GEISHA - A Chicken Embryo Gene Expression Database
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IRX1
iroquois homeobox 1

Gene
Official SymbolIRX1
Official Full Nameiroquois homeobox 1
CGNC ID9961
also known asiroquois-class homeodomain protein IRX-1|iroquois homeobox protein 1|iroquois homologue-1
gene typeprotein-coding
Genomic Map
 Ensembl ID not known
NCBI
UCSC
Gallus-Browse
Sequence Information
Genomic
RNANM_001030338
PolypeptideNP_001025509
Sequence Clusters/ESTsUnigene
Gene Expression
In Situ HybridizationGEISHA
EST ProfileGga.2699
Orthology
Entrez GeneEnsembl GeneGenetic PhenotypesMOD
Fruit Fly
Human79192ENSG00000170549MIM:606197
Mouse16371ENSMUSG00000060969All phenotypic alleles (1):Targeted, knock-out(1) MGI:1197515
Xenopus100038208, 397976, 735237486816
Zebrafish403019, 114430ENSDARG00000009510, ENSDARG00000056594ZDB-GENE-040707-1, ZDB-GENE-010716-1ZFIN:ZDB-GENE-040707-1, ZFIN:ZDB-GENE-010716-1
Gene Ontology
Molecular Function
Biological Process
Cellular Component
Links to other databases
Entrez Gene374185
Ensembl Gene
KEGGgga:374185

Entry 1

GEISHA IdIRX1.UApcrData SourceGEISHA ISH Analysis
Forward cDNA Template PrimerAACACCGCAAGAACCCCTACCC
Reverse cDNA Template PrimerAATTAACCCTCACTAAAGGAAGCCCCATTTGTCCAGTTGTGcDNA Template Length675
Forward cDNA Template Probeshow
NTTATCCATGCGTTGGACTGCCATCGGACGTGTGAGTCCATGGCTGGGGAGAAAGGCGGGATGCTGGATCTGTGAAGAA
GTGTGGGTGACCTGGGCAGGGGGAGGTGGTGGGGGGGAGGATTTCAGGGCACCATCAGGGCTGGTCGCAGTCTCTGCCA
AAGACCAGATCTTGGGTTTGCTGTGAGATGGCATCTGTAAATTGCTCTGTCCCCCGGGGCTAATGATTCGCGTGCTGTT
GTCAGAGGCCTCCTTCACCATGGCCAGAGCATCTTTGGGTTTCAGCCCTTCAGATCCTGACAGTGACAATTCCTTGTCT
TTTTCCAAGCGCTCCTCTTCACTGCTTTGTCTCAGGAGCTCAGGCTTCTCCTCCTCTTCCTCATTGCTCTGTTCCCCAT
CGTTTTCATCAATTTTATCTATGTCTATGCTCTCCAGGTCGATCTCCTCATCGTCTTCGGTCTTCTCAGGGTCCCCCTC
GTTATCGCTGCCAAAAAGGTTAGCATCTTCTTGGTCCTTACTCCTGGAGCCCCAGGTCACCTTGTTCTCCTTCTTGAGG
CGGCGGCGGGCGTTGGCGAACCAGGTGGAGACCTGGGTGAGGGTCATCTTGGTGATGATGGCCAGCATGATCTTCTCGC
CCTTGGTAGGGTAGGGGTTCTTGCAGTATTAAACN
StageImage (click image to view full size)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
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 7
stage 7
stage 8
stage 9
stage 9
stage 10
stage 10
stage 11
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 21
stage 22
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 25
stage 26
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 IdIRX1.Khudyakov.2009Data SourcePublication
Complete cDNA Template Probeshow
GCGGCTCGAGGGGGAACAGAGCAATGAGGAAGAGGAGGAGAAGCCTGAGCTCCTGAGACAAAGCAGTGAAGAGGAGCGC
TTGGAAAAAGACAAGGAATTGTCACTGTCAGGATCTGAAGGGCTGAAACCCAAAGATGCTCTGGCCATGGTGAAGGAGG
CCTCTGACAACAGCACGCGAATCATTAGCCCCGGGGGACAGAGCAATTTACAGATGCCATCTCACAGCAAACCCAAGAT
CTGGTCTTTGGCAGAGACTGCGACCAGCCCTGATGGTGCCCTGAAATCCTCCCCCCCACCACCTCCCCCTGCCCAGGTC
ACCCACACTTCGCCACAGATCCAGCATCCCGCCTTTCTCCCCAGCCATGGACTCTACACGTGCCAGATTGGCAAGTTTC
ACAACTGGACAAATGGGGCTTTTCTCACGCAGAGTTCCCTGCTAAACGTGAGGTCGTTTTTGGGAGTAAATCACCACCA
TGCCACTCACCACAAACACCAACTCCAGGCCCAGCAGCAGCCTTCTGTTTTAACAGCCACCCTGGGAGCCCTAAGCAGT
GAAAAGCCTTCAGAGAGGACCAGTCCCAAACACATAGAAAATGTCCCAAGAACCGATTCCCCACCTCAGCCACTCAAAT
CGCCCTTCCAGCCTGTCCGTGACAACTCTTTGCCTCAGCAAGAGGGAACACCGAGAATTTTAACAGCTCTCCCTTCGGC
TTGATTAAATGGTTTGCTGAAAAACCACAATATTACAGAGACTTGGTCTTTAAGGACAGAAAACCAAAACACAACGACA
CAC
CitationKhudyakov J, Bronner-Fraser M. Comprehensive spatiotemporal analysis of early chick neural crest network genes. Dev Dyn. 2009 Mar;238(3):716-23.
CopyrightPublished Online: 22 Feb 2009 Copyright © 2009 Wiley-Liss, Inc.
CommentsThe sequence below was obtained from NCBI (BU365297) using the information provided in the publication.
StageImage (click image to view full size)Location (click to highlight)Comments (click to highlight)
4
stage 4
Placcode
preplacodal region

Entry 3

GEISHA IdIRX1.Abello.2010Data SourcePublication
Complete cDNA Template Probeshow
ATGTCCTTCCCCCAGCTGGGCTACCCGCAGTACCTCAGCGCCAGCCAGGCGGTGTACGGCAGCGAGCGGCCCGGGGTGC
TGGCCGCCGCCGCCGCAGCCGCCGCAGCCGCCGCCGCCGCCTCGGGCCGGCCCGCGGGCGCCGAACTGGGCAGCGGCTC
GGCCGCTGTCACCTCGGTGCTGGGCATGTACGCGGGGCCCTACAGCGCCCCCAACTACAGCGCCTTCCTGCCCTACACC
GCCGACCTCGGCCTCTTCTCGCAGATGGGCTCCCAGTACGAGCTGAAAGATAATCCGGGTGTCCATCCTGCTACCTTCG
CAGCCCACACCGCCCCCGGCTATTATCCCTACGGACAGTTCCAGTATGGGGACCCGGGGCGACCCAAAAATGCCACCCG
GGAGAGTACCAGCACCCTCAAGGCCTGGCTCAATGAACACCGCAAGAACCCCTACCCTACCAAGGGCGAGAAGATCATG
CTGGCCATCATCACCAAGATGACCCTCACCCAGGTCTCCACCTGGTTCGCCAACGCCCGCCGCCGCCTCAAGAAGGAGA
ACAAGGTGACCTGGGGCTCCAGGAGTAAGGACCAAGAAGATGCTAACCTTTTTGGCAGCGATAACGAGGGGGACCCTGA
GAAGACCGAAGACGATGAGGAGATCGACCTGGAGAGCATAGACATAGATAAAATTGATGAAAACGATGGGGAACAGAGC
AATGAGGAAGAGGAGGAGAAGCCTGAGCTCCTGAGACAAAGCAGTGAAGAGGAGCGCTTGGAAAAAGACAAGGAATTGT
CACTGTCAGGATCTGAAGGGCTGAAACCCAAAGATGCTCTGGCCATGGTGAAGGAGGCCTCTGACAACAGCACGCGAAT
CATTAGCCCCGGGGGACAGAGCAATTTACAGATGCCATCTCACAGCAAACCCAAGATCTGGTCTTTGGCAGAGACTGCG
ACCAGCCCTGATGGTGCCCTGAAATCCTCCCCCCCACCACCTCCCCCTGCCCAGGTCACCCACACTTTGCCACAGATCC
AGCATCCCGCCTTTCTCCCCAGCCATGGACTCTACACGTGCCAGATTGGCAAGTTTCACAACTGGACAAATGGGGCTTT
TCTCACGCAGAGTTCCCTGCTAAACGTGAGGTCGTTTTTGGGAGTAAATCACCACCATGCCACTCACCACAACCACCAC
CTCCAGGCCCAGCAGCAGCCTTCTGTTTTAACAGCCACCCTGGGAGCCCTAAGCAGTGAAAAGCCTTCAGAGAGGACCA
GTCCCAAACACATAGAAAATGTCCCAAGAACCGATTCCCCACCTCAGCCACTCAAATCGCCCTTCCAGCCTGTCCGCGA
CAACTCTTTGCCTCAGCAAGAGGGAACTCCGAGAATTTTAACAGCTCTCCCTTCGGCTTGA
CitationAbelló 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.
CopyrightCopyright © 2009 Elsevier Inc. All rights reserved.
CommentsAs 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).
StageImage (click image to view full size)Location (click to highlight)Comments (click to highlight)
1
stage 1
Ear/Otic Placode
 

Entry 4

GEISHA IdIRX3.GarciaCampmany.2007Data SourcePublication
Complete cDNA Template Probeshow
GCCGCCTTCCCGCACCACCACCCCGCTTTCTACCCCTACGGGCAGTACCAGTTCGGGGACCCGTCGCGGCCCAAGAACG
CCACCCGCGAGAGCACCAGCACGCTCAAGGCCTGGCTCAACGAGCACCGCAAGAACCCGTACCCCACCAAGGGTGAGAA
GATCATGCTGGCCATCATCACCAAGATGACCCTCACCCAGGTCTCCACCTGGTTCGCCAACGCTCGGCGGCGGCTCAAG
AAGGAGAACAAGATGACCTGGGCCCCCCGCAGCAGGACGGACGAGGAGGGCAACTCCTACGGC
CitationGarcía-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.
CopyrightCopyright by the authors. Published by the Company of Biologists Ltd.
CommentsAs insufficient information is provided in publication to verify exact sequence used to synthesize probe, the sequence below was obtained from NCBI NM_001030338
StageImage (click image to view full size)Location (click to highlight)Comments (click to highlight)
13-18
stage 18
stage 18
Spinal Cord
 

Entry 5

GEISHA IdIRX1.Anderson.2021Data SourceDirect Submission
Complete cDNA Template Probeshow
ATATTTCTGCCGCTCCTGCCGCCGACGCCAGTGCTGCCAGTGCCGCCGCCCCGGAGATGTCCTTCCCCCAGCTGGGCTA
CCCGCAGTACCTCAGCGCCAGCCAGGCGGTGTACGGCAGCGAGCGGCCCGGGGTGCTGGCCGCCGCCGCCGCAGCCGCC
GCAGCCGCCGCCGCCGCCTCGGGCCGGCCCGCGGGCGCCGAACTGGGCAGCGGCTCGGCCGCTGTCACCTCGGTGCTGG
GCATGTACGCGGGGCCCTACAGCGCCCCCAACTACAGCGCCTTCCTGCCCTACACCGCCGACCTCGGCCTCTTCTCGCA
GATGGGCTCCCAGTACGAGCTGAAAGATAATCCGGGTGTCCATCCTGCTACCTTCGCAGCCCACACCGCCCCCGGCTAT
TATCCCTACGGACAGTTCCAGTACGGGGACCCGGGGCGACCCAAAAATGCCACCCGGGAGAGTACCAGCACCCTCAAGG
CCTGGCTCAATGAACACCGCAAGAACCCCTACCCTACCAAGGGCGAGAAGATCATGCTGGCCATCATCACCAAGATGAC
CCTCACCCAGGTCTCCACCTGGTTCGCCAACGCCCGCCGCCGCCTCAAGAAGGAGAACAAGGTGACCTGGGGCTCCAGG
AGTAAGGACCAAGAAGATGCTAACCTTTTTGGCAGCGATAACGAGGGGGACCCTGAGAAGACCGAAGACGATGAGGAGA
TCGACCTGGAGAGCATAGACATAGATAAAATTGATGAAAACGATGGGGAACAGAGCAATGAGGAAGAGGAGGAGAAGCC
TGAGCTCCTGAGACAAAGCAGTGAAGAGGAGCGCTTGGAAAAAGACAAGGAATTGTCACTGTCAGGATCTGAAGGGCTG
AAACCCAAAGATGCTCTGGCCATGGTGAAGGAGGCCTCTGACAACAGCACGCGAATCATTAGCCCCGGGGGACAGAGCA
ATTTACAGATGCCATCTCACAGCAAACCCAAGATCTGGTCTTTGGCAGAGACTGCGACCAGCCCTGATGGTGCCCTGAA
ATCCTCCCCCCCACCACCTCCCCCTGCCCAGGTCACCCACACTTCGCCACAGATCCAGCATCCCGCCTTTCTCCCCAGC
CATGGACTCTACACGTGCCAGATTGGCAAGTTTCACAACTGGACAAATGGGGCTTTTCTCACGCAGAGTTCCCTGCTAA
ACGTGAGGTCGTTTTTGGGAGTAAATCACCACCATGCCACTCACCACAACCACCACCTCCAGGCCCAGCAGCAGCCTTC
TGTTTTAACAGCCACCCTGGGAGCCCTAAGCAGTGAAAAGCCTTCAGAGAGGACCAGTCCCAAACACATAGAAAATGTC
CCAAGAACCGATTCCCCACCTCAGCCACTCAAATCGCCCTTCCAGCCTGTCCGTGACAACTCTTTGCCTCAGCAAGAGG
GAACACCGAGAATTTTAACAGCTCTCCCTTCGGCTTGATTAAATGGTTTGCTGAAAAACAAAATATTACAGAGACTGGT
CTTAAGGACAGAAAAACAAAACAAAAAGAAAAAAAAAAAAAAGGAAACTGTATAAACGACTCTCATCCATCTCTTTTTT
GCAATAAGGTGGTGCAAATCCATTAAGGCGATTAAACAATTCTGTAGATGGATCCCCTCCTTCATTGTACCATTTCAGA
TCGTGTTATTCTAACCATTCTTGGATTATTTGTTTGGTAAATGTTTCCCATGTGTTTGTGTTTTTTCTGTATATAGAGT
GATTTCAGATTGTAAATAGCGCGTCAGCAAAACTTGTCTAAATCATATATTTTTGTCTAATAAACTAAATGAAATTA
CommentsImages 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.
StageImage (click image to view full size)Location (click to highlight)Comments (click to highlight)
7-12
stage 12
stage 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 IdIRX1.Anderson.2019Data SourcePublication
Complete cDNA Template Probeshow
ATATTTCTGCCGCTCCTGCCGCCGACGCCAGTGCTGCCAGTGCCGCCGCCCCGGAGATGTCCTTCCCCCAGCTGGGCTA
CCCGCAGTACCTCAGCGCCAGCCAGGCGGTGTACGGCAGCGAGCGGCCCGGGGTGCTGGCCGCCGCCGCCGCAGCCGCC
GCAGCCGCCGCCGCCGCCTCGGGCCGGCCCGCGGGCGCCGAACTGGGCAGCGGCTCGGCCGCTGTCACCTCGGTGCTGG
GCATGTACGCGGGGCCCTACAGCGCCCCCAACTACAGCGCCTTCCTGCCCTACACCGCCGACCTCGGCCTCTTCTCGCA
GATGGGCTCCCAGTACGAGCTGAAAGATAATCCGGGTGTCCATCCTGCTACCTTCGCAGCCCACACCGCCCCCGGCTAT
TATCCCTACGGACAGTTCCAGTACGGGGACCCGGGGCGACCCAAAAATGCCACCCGGGAGAGTACCAGCACCCTCAAGG
CCTGGCTCAATGAACACCGCAAGAACCCCTACCCTACCAAGGGCGAGAAGATCATGCTGGCCATCATCACCAAGATGAC
CCTCACCCAGGTCTCCACCTGGTTCGCCAACGCCCGCCGCCGCCTCAAGAAGGAGAACAAGGTGACCTGGGGCTCCAGG
AGTAAGGACCAAGAAGATGCTAACCTTTTTGGCAGCGATAACGAGGGGGACCCTGAGAAGACCGAAGACGATGAGGAGA
TCGACCTGGAGAGCATAGACATAGATAAAATTGATGAAAACGATGGGGAACAGAGCAATGAGGAAGAGGAGGAGAAGCC
TGAGCTCCTGAGACAAAGCAGTGAAGAGGAGCGCTTGGAAAAAGACAAGGAATTGTCACTGTCAGGATCTGAAGGGCTG
AAACCCAAAGATGCTCTGGCCATGGTGAAGGAGGCCTCTGACAACAGCACGCGAATCATTAGCCCCGGGGGACAGAGCA
ATTTACAGATGCCATCTCACAGCAAACCCAAGATCTGGTCTTTGGCAGAGACTGCGACCAGCCCTGATGGTGCCCTGAA
ATCCTCCCCCCCACCACCTCCCCCTGCCCAGGTCACCCACACTTCGCCACAGATCCAGCATCCCGCCTTTCTCCCCAGC
CATGGACTCTACACGTGCCAGATTGGCAAGTTTCACAACTGGACAAATGGGGCTTTTCTCACGCAGAGTTCCCTGCTAA
ACGTGAGGTCGTTTTTGGGAGTAAATCACCACCATGCCACTCACCACAACCACCACCTCCAGGCCCAGCAGCAGCCTTC
TGTTTTAACAGCCACCCTGGGAGCCCTAAGCAGTGAAAAGCCTTCAGAGAGGACCAGTCCCAAACACATAGAAAATGTC
CCAAGAACCGATTCCCCACCTCAGCCACTCAAATCGCCCTTCCAGCCTGTCCGTGACAACTCTTTGCCTCAGCAAGAGG
GAACACCGAGAATTTTAACAGCTCTCCCTTCGGCTTGATTAAATGGTTTGCTGAAAAACAAAATATTACAGAGACTGGT
CTTAAGGACAGAAAAACAAAACAAAAAGAAAAAAAAAAAAAAGGAAACTGTATAAACGACTCTCATCCATCTCTTTTTT
GCAATAAGGTGGTGCAAATCCATTAAGGCGATTAAACAATTCTGTAGATGGATCCCCTCCTTCATTGTACCATTTCAGA
TCGTGTTATTCTAACCATTCTTGGATTATTTGTTTGGTAAATGTTTCCCATGTGTTTGTGTTTTTTCTGTATATAGAGT
GATTTCAGATTGTAAATAGCGCGTCAGCAAAACTTGTCTAAATCATATATTTTTGTCTAATAAACTAAATGAAATTA
CitationAnderson 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.
CopyrightCopyright © 2019 Elsevier Inc. All rights reserved.
CommentsInsufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (NM_001030338 ).
StageImage (click image to view full size)Location (click to highlight)Comments (click to highlight)
7-12
stage 12
Heart
 
 Data from NCBI Unigene EST Profile
Unigene ID: Gga.2699

Mouse

EmageMGI:1197515
EurexpressMGI:1197515
MGI GXDMGI:1197515

Frog

Xenbase486816

Fruit Fly

BDGP

Zebra Finch

ZEBrA

Zebrafish

ZFINZDB-GENE-040707-1, ZDB-GENE-010716-1
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