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A chicken embryo gene expression database

	Anatomical Location
	Stage
	Gene Name
	GEISHA ID
	Multiple Parameters

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IRX1
iroquois homeobox 1

Gene

Official Symbol	IRX1
Official Full Name	iroquois homeobox 1
CGNC ID	9961
also known as	iroquois-class homeodomain protein IRX-1\|iroquois homeobox protein 1\|iroquois homologue-1
gene type	protein-coding

Genomic Map

	Ensembl ID not known
	NCBI
	UCSC
	Gallus-Browse

Sequence Information

Genomic
RNA	NM_001030338
Polypeptide	NP_001025509
Sequence Clusters/ESTs	Unigene

Gene Expression

In Situ Hybridization	GEISHA
EST Profile	Gga.2699

Orthology

	Entrez Gene	Ensembl Gene	Genetic Phenotypes	MOD
Fruit Fly
Human	79192	ENSG00000170549		MIM:606197
Mouse	16371	ENSMUSG00000060969	All phenotypic alleles (1):Targeted, knock-out(1)	MGI:1197515
Xenopus	100038208, 397976, 735237			486816
Zebrafish	403019, 114430	ENSDARG00000009510, ENSDARG00000056594	ZDB-GENE-040707-1, ZDB-GENE-010716-1	ZFIN:ZDB-GENE-040707-1, ZFIN:ZDB-GENE-010716-1

Gene Ontology

Molecular Function
Biological Process
Cellular Component

Links to other databases

Entrez Gene	374185
Ensembl Gene
KEGG	gga:374185

Entry 1

GEISHA Id	IRX1.UApcr	Data Source	GEISHA ISH Analysis
Forward cDNA Template Primer	AACACCGCAAGAACCCCTACCC
Reverse cDNA Template Primer	AATTAACCCTCACTAAAGGAAGCCCCATTTGTCCAGTTGTG	cDNA Template Length	675
Forward cDNA Template Probe	show NTTATCCATGCGTTGGACTGCCATCGGACGTGTGAGTCCATGGCTGGGGAGAAAGGCGGGATGCTGGATCTGTGAAGAA GTGTGGGTGACCTGGGCAGGGGGAGGTGGTGGGGGGGAGGATTTCAGGGCACCATCAGGGCTGGTCGCAGTCTCTGCCA AAGACCAGATCTTGGGTTTGCTGTGAGATGGCATCTGTAAATTGCTCTGTCCCCCGGGGCTAATGATTCGCGTGCTGTT GTCAGAGGCCTCCTTCACCATGGCCAGAGCATCTTTGGGTTTCAGCCCTTCAGATCCTGACAGTGACAATTCCTTGTCT TTTTCCAAGCGCTCCTCTTCACTGCTTTGTCTCAGGAGCTCAGGCTTCTCCTCCTCTTCCTCATTGCTCTGTTCCCCAT CGTTTTCATCAATTTTATCTATGTCTATGCTCTCCAGGTCGATCTCCTCATCGTCTTCGGTCTTCTCAGGGTCCCCCTC GTTATCGCTGCCAAAAAGGTTAGCATCTTCTTGGTCCTTACTCCTGGAGCCCCAGGTCACCTTGTTCTCCTTCTTGAGG CGGCGGCGGGCGTTGGCGAACCAGGTGGAGACCTGGGTGAGGGTCATCTTGGTGATGATGGCCAGCATGATCTTCTCGC CCTTGGTAGGGTAGGGGTTCTTGCAGTATTAAACN

Stage

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Location (click to highlight)

Comments (click to highlight)

1-3

stage 3

Area Pellucida

Low level expression. Will redo to confirm.

4-6

stage 4

stage 6

Area Pellucida
Ectoderm
Lateral Plate Mesoderm
Neural Plate/Tube
Primitive Streak

Low level expression. Will redo to confirm.

7-12

stage 7

stage 8

stage 9

stage 10

stage 11

Ectoderm
Hindbrain
Lateral Plate Mesoderm
Midbrain
Neural Plate/Tube

Dorsal view.
Ventral view.

13-18

stage 16

stage 18

Ear/Otic Placode
Eye
Gut
Heart
Hindbrain
Midbrain
Pharyngeal Arches and Clefts
Spinal Cord

19-24

stage 21

stage 22

Ear/Otic Placode
Endocardium
Eye
Forebrain
Gut
Hindbrain
Leg Mesenchyme
Lung
Midbrain
Spinal Cord
Spinal Ganglia and Nerves
Wing Mesenchyme

25-26

stage 25

stage 26

Ear/Otic Placode
Eye
Forebrain
Gut
Heart
Hindbrain
Leg Mesenchyme
Lung
Midbrain
Nephric Ducts
Spinal Cord
Spinal Ganglia and Nerves
Wing Mesenchyme

Entry 2

GEISHA Id	IRX1.Khudyakov.2009	Data Source	Publication
Complete cDNA Template Probe	show GCGGCTCGAGGGGGAACAGAGCAATGAGGAAGAGGAGGAGAAGCCTGAGCTCCTGAGACAAAGCAGTGAAGAGGAGCGC TTGGAAAAAGACAAGGAATTGTCACTGTCAGGATCTGAAGGGCTGAAACCCAAAGATGCTCTGGCCATGGTGAAGGAGG CCTCTGACAACAGCACGCGAATCATTAGCCCCGGGGGACAGAGCAATTTACAGATGCCATCTCACAGCAAACCCAAGAT CTGGTCTTTGGCAGAGACTGCGACCAGCCCTGATGGTGCCCTGAAATCCTCCCCCCCACCACCTCCCCCTGCCCAGGTC ACCCACACTTCGCCACAGATCCAGCATCCCGCCTTTCTCCCCAGCCATGGACTCTACACGTGCCAGATTGGCAAGTTTC ACAACTGGACAAATGGGGCTTTTCTCACGCAGAGTTCCCTGCTAAACGTGAGGTCGTTTTTGGGAGTAAATCACCACCA TGCCACTCACCACAAACACCAACTCCAGGCCCAGCAGCAGCCTTCTGTTTTAACAGCCACCCTGGGAGCCCTAAGCAGT GAAAAGCCTTCAGAGAGGACCAGTCCCAAACACATAGAAAATGTCCCAAGAACCGATTCCCCACCTCAGCCACTCAAAT CGCCCTTCCAGCCTGTCCGTGACAACTCTTTGCCTCAGCAAGAGGGAACACCGAGAATTTTAACAGCTCTCCCTTCGGC TTGATTAAATGGTTTGCTGAAAAACCACAATATTACAGAGACTTGGTCTTTAAGGACAGAAAACCAAAACACAACGACA CAC
Citation	Khudyakov J, Bronner-Fraser M. Comprehensive spatiotemporal analysis of early chick neural crest network genes. Dev Dyn. 2009 Mar;238(3):716-23.
Copyright	Published Online: 22 Feb 2009 Copyright © 2009 Wiley-Liss, Inc.
Comments	The sequence below was obtained from NCBI (BU365297) using the information provided in the publication.

Stage

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stage 4

Placcode

preplacodal region

Entry 3

GEISHA Id	IRX1.Abello.2010	Data Source	Publication
Complete cDNA Template Probe	show ATGTCCTTCCCCCAGCTGGGCTACCCGCAGTACCTCAGCGCCAGCCAGGCGGTGTACGGCAGCGAGCGGCCCGGGGTGC TGGCCGCCGCCGCCGCAGCCGCCGCAGCCGCCGCCGCCGCCTCGGGCCGGCCCGCGGGCGCCGAACTGGGCAGCGGCTC GGCCGCTGTCACCTCGGTGCTGGGCATGTACGCGGGGCCCTACAGCGCCCCCAACTACAGCGCCTTCCTGCCCTACACC GCCGACCTCGGCCTCTTCTCGCAGATGGGCTCCCAGTACGAGCTGAAAGATAATCCGGGTGTCCATCCTGCTACCTTCG CAGCCCACACCGCCCCCGGCTATTATCCCTACGGACAGTTCCAGTATGGGGACCCGGGGCGACCCAAAAATGCCACCCG GGAGAGTACCAGCACCCTCAAGGCCTGGCTCAATGAACACCGCAAGAACCCCTACCCTACCAAGGGCGAGAAGATCATG CTGGCCATCATCACCAAGATGACCCTCACCCAGGTCTCCACCTGGTTCGCCAACGCCCGCCGCCGCCTCAAGAAGGAGA ACAAGGTGACCTGGGGCTCCAGGAGTAAGGACCAAGAAGATGCTAACCTTTTTGGCAGCGATAACGAGGGGGACCCTGA GAAGACCGAAGACGATGAGGAGATCGACCTGGAGAGCATAGACATAGATAAAATTGATGAAAACGATGGGGAACAGAGC AATGAGGAAGAGGAGGAGAAGCCTGAGCTCCTGAGACAAAGCAGTGAAGAGGAGCGCTTGGAAAAAGACAAGGAATTGT CACTGTCAGGATCTGAAGGGCTGAAACCCAAAGATGCTCTGGCCATGGTGAAGGAGGCCTCTGACAACAGCACGCGAAT CATTAGCCCCGGGGGACAGAGCAATTTACAGATGCCATCTCACAGCAAACCCAAGATCTGGTCTTTGGCAGAGACTGCG ACCAGCCCTGATGGTGCCCTGAAATCCTCCCCCCCACCACCTCCCCCTGCCCAGGTCACCCACACTTTGCCACAGATCC AGCATCCCGCCTTTCTCCCCAGCCATGGACTCTACACGTGCCAGATTGGCAAGTTTCACAACTGGACAAATGGGGCTTT TCTCACGCAGAGTTCCCTGCTAAACGTGAGGTCGTTTTTGGGAGTAAATCACCACCATGCCACTCACCACAACCACCAC CTCCAGGCCCAGCAGCAGCCTTCTGTTTTAACAGCCACCCTGGGAGCCCTAAGCAGTGAAAAGCCTTCAGAGAGGACCA GTCCCAAACACATAGAAAATGTCCCAAGAACCGATTCCCCACCTCAGCCACTCAAATCGCCCTTCCAGCCTGTCCGCGA CAACTCTTTGCCTCAGCAAGAGGGAACTCCGAGAATTTTAACAGCTCTCCCTTCGGCTTGA
Citation	Abelló G, Khatri S, Radosevic M, Scotting PJ, Giráldez F, Alsina B., Independent regulation of Sox3 and Lmx1b by FGF and BMP signaling influences the neurogenic and non-neurogenic domains in the chick otic placode. Dev Biol. 2010 Mar 1;339(1):166-78. Epub 2010 Jan 4.
Copyright	Copyright © 2009 Elsevier Inc. All rights reserved.
Comments	As insufficient information is provided in publication to verify exact sequence used to synthesize probe, the sequence below was obtained from NCBI (acc #NM_001030338.1).

Stage

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Location (click to highlight)

Comments (click to highlight)

stage 1

Ear/Otic Placode

Entry 4

GEISHA Id	IRX3.GarciaCampmany.2007	Data Source	Publication
Complete cDNA Template Probe	show `GCCGCCTTCCCGCACCACCACCCCGCTTTCTACCCCTACGGGCAGTACCAGTTCGGGGACCCGTCGCGGCCCAAGAACG CCACCCGCGAGAGCACCAGCACGCTCAAGGCCTGGCTCAACGAGCACCGCAAGAACCCGTACCCCACCAAGGGTGAGAA GATCATGCTGGCCATCATCACCAAGATGACCCTCACCCAGGTCTCCACCTGGTTCGCCAACGCTCGGCGGCGGCTCAAG AAGGAGAACAAGATGACCTGGGCCCCCCGCAGCAGGACGGACGAGGAGGGCAACTCCTACGGC`
Citation	García-Campmany L, Martí E. The TGFbeta intracellular effector Smad3 regulates neuronal differentiation and cell fate specification in the developing spinal cord. Development. 2007 Jan;134(1):65-75. Epub 2006 Nov 30.
Copyright	Copyright by the authors. Published by the Company of Biologists Ltd.
Comments	As insufficient information is provided in publication to verify exact sequence used to synthesize probe, the sequence below was obtained from NCBI NM_001030338

Stage

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Location (click to highlight)

Comments (click to highlight)

13-18

stage 18

Spinal Cord

Entry 5

GEISHA Id	IRX1.Anderson.2021	Data Source	Direct Submission
Complete cDNA Template Probe	show ATATTTCTGCCGCTCCTGCCGCCGACGCCAGTGCTGCCAGTGCCGCCGCCCCGGAGATGTCCTTCCCCCAGCTGGGCTA CCCGCAGTACCTCAGCGCCAGCCAGGCGGTGTACGGCAGCGAGCGGCCCGGGGTGCTGGCCGCCGCCGCCGCAGCCGCC GCAGCCGCCGCCGCCGCCTCGGGCCGGCCCGCGGGCGCCGAACTGGGCAGCGGCTCGGCCGCTGTCACCTCGGTGCTGG GCATGTACGCGGGGCCCTACAGCGCCCCCAACTACAGCGCCTTCCTGCCCTACACCGCCGACCTCGGCCTCTTCTCGCA GATGGGCTCCCAGTACGAGCTGAAAGATAATCCGGGTGTCCATCCTGCTACCTTCGCAGCCCACACCGCCCCCGGCTAT TATCCCTACGGACAGTTCCAGTACGGGGACCCGGGGCGACCCAAAAATGCCACCCGGGAGAGTACCAGCACCCTCAAGG CCTGGCTCAATGAACACCGCAAGAACCCCTACCCTACCAAGGGCGAGAAGATCATGCTGGCCATCATCACCAAGATGAC CCTCACCCAGGTCTCCACCTGGTTCGCCAACGCCCGCCGCCGCCTCAAGAAGGAGAACAAGGTGACCTGGGGCTCCAGG AGTAAGGACCAAGAAGATGCTAACCTTTTTGGCAGCGATAACGAGGGGGACCCTGAGAAGACCGAAGACGATGAGGAGA TCGACCTGGAGAGCATAGACATAGATAAAATTGATGAAAACGATGGGGAACAGAGCAATGAGGAAGAGGAGGAGAAGCC TGAGCTCCTGAGACAAAGCAGTGAAGAGGAGCGCTTGGAAAAAGACAAGGAATTGTCACTGTCAGGATCTGAAGGGCTG AAACCCAAAGATGCTCTGGCCATGGTGAAGGAGGCCTCTGACAACAGCACGCGAATCATTAGCCCCGGGGGACAGAGCA ATTTACAGATGCCATCTCACAGCAAACCCAAGATCTGGTCTTTGGCAGAGACTGCGACCAGCCCTGATGGTGCCCTGAA ATCCTCCCCCCCACCACCTCCCCCTGCCCAGGTCACCCACACTTCGCCACAGATCCAGCATCCCGCCTTTCTCCCCAGC CATGGACTCTACACGTGCCAGATTGGCAAGTTTCACAACTGGACAAATGGGGCTTTTCTCACGCAGAGTTCCCTGCTAA ACGTGAGGTCGTTTTTGGGAGTAAATCACCACCATGCCACTCACCACAACCACCACCTCCAGGCCCAGCAGCAGCCTTC TGTTTTAACAGCCACCCTGGGAGCCCTAAGCAGTGAAAAGCCTTCAGAGAGGACCAGTCCCAAACACATAGAAAATGTC CCAAGAACCGATTCCCCACCTCAGCCACTCAAATCGCCCTTCCAGCCTGTCCGTGACAACTCTTTGCCTCAGCAAGAGG GAACACCGAGAATTTTAACAGCTCTCCCTTCGGCTTGATTAAATGGTTTGCTGAAAAACAAAATATTACAGAGACTGGT CTTAAGGACAGAAAAACAAAACAAAAAGAAAAAAAAAAAAAAGGAAACTGTATAAACGACTCTCATCCATCTCTTTTTT GCAATAAGGTGGTGCAAATCCATTAAGGCGATTAAACAATTCTGTAGATGGATCCCCTCCTTCATTGTACCATTTCAGA TCGTGTTATTCTAACCATTCTTGGATTATTTGTTTGGTAAATGTTTCCCATGTGTTTGTGTTTTTTCTGTATATAGAGT GATTTCAGATTGTAAATAGCGCGTCAGCAAAACTTGTCTAAATCATATATTTTTGTCTAATAAACTAAATGAAATTA
Comments	Images provided by Claire Anderson. As insufficient information was provided to verify sequence used to synthesize probe, the sequence above was obtained from NCBI (accession number NM_001030338.2). Related paper: Anderson C, Hill B, Lu HC, Moverley A, Yang Y, Oliveira NMM, Baldock RA, Stern CD. A 3D molecular atlas of the chick embryonic heart. Dev Biol. 2019 Dec 1;456(1):40-46. doi: 10.1016/j.ydbio.2019.07.003. Epub 2019 Jul 5.

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

7-12

stage 12

Ear/Otic Placode
Ectoderm
Forebrain
Hindbrain
Lateral Plate Mesoderm
Mesencephalon
Midbrain
Neural Plate/Tube
Pharynx
Splanchnic Mesoderm

dorsal mesocardium

Entry 6

GEISHA Id	IRX1.Anderson.2019	Data Source	Publication
Complete cDNA Template Probe	show ATATTTCTGCCGCTCCTGCCGCCGACGCCAGTGCTGCCAGTGCCGCCGCCCCGGAGATGTCCTTCCCCCAGCTGGGCTA CCCGCAGTACCTCAGCGCCAGCCAGGCGGTGTACGGCAGCGAGCGGCCCGGGGTGCTGGCCGCCGCCGCCGCAGCCGCC GCAGCCGCCGCCGCCGCCTCGGGCCGGCCCGCGGGCGCCGAACTGGGCAGCGGCTCGGCCGCTGTCACCTCGGTGCTGG GCATGTACGCGGGGCCCTACAGCGCCCCCAACTACAGCGCCTTCCTGCCCTACACCGCCGACCTCGGCCTCTTCTCGCA GATGGGCTCCCAGTACGAGCTGAAAGATAATCCGGGTGTCCATCCTGCTACCTTCGCAGCCCACACCGCCCCCGGCTAT TATCCCTACGGACAGTTCCAGTACGGGGACCCGGGGCGACCCAAAAATGCCACCCGGGAGAGTACCAGCACCCTCAAGG CCTGGCTCAATGAACACCGCAAGAACCCCTACCCTACCAAGGGCGAGAAGATCATGCTGGCCATCATCACCAAGATGAC CCTCACCCAGGTCTCCACCTGGTTCGCCAACGCCCGCCGCCGCCTCAAGAAGGAGAACAAGGTGACCTGGGGCTCCAGG AGTAAGGACCAAGAAGATGCTAACCTTTTTGGCAGCGATAACGAGGGGGACCCTGAGAAGACCGAAGACGATGAGGAGA TCGACCTGGAGAGCATAGACATAGATAAAATTGATGAAAACGATGGGGAACAGAGCAATGAGGAAGAGGAGGAGAAGCC TGAGCTCCTGAGACAAAGCAGTGAAGAGGAGCGCTTGGAAAAAGACAAGGAATTGTCACTGTCAGGATCTGAAGGGCTG AAACCCAAAGATGCTCTGGCCATGGTGAAGGAGGCCTCTGACAACAGCACGCGAATCATTAGCCCCGGGGGACAGAGCA ATTTACAGATGCCATCTCACAGCAAACCCAAGATCTGGTCTTTGGCAGAGACTGCGACCAGCCCTGATGGTGCCCTGAA ATCCTCCCCCCCACCACCTCCCCCTGCCCAGGTCACCCACACTTCGCCACAGATCCAGCATCCCGCCTTTCTCCCCAGC CATGGACTCTACACGTGCCAGATTGGCAAGTTTCACAACTGGACAAATGGGGCTTTTCTCACGCAGAGTTCCCTGCTAA ACGTGAGGTCGTTTTTGGGAGTAAATCACCACCATGCCACTCACCACAACCACCACCTCCAGGCCCAGCAGCAGCCTTC TGTTTTAACAGCCACCCTGGGAGCCCTAAGCAGTGAAAAGCCTTCAGAGAGGACCAGTCCCAAACACATAGAAAATGTC CCAAGAACCGATTCCCCACCTCAGCCACTCAAATCGCCCTTCCAGCCTGTCCGTGACAACTCTTTGCCTCAGCAAGAGG GAACACCGAGAATTTTAACAGCTCTCCCTTCGGCTTGATTAAATGGTTTGCTGAAAAACAAAATATTACAGAGACTGGT CTTAAGGACAGAAAAACAAAACAAAAAGAAAAAAAAAAAAAAGGAAACTGTATAAACGACTCTCATCCATCTCTTTTTT GCAATAAGGTGGTGCAAATCCATTAAGGCGATTAAACAATTCTGTAGATGGATCCCCTCCTTCATTGTACCATTTCAGA TCGTGTTATTCTAACCATTCTTGGATTATTTGTTTGGTAAATGTTTCCCATGTGTTTGTGTTTTTTCTGTATATAGAGT GATTTCAGATTGTAAATAGCGCGTCAGCAAAACTTGTCTAAATCATATATTTTTGTCTAATAAACTAAATGAAATTA
Citation	Anderson C, Hill B, Lu HC, Moverley A, Yang Y, Oliveira NMM, Baldock RA, Stern CD. A 3D molecular atlas of the chick embryonic heart. Dev Biol. 2019 Dec 1;456(1):40-46. doi: 10.1016/j.ydbio.2019.07.003. Epub 2019 Jul 5.
Copyright	Copyright © 2019 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 (NM_001030338 ).