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A chicken embryo gene expression database

	Anatomical Location
	Stage
	Gene Name
	GEISHA ID
	Multiple Parameters

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SIX1
SIX homeobox 1

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

Gene

Official Symbol	SIX1
Official Full Name	SIX homeobox 1
CGNC ID	54357
also known as	homeobox protein SIX1\|sine oculis homeobox homolog 1
gene type	protein-coding

Genomic Map

	Ensembl ID not known
	NCBI
	UCSC
	Gallus-Browse

Sequence Information

Genomic
RNA	NM_001044685
Polypeptide	NP_001038150
Sequence Clusters/ESTs	Unigene

Gene Expression

In Situ Hybridization	GEISHA
EST Profile	Gga.20089

Orthology

	Entrez Gene	Ensembl Gene	Genetic Phenotypes	MOD
Fruit Fly
Human	6495		MIM:608389	MIM:601205
Mouse	20471	ENSMUSG00000051367	All phenotypic alleles (5):Chemically induced(1) Targeted, knock-out(2) Targeted, other(2)	MGI:102780
Xenopus	100101784, 373734, 100101702, 398185			480716, 481503
Zebrafish	404627, 494168	ENSDARG00000039304	ZDB-GENE-040426-2308, ZDB-GENE-040718-155	ZFIN:ZDB-GENE-040426-2308, ZFIN:ZDB-GENE-040718-155

Gene Ontology

Molecular Function
Biological Process
Cellular Component

Links to other databases

Entrez Gene	693262
Ensembl Gene
KEGG	gga:693262

Entry 1

GEISHA Id	SIX1.UApcr	Data Source	GEISHA ISH Analysis
Forward cDNA Template Primer	GGAGAACACGGAGAACAACAACG
Reverse cDNA Template Primer	AATTAACCCTCACTAAAGGGAGGCAGACAGAGAGAGACGC	cDNA Template Length	944
Forward cDNA Template Probe	show `CCCANNCCCCNCCNNNCCCCCCCGCCCTCTCCCTTCATTTTATTTCTGCTGCTGTAATTCCCCCTCACTTGAACTCAAA AGGCCAAGGGCTTTCTGCCCCTCTCTGCTTTTGGCTCCTTGAAAATTATTATTACCATTATTATTATTATTATTAAAAA AACCACCGTTGAAAAAGGAGGGTGGGGGGGGACCCACCCTGCTTTTAACACCTTGAAAAAAAACCAACTTCTTTTTCAT GACCACCCCCCCTTTTTTACAACCAAAATTCGTTTCCCACCACCTCCTTTTATAACCCAACCCCCCCCAGCCTGGAGGT AAGCGCCCCCCCCACCAATTCTTGAATTTAATGCCCCGCCAGGTTTTCCTTCCCCGGGGGGGCGGCCAGGAACCCCACC GGTTACCAAAACCTCCTCCCTGAAGGAAGTTTCCCCCCCAAAAGAAGAACGAATTTATAAATAA`

Stage

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Location (click to highlight)

Comments (click to highlight)

4-6

stage 5

stage 6

Early Endoderm
Early Mesoderm
Headfold

7-12

stage 8

stage 9

stage 10

stage 11

Ear/Otic Placode
Endoderm
Forebrain
Head Mesenchyme
Neural Plate/Tube
Somatic Mesoderm
Somites
Splanchnic Mesoderm

13-18

stage 13

stage 17

stage 18

Ear/Otic Placode
Foregut
Head Mesenchyme
Leg Mesenchyme
Nasal Placode/Nerve
Pharyngeal Arches and Clefts
Pharynx
Somites
Wing Mesenchyme

19-24

stage 21

stage 23

stage 24

Head Mesenchyme
Leg Mesenchyme
Nasal Placode/Nerve
Pharyngeal Arches and Clefts
Somites
Wing Mesenchyme

Entry 2

GEISHA Id	Six1.Barembaum.2007	Data Source	Publication
Complete cDNA Template Probe	show GCCGAGCATCCCCCGCTCCGCCGCCGCGGCCGCCTCCGCGCCTCCCCGCTCTGGGGACGGGACCGGGCCCGGGGCTCTC CCCGCCCCTCCGCCGCCTCCCGGTGCCGCACGCAGCCCCGAGCCGCCCCTCGGCGCCCGGCCCCGGCCATGTCGATGCT GCCGTCGTTCGGCTTCACGCAGGAGCAGGTCGCCTGCGTGTGCGAGGTGCTGCAGCAGGGGGGGAACCTGGAGCGCCTG GGCCGCTTCCTCTGGTCGCTGCCGGCGTGCGACCACCTGCACAAGAACGAGAGCGTCCTCAAGGCCAAAGCGGTGGTGG CCTTCCACCGGGGCAACTTCCGCGAGCTCTACAAGATCCTGGAGAGCCACCAGTTCTCGCCCCACAACCACCCCAAGCT GCAGCAGCTCTGGCTCAAGGCGCACTACGTGGAAGCCGAGAAGCTGCGCGGGCGGCCGCTGGGCGCCGTGGGCAAATAC CGGGTGCGCCGAAAGTTCCCCCTGCCCCGCACCATCTGGGACGGCGAGGAGACGAGCTACTGCTTCAAGGAGAAGTCGC GGGGGGTGCTGCGGGAGTGGTACGCGCACAACCCCTACCCCTCGCCCCGCGAGAAGCGGGAGCTGGCCGAGGCCACCGG GCTCACCACCACGCAGGTCAGCAACTGGTTCAAGAACCGGCGGCAGCGGGACCGGGCGGCGGAGGCCAAGGAGAGGGAG AACACGGAGAACAACAACGCGGCCACCAACAAACCCAACCAGCTCTCCCCCCTGGACGGGAGCAAACCCCTCATGTCCA GCTCCGAGGAAGAATTTTCACCCCCGCAGAGCCCGGATCAGAACTCGGTCCTCCTGTTGCAGGGGAACCTCGCTCACGG CAGGAGCTCCGCGTACCCGCTGGGCTCCCTGCCCGCCCCCCCGGGCACGCACAGCCTCCCGGGCCATCAGCTCCAGGAC TCGCTGCTGGGGCCGCTCACCTCCAGCCTGGTGGACCTGGGCTCCTAAAGGGAGCTCGTGGACACGGACTCTCGGTTGT ACATAGCGGACGGTGATCCTGAACGTGACTCGGCTCTCTCCACGGTCTCAGCTGCAGGTCCGGTCCCCCCCCACCTCCC TTCTCCACTGTCGTTATTTTTATTATTATTATTCATTATTGTTATTATTATTTTTCACGTAGCCAAATGCAGAGAGCGG CAGAAAGCCCTCGGCCTTTCGAGTTCAAGTGAGCGGGAATTACAGCAGCAGAAATAGAAATAGAAGGGGAGAGGGTGAG GGGAAAAAAAACCCAACCCCGAACCCCGGATCCCATTGCGCCCCATAAATCCCGGCTGTTGCGGCCCAGAGGCAGAGGG AGCGCGGGGCCCTTTGCGGCAGCGGGAGGAGGGAGGGGAACTTTTTCGTTTACATTTCTTTTTTTTCATATTTAGCTTC ACCGGAAGGATTTCGATGTAGTTTAAAATTAAAAAAAAAAAAAAAAAGAGGGGAAAAAAAAATAGATAATTAGGAAGCG GCAGTCTGAGTGCCTCTGTCTTAACGCGGCGGTGCTGCTCCCCGGCCGGGACACGCAGCGATGCGGCTGCACTTTAGGA CAGTAACAACAGCGATAATAAATGCGGATGGCCCTTTCCTTCCGCAGGAGCGTCTCTCTCTGTCTGCCTCCCCCAACCC CCAGCTCTGCCTCGCAGTGAGCCCGCAGCTGTCTGTCTCGAGTCTGTGTTACCGACCTCGCGTGTGCTTTCAGGTTTCT TTTCTATTGTACCCGAACAGCCGAAATTAAACACTGCTGATGGCAGAAAAAAAAAAAAAAAAAAAAAAAAAA
Citation	Barembaum M, Bronner-Fraser M. Spalt4 mediates invagination and otic placode gene expression in cranial ectoderm. Development. 2007 Nov;134(21):3805-14.
Copyright	Published by The Company of Biologists 2007
Comments	Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (NM_001044685).

Stage

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Location (click to highlight)

Comments (click to highlight)

4-6

stage 5

Ectoderm

Preplacode Ectoderm

stage 13

Ear/Otic Placcode

Entry 3

GEISHA Id	SIX1.Sato.2012	Data Source	Publication
Complete cDNA Template Probe	show GCCGAGCATCCCCCGCTCCGCCGCCGCGGCCGCCTCCGCGCCTCCCCGCTCTGGGGACGGGACCGGGCCCGGGGCTCTC CCCGCCCCTCCGCCGCCTCCCGGTGCCGCACGCAGCCCCGAGCCGCCCCTCGGCGCCCGGCCCCGGCCATGTCGATGCT GCCGTCGTTCGGCTTCACGCAGGAGCAGGTCGCCTGCGTGTGCGAGGTGCTGCAGCAGGGGGGGAACCTGGAGCGCCTG GGCCGCTTCCTCTGGTCGCTGCCGGCGTGCGACCACCTGCACAAGAACGAGAGCGTCCTCAAGGCCAAAGCGGTGGTGG CCTTCCACCGGGGCAACTTCCGCGAGCTCTACAAGATCCTGGAGAGCCACCAGTTCTCGCCCCACAACCACCCCAAGCT GCAGCAGCTCTGGCTCAAGGCGCACTACGTGGAAGCCGAGAAGCTGCGCGGGCGGCCGCTGGGCGCCGTGGGCAAATAC CGGGTGCGCCGAAAGTTCCCCCTGCCCCGCACCATCTGGGACGGCGAGGAGACGAGCTACTGCTTCAAGGAGAAGTCGC GGGGGGTGCTGCGGGAGTGGTACGCGCACAACCCCTACCCCTCGCCCCGCGAGAAGCGGGAGCTGGCCGAGGCCACCGG GCTCACCACCACGCAGGTCAGCAACTGGTTCAAGAACCGGCGGCAGCGGGACCGGGCGGCGGAGGCCAAGGAGAGGGAG AACACGGAGAACAACAACGCGGCCACCAACAAACCCAACCAGCTCTCCCCCCTGGACGGGAGCAAACCCCTCATGTCCA GCTCCGAGGAAGAATTTTCACCCCCGCAGAGCCCGGATCAGAACTCGGTCCTCCTGTTGCAGGGGAACCTCGCTCACGG CAGGAGCTCCGCGTACCCGCTGGGCTCCCTGCCCGCCCCCCCGGGCACGCACAGCCTCCCGGGCCATCAGCTCCAGGAC TCGCTGCTGGGGCCGCTCACCTCCAGCCTGGTGGACCTGGGCTCCTAAAGGGAGCTCGTGGACACGGACTCTCGGTTGT ACATAGCGGACGGTGATCCTGAACGTGACTCGGCTCTCTCCACGGTCTCAGCTGCAGGTCCGGTCCCCCCCCACCTCCC TTCTCCACTGTCGTTATTTTTATTATTATTATTCATTATTGTTATTATTATTTTTCACGTAGCCAAATGCAGAGAGCGG CAGAAAGCCCTCGGCCTTTCGAGTTCAAGTGAGCGGGAATTACAGCAGCAGAAATAGAAATAGAAGGGGAGAGGGTGAG GGGAAAAAAAACCCAACCCCGAACCCCGGATCCCATTGCGCCCCATAAATCCCGGCTGTTGCGGCCCAGAGGCAGAGGG AGCGCGGGGCCCTTTGCGGCAGCGGGAGGAGGGAGGGGAACTTTTTCGTTTACATTTCTTTTTTTTCATATTTAGCTTC ACCGGAAGGATTTCGATGTAGTTTAAAATTAAAAAAAAAAAAAAAAAGAGGGGAAAAAAAAATAGATAATTAGGAAGCG GCAGTCTGAGTGCCTCTGTCTTAACGCGGCGGTGCTGCTCCCCGGCCGGGACACGCAGCGATGCGGCTGCACTTTAGGA CAGTAACAACAGCGATAATAAATGCGGATGGCCCTTTCCTTCCGCAGGAGCGTCTCTCTCTGTCTGCCTCCCCCAACCC CCAGCTCTGCCTCGCAGTGAGCCCGCAGCTGTCTGTCTCGAGTCTGTGTTACCGACCTCGCGTGTGCTTTCAGGTTTCT TTTCTATTGTACCCGAACAGCCGAAATTAAACACTGCTGATGGCAGAAAAAAAAAAAAAAAAAAAAAAAAAA
Citation	Sato S, Ikeda K, Shioi G, Nakao K, Yajima H, Kawakami K. Regulation of Six1 expression by evolutionarily conserved enhancers in tetrapods. Dev Biol. 2012 Aug 1;368(1):95-108. doi: 10.1016/j.ydbio.2012.05.023. Epub 2012 May 30.
Copyright	Copyright © 2012 Elsevier Inc.
Comments	The sequence below was obtained from NCBI (acc # AB199734.1) using the information provided in the publication as described in Sato et al.

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

4-6

stage 5

Ectoderm
Head Process

Preplacode ectoderm

7-12

stage 7

stage 8

stage 10

stage 11

Ear/Otic Placode
Ectoderm
Neural Plate/Tube
Somites

HH8+ embryo
preplacode ectoderm

13-18

stage 14

stage 15

stage 18

Ear/Otic Placode
Nasal Placode/Nerve
Neural Plate/Tube
Pharyngeal Arches and Clefts
Somites

19-21

stage 21

Leg
Nasal Placode/Nerve
Pharyngeal Arches and Clefts
Somites
Wing

Entry 4

GEISHA Id	SIX1.Litsiou.2005	Data Source	Publication
Complete cDNA Template Probe	show GCCGAGCATCCCCCGCTCCGCCGCCGCGGCCGCCTCCGCGCCTCCCCGCTCTGGGGACGGGACCGGGCCCGGGGCTCTC CCCGCCCCTCCGCCGCCTCCCGGTGCCGCACGCAGCCCCGAGCCGCCCCTCGGCGCCCGGCCCCGGCCATGTCGATGCT GCCGTCGTTCGGCTTCACGCAGGAGCAGGTCGCCTGCGTGTGCGAGGTGCTGCAGCAGGGGGGGAACCTGGAGCGCCTG GGCCGCTTCCTCTGGTCGCTGCCGGCGTGCGACCACCTGCACAAGAACGAGAGCGTCCTCAAGGCCAAAGCGGTGGTGG CCTTCCACCGGGGCAACTTCCGCGAGCTCTACAAGATCCTGGAGAGCCACCAGTTCTCGCCCCACAACCACCCCAAGCT GCAGCAGCTCTGGCTCAAGGCGCACTACGTGGAAGCCGAGAAGCTGCGCGGGCGGCCGCTGGGCGCCGTGGGCAAATAC CGGGTGCGCCGAAAGTTCCCCCTGCCCCGCACCATCTGGGACGGCGAGGAGACGAGCTACTGCTTCAAGGAGAAGTCGC GGGGGGTGCTGCGGGAGTGGTACGCGCACAACCCCTACCCCTCGCCCCGCGAGAAGCGGGAGCTGGCCGAGGCCACCGG GCTCACCACCACGCAGGTCAGCAACTGGTTCAAGAACCGGCGGCAGCGGGACCGGGCGGCGGAGGCCAAGGAGAGGGAG AACACGGAGAACAACAACGCGGCCACCAACAAACCCAACCAGCTCTCCCCCCTGGACGGGAGCAAACCCCTCATGTCCA GCTCCGAGGAAGAATTTTCACCCCCGCAGAGCCCGGATCAGAACTCGGTCCTCCTGTTGCAGGGGAACCTCGCTCACGG CAGGAGCTCCGCGTACCCGCTGGGCTCCCTGCCCGCCCCCCCGGGCACGCACAGCCTCCCGGGCCATCAGCTCCAGGAC TCGCTGCTGGGGCCGCTCACCTCCAGCCTGGTGGACCTGGGCTCCTAAAGGGAGCTCGTGGACACGGACTCTCGGTTGT ACATAGCGGACGGTGATCCTGAACGTGACTCGGCTCTCTCCACGGTCTCAGCTGCAGGTCCGGTCCCCCCCCACCTCCC TTCTCCACTGTCGTTATTTTTATTATTATTATTCATTATTGTTATTATTATTTTTCACGTAGCCAAATGCAGAGAGCGG CAGAAAGCCCTCGGCCTTTCGAGTTCAAGTGAGCGGGAATTACAGCAGCAGAAATAGAAATAGAAGGGGAGAGGGTGAG GGGAAAAAAAACCCAACCCCGAACCCCGGATCCCATTGCGCCCCATAAATCCCGGCTGTTGCGGCCCAGAGGCAGAGGG AGCGCGGGGCCCTTTGCGGCAGCGGGAGGAGGGAGGGGAACTTTTTCGTTTACATTTCTTTTTTTTCATATTTAGCTTC ACCGGAAGGATTTCGATGTAGTTTAAAATTAAAAAAAAAAAAAAAAAGAGGGGAAAAAAAAATAGATAATTAGGAAGCG GCAGTCTGAGTGCCTCTGTCTTAACGCGGCGGTGCTGCTCCCCGGCCGGGACACGCAGCGATGCGGCTGCACTTTAGGA CAGTAACAACAGCGATAATAAATGCGGATGGCCCTTTCCTTCCGCAGGAGCGTCTCTCTCTGTCTGCCTCCCCCAACCC CCAGCTCTGCCTCGCAGTGAGCCCGCAGCTGTCTGTCTCGAGTCTGTGTTACCGACCTCGCGTGTGCTTTCAGGTTTCT TTTCTATTGTACCCGAACAGCCGAAATTAAACACTGCTGATGGCAGAAAAAAAAAAAAAAAAAAAAAAAAAA
Citation	Litsiou A, Hanson S, Streit A. A balance of FGF, BMP and WNT signalling positions the future placode territory in the head. Development. 2005 Sep;132(18):4051-62. Epub 2005 Aug 10
Copyright	Authors hold the copyright. 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_001044685.1

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

4-6

stage 6

Early Endoderm
Early Mesoderm
Neural Crest

7-8

stage 7

stage 8

Early Endoderm
Epiblast
Head Mesenchyme
Neural Crest

Entry 5

GEISHA Id	SIX1.Anderson.2019	Data Source	Publication
Complete cDNA Template Probe	show AAAGTTCCCCCCGGCGCTCCGCCGAGCATCCCCCGCTCCGCCGCCGCGGCCGCCTCCGCGCCTCCCCGCTCTGGGGACG GGACCGGGCCCGGGGCTCTCCCCGCCCCTCCGCCGCCTCCCGGTGCCGCACGCAGCCCCGAGCCGCCCCTCGGCGCCCG GCCCCGGCCATGTCGATGCTGCCGTCGTTCGGCTTCACGCAGGAGCAGGTCGCCTGCGTGTGCGAGGTGCTGCAGCAGG GGGGGAACCTGGAGCGCCTGGGCCGCTTCCTCTGGTCGCTGCCGGCGTGCGACCACCTGCACAAGAACGAGAGCGTCCT CAAGGCCAAAGCGGTGGTGGCCTTCCACCGGGGCAACTTCCGCGAGCTCTACAAGATCCTGGAGAGCCACCAGTTCTCG CCCCACAACCACCCCAAGCTGCAGCAGCTCTGGCTCAAGGCGCACTACGTGGAAGCCGAGAAGCTGCGCGGGCGGCCGC TGGGCGCCGTGGGCAAATACCGGGTGCGCCGAAAGTTCCCCCTGCCCCGCACCATCTGGGACGGCGAGGAGACGAGCTA CTGCTTCAAGGAGAAGTCGCGGGGGGTGCTGCGGGAGTGGTACGCGCACAACCCCTACCCCTCGCCCCGCGAGAAGCGG GAGCTGGCCGAGGCCACCGGGCTCACCACCACGCAGGTCAGCAACTGGTTCAAGAACCGGCGGCAGCGGGACCGGGCGG CGGAGGCCAAGGAGAGGGAGAACACGGAGAACAACAACGCGGCCACCAACAAACCCAACCAGCTCTCCCCCCTGGACGG GAGCAAACCCCTCATGTCCAGCTCCGAGGAAGAATTTTCACCCCCGCAGAGCCCGGATCAGAACTCGGTCCTCCTGTTG CAGGGGAACCTCGCTCACGGCAGGAGCTCCGCGTACCCGCTGGGCTCCCTGCCCGCCCCCCCGGGCACGCACAGCCTCC CGGGCCATCAGCTCCAGGACTCGCTGCTGGGGCCGCTCACCTCCAGCCTGGTGGACCTGGGCTCCTAAAGGGAGCTCGT GGACACGGACTCTCGGTTGTACATAGCGGACGGTGATCCTGAACGTGACTTCGGCTCTTCTCCACGGTCTCAGCTCCAG GTCCGGTCCCCCCCCACCTCCCTTCTCCACTGTCGTTATTTTTATTATTATTATTATTATTGTTATTATTATTTTTCAC GTAGCCAAATGCAGAGAGCGGCAGAAAGCCCTCGGCCTTTCGAGTTCAAGTGAGCGGGAATTACAGCAGCAGAAATAGA AATAGAAGGGGAGAGGGTGGGGGGGAAAAAAACCCAACCCCGAACCCCGGATCCCATTGCGCCCCATAAATCCCGGCTG TTGCGGCCCAGAGGCAGAGGGAGCGCGGGGCCCTTTGCGGCAGCGGGAGGAGGGAGGGGAACTTTTTCGTTTACATTTC TTTTTTTTTCATATTTAGCTTCACCGGAAGGATTTCGATGTAGTTTAAAATTAAAAAAAAAAAAAAAAAAGAGGGGAAA AAAAAAATAGATAATTAGGAAGCGGCAGTCTGAGTGCCTCTGTCTTAACGCGGCGGTGCTGCTCCCCGGCCGGGACACG CAGCGATGCGGCTGCACTTTAGGACAGTAACAACAGCGATAATAAATGCGGATGGCCCTTTCCTTCCGCAGGAGCGTCT CTCTCTGTCTGCCTCCCCCAACCCCCAGCTCTGCCTCGCAGTGAGCCCGCAGCTGTCTGTCTCGAGTCTGTGTTACCGA CCTCGCGTGTGCTTTCAGGTTTCTTTTCTATTGTACCCGAACAGCCGAAATTAAACACTGCTGATGGCAGAA
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_001044685 ).