCATCACGGA CCAAGTGAGCGACACCTCGTCGTACCCCAGCCCCAAGGTGGAGGAGTGGAGCAGCCTGGGCCGGAGCAGCTTCCCCGCT GCAGCCCAGCATGCCGTGAACGGGCTGGAGAAGAGCTCCCTGGAACAGGAGGCCAAGTACAGCCAGGCACACAATGGCC TCCCAGCAGTTGGAAGCTTTGTATCAGCACCAGCCATGTCTCCCTACGCCACGTCGGCTCAGGTGTCACCCTACATGCC ATACAGCGCAGCTCCCTCCAGCTACATGGCAGGCCATGGTTGGCAGCATACTGCAGGCACGCCTCTCTCCCCTCATGGC TGTGACCTCCCTGCCTCGCTGGCCTTCAAGGGCGTGCAGACAGCCAGGGAAGGCAGCCACTCAGTCACGGCCTCCGCTC TCTGATGCAGGAGTTGCTCCAGGCCAAGCGTCCCCAGCACCGGGCTCACAGACTGCTCTCCTCATGCTGGTGGAACTGG GTCTTTCCCCTCCTGACTTGTCTCCTGCAGGACTTTTCGGGACTGAAAGAGCTGAAGGCAGCATCAGAAGCAGAGGGGA GCGTGCTGATGCCCTTGCACTCTCTAAGATCTTGTGTCCCTCAAAGGGCCCGTGGAAACTTGTATAACACTCCTCTGGT CAAACCACACATATTTATTCTTAATCACCACAGAGTTGTTAAATGTGCAATTGTTGTTAAGATTTGTGTAGAAATCAAT AAAGAAAACTAATCACAGGAAATTCTGCCACGCCTCAAATCAGCAAAGGTGGTTAAATTAAAGGTATTTGCCAATGACC TGTCTCTAGAGCACAAATAAGGTTATGCGATCCACTGCTATTGAGATCACGT

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

7-12

stage 9

stage 10

Head Mesenchyme
Pharynx
Unlabeled

13-18

stage 13

stage 18

Head Mesenchyme
Pharyngeal Arches and Clefts
Pharynx
Sclerotome

19-24

stage 20

stage 23

stage 24

Head Mesenchyme
Leg Mesenchyme
Lung
Nasal Placode/Nerve
Pharyngeal Arches and Clefts
Pharynx
Sclerotome

25-26

stage 26

Head Mesenchyme
Leg Mesenchyme
Pharyngeal Arches and Clefts
Sclerotome
Wing Mesenchyme

Entry 2

GEISHA Id	PAX1.Christ.2007	Data Source	Publication
Complete cDNA Template Probe	show `CGTCCGCTGCCCAACGCCATCCGCCTGCGGATCGTGGAGCTGGCCCAGCTCGGCATTCGACCGTGCGACATCAGCCGCC AGCTGCGGGTCTCGCACGGCTGCGTCAGCAAGATCCTGGCCCGCTACAACGAGACCGGCTCCATCCTGCCCGGAGCCAT CGGAGGCAGCAAGCCGCGGGTCACCACCCCCAACGTGGTCAAGCACATCCGCGACTACAAGCAGGGAGACCCCGGCATC TTCGCCTGGGAGATCCGCGACCGGCTGCTGGCCGACGGCGTC`
Citation	Christ B, Huang R, Scaal M. Amniote somite derivatives. Dev Dyn. 2007 Sep;236(9):2382-96.
Copyright	Copyright © 2007 Wiley-Liss, Inc.
Comments	Insufficient information provided in publication to verify exact sequence used to synthesize probe. The sequence below was obtained from NCBI (acc #X82442).

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

13-18

stage 18

Sclerotome
Somites

Entry 3

GEISHA Id	PAX1.Wang.2005	Data Source	Publication
Complete cDNA Template Probe	show `CGTCCGCTGCCCAACGCCATCCGCCTGCGGATCGTGGAGCTGGCCCAGCTCGGCATTCGACCGTGCGACATCAGCCGCC AGCTGCGGGTCTCGCACGGCTGCGTCAGCAAGATCCTGGCCCGCTACAACGAGACCGGCTCCATCCTGCCCGGAGCCAT CGGAGGCAGCAAGCCGCGGGTCACCACCCCCAACGTGGTCAAGCACATCCGCGACTACAAGCAGGGAGACCCCGGCATC TTCGCCTGGGAGATCCGCGACCGGCTGCTGGCCGACGGCGTC`
Citation	Wang B, He L, Ehehalt F, Geetha-Loganathan P, Nimmagadda S, Christ B, Scaal M, Huang R. (2005) The formation of the avian scapula blade takes place in the hypaxial domain of the somites and requires somatopleure-derived BMP signals. Dev Biol. 2005 Nov 1;287(1):11-8. Epub 2005 Oct 3.
Copyright	Copyright © 2005 Elsevier Inc. All rights reserved.
Comments	Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (X82442).

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

25-28

stage 27

stage 28

Somites
Wing

Scapula

Entry 4

GEISHA Id	Pax‐9.LeClair.1999	Data Source	Publication
Complete cDNA Template Probe	show `CCCGTGGAAACTTGTATAACACTCCTCTGGTCAAACCACACATATTTATTCTTAATCACCACAGAGTTGTTAAATGTGC AATTGTTGTTAAGATTTGTGTAGAAATCAATAAAGAAAACTAATCACAGGAAATTCTGCCACGCCTCAAATCAGCAAAG GTGGTTAAATTAAAGGTATTTGCCAATGACCTGTCTCTAGAGCACAAATAAGGTTATGCGATCCACTGCTATTGA`
Citation	LeClair EE, Bonfiglio L, Tuan RS. Expression of the paired-box genes Pax-1 and Pax-9 in limb skeleton development. Dev Dyn. 1999 Feb;214(2):101-15.
Copyright	Copyright © 1999 Wiley‐Liss, Inc.
Comments	The complete cDNA template sequence was obtained from the information from the publication as described in LeClair et al. 1999.