Geisha

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A chicken embryo gene expression database

	Anatomical Location
	Stage
	Gene Name
	GEISHA ID
	Multiple Parameters

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HOXB1
homeobox B1

Gene

Official Symbol	HOXB1
Official Full Name	homeobox B1
CGNC ID	10116
also known as	Ghox-lab, HOXB-1, homeobox protein Hox-B1\|homeobox-containing transcription factor Hoxb-1
gene type	protein-coding

Genomic Map

	Ensembl
	NCBI
	UCSC
	Gallus-Browse

Sequence Information

Genomic
RNA	NM_001080859
Polypeptide	NP_001074328
Sequence Clusters/ESTs	Unigene

Gene Expression

In Situ Hybridization	GEISHA
EST Profile	Gga.533

Orthology

	Entrez Gene	Ensembl Gene	Genetic Phenotypes	MOD
Fruit Fly
Human	3211			MIM:142968
Mouse	15407	ENSMUSG00000018973	All phenotypic alleles (16):Targeted, knock-out(2) Targeted, other(14)	MGI:96182
Xenopus	100493290, 100301962			485771
Zebrafish	30337, 30374	ENSDARG00000008174	ZDB-GENE-990415-101, ZDB-GENE-980526-290	ZFIN:ZDB-GENE-990415-101, ZFIN:ZDB-GENE-980526-290

Gene Ontology

Molecular Function
Biological Process
Cellular Component

Links to other databases

Entrez Gene	395900
Ensembl Gene	ENSGALG00000013454
KEGG	gga:395900

Entry 1

GEISHA Id	W24	Data Source	GEISHA ISH Analysis
Forward cDNA Template Probe	show GAGCAGCAGCACCTTTACGGGCAGGAGCAGCCCGGTTACTTGCCCGGGGTTTACGGCAACCTCTCGCCTTCCCTAAATG AGGACAAAGACCCCGCGTGCCCCTCCGAGCCGTGCCCCAATGCCAGCGCGGCGCGGACCTTCGATTGGATGAAAGTGAA GAGGAACCCCCCCAAGACAGCCAAAGTGTCGGAATACGGGCTGCTGGGACAGCCCAACACCATTCGCACCAACTTCACC ACCAAGCAGCTGACGGAGCTGGAGAAGGAGTTTCACTTTAACAAGTACCTCACCCGGGCCCGGAGGGTGGAGATCGCCG CTACACTGGAGCTCAACGAAACCCAAGTCAAGATCTGGTTCCAGAACAGGCGGATGAAACAGAAGAAGAGGGAAAAGGA AGGTCTTGCTCCTCCTGCTGCCTCCAGGTCCGCGAAGGAAGCGAGTGAAGCCTCGGATCAGTCCAACTGCACCTCACCT GATGCCTCCCCCAACTCCGTGTCCTCCTGAGCCGCGGTCCCGCGGGGCACAACGACCGGATCGGGGCTGCCTTCGAAGG CCGCTGCATCCCCG
Reverse cDNA Template Probe	show GCCATTTTGCACTATCGTCGCTTTACAGGGTTTCCTACACGCTCTCCGCCTGTATTACCGATCCTGGGGGTGGGAGCGT TGTGCTATCAGATAAAACGAGATAAGGGGAAGGCTGAGCCCGGGGTGCTTTGGGCAACGGTCATTGCCGCACCGAGTGT GAACGTGCACGGGACGAAGGCCGGGGGGGTCCGCACTGCGCTCCCCCAACCGCGATGCACTGACTGCTATTTATTGTAC GTCTCGATAGCCTCACGTCTTGGGGCGAAGCTGCACGGCTCCTCGTATCCCCACCCCCTCAGGCTTATCGGAGTCCGAG AAAAACATAATTAACCACGGCCAGTTGCTACCCTTTACCACCAGAAGCTTTAGCGCAGGGCGAAGTGAAAACCACGGCG AGTTTCGTTAAAGGTTGTTTTAAAGAGATAAAGGGTCATCCTGAAAAGCCTGTGGTTTCTTAATCGGAATCTGTTTTCC CTCTACTCCCTTCCCTGTTTTTCGAAATGAAACTACCTCAGTCTAATAAAGTTTACTTTTTCCAAAAAAAAAAAAAAAA AA

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

4-6

stage 4

stage 6

Epiblast
Primitive Streak
Surface Ectoderm

13-18

stage 13

Hindbrain
Intermediate Mesoderm
Lateral Plate Mesoderm
Paraxial Mesoderm

stage 19

Hindbrain
Rhombomeres
Spinal Cord
Trunk Mesenchyme

Entry 2

GEISHA Id	Hoxb-1.Reijntjes.2004	Data Source	Publication
Complete cDNA Template Probe	show ATGGACAATACTAGGATGAACTCCTTCTTAGAGTATGCAATTTGTAACCGTGGGACGGGCGCCTACCACCATTTAGAGC AAAGCTCCCCTTCCTTCCCCTCTTGCTCAGGTAGCCCCTCCAGTGACACTTTTCATGGAGAAGGGGCGTACGGTGCGGG GGGCAGCCCGGTCGCGGCCGCCCATCTCCCCCCGCAGAGCCCCGGCTTCTTCCCCGCGCCTCCGGGCGCTCCGTCCCTT CGCGGCCGCTGCCCCGAGCGCCGGGTACCCAACCCAAAACTGCAGCCCCGGCTACGGCACCACCAGCTCTACCTCGGCC AGCAGGACGCGGACGCGGTGTACTTCCAGGCGGCCGGGTACTCCTCCAGCACCGGACCCCACCTCGGCTCCCTGGCAGA GGGCTATTGTGGGGCCGTAGGGCAGTACCAGCAGCAGCAGCACCTTTACGGGCAGGAGCAGCCCAGCTACTTGCCCGGG GTTTACGGCAACCTCTCGCCTTCCCTAAATGAGGACAAAGACCCCGCGTGCCCCTCCGAGCCGTGCCCCAATGCCAGCC GGGCGCGGACCTTCGATTGGATGAAAGTGAAGAGGAACCCCCCCAAGACAGCCAAAGTGTCGGAATACGGGCTGCTGGG ACAGCCCAACACCATTCGCACCAACTTCACCACCAAGCAGCTGACGGAGCTGGAGAAGGAGTTTCACTTTAACAAGTAC CTCACCCGGGCCCGGAGGGTGGAGATCGCCGCTACACTGGAGCTCAACGAAACCCAAGTCAAGATCTGGTTCCAGAACA GGCGGATGAAACAGAAGAAGAGGGAAAAGGAAGGTCTCGCCCCTCCTGCTGCCTCCAGGTCCGCGAAGGAAGCGAGTGA AGCCTCGGATCAGTCCAACTGCACCTCACCTGAGGCCTCCCCCAGCTCCGTGTCCTCCTGA
Citation	Reijntjes S, Gale E, Maden M. Generating gradients of retinoic acid in the chick embryo: Cyp26C1 expression and a comparative analysis of the Cyp26 enzymes. Dev Dyn. 2004 Jul;230(3):509-17.
Copyright	Wiley-Liss, Inc. 2004

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

4-6

stage 6

Hindbrain
Neural Plate/Tube
Spinal Cord

7-9

stage 9

Hindbrain
Neural Plate/Tube
Spinal Cord

Entry 3

GEISHA Id	HOXB1.Bok.2005	Data Source	Publication
Complete cDNA Template Probe	show ATGGACAATACTAGGATGAACTCCTTCTTAGAGTATGCAATTTGTAACCGTGGGACGGGCGCCTACCACCATTTAGAGC AAAGCTCCCCTTCCTTCCCCTCTTGCTCAGGTAGCCCCTCCAGTGACACTTTTCATGGAGAAGGGGCGTACGGTGCGGG GGGCAGCCCGGTCGCGGCCGCCCATCTCCCCCCGCAGAGCCCCGGCTTCTTCCCCGCGCCTCCGGGCGCTCCGTCCCTT CGCGGCCGCTGCCCCGAGCGCCGGGTACCCAACCCAAAACTGCAGCCCCGGCTACGGCACCACCAGCTCTACCTCGGCC AGCAGGACGCGGACGCGGTGTACTTCCAGGCGGCCGGGTACTCCTCCAGCACCGGACCCCACCTCGGCTCCCTGGCAGA GGGCTATTGTGGGGCCGTAGGGCAGTACCAGCAGCAGCAGCACCTTTACGGGCAGGAGCAGCCCAGCTACTTGCCCGGG GTTTACGGCAACCTCTCGCCTTCCCTAAATGAGGACAAAGACCCCGCGTGCCCCTCCGAGCCGTGCCCCAATGCCAGCC GGGCGCGGACCTTCGATTGGATGAAAGTGAAGAGGAACCCCCCCAAGACAGCCAAAGTGTCGGAATACGGGCTGCTGGG ACAGCCCAACACCATTCGCACCAACTTCACCACCAAGCAGCTGACGGAGCTGGAGAAGGAGTTTCACTTTAACAAGTAC CTCACCCGGGCCCGGAGGGTGGAGATCGCCGCTACACTGGAGCTCAACGAAACCCAAGTCAAGATCTGGTTCCAGAACA GGCGGATGAAACAGAAGAAGAGGGAAAAGGAAGGTCTCGCCCCTCCTGCTGCCTCCAGGTCCGCGAAGGAAGCGAGTGA AGCCTCGGATCAGTCCAACTGCACCTCACCTGAGGCCTCCCCCAGCTCCGTGTCCTCCTGA
Citation	Bok J, Bronner-Fraser M, Wu DK. Role of the hindbrain in dorsoventral but not anteroposterior axial specification of the inner ear. Development. 2005 May;132(9):2115-24. Epub 2005 Mar 23.
Copyright	Copyright for articles in Development are retained by the authors. Permission granted by MBF.
Comments	Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (NM_001080859).

no images

Entry 4

GEISHA Id	HOXB1.Paxton.2010	Data Source	Publication
Complete cDNA Template Probe	show ATGGACAATACTAGGATGAACTCCTTCTTAGAGTATGCAATTTGTAACCGTGGGACGGGCGCCTACCACCATTTAGAGC AAAGCTCCCCTTCCTTCCCCTCTTGCTCAGGTAGCCCCTCCAGTGACACTTTTCATGGAGAAGGGGCGTACGGTGCGGG GGGCAGCCCGGTCGCGGCCGCCCATCTCCCCCCGCAGAGCCCCGGCTTCTTCCCCGCGCCTCCGGGCGCTCCGTCCCTT CGCGGCCGCTGCCCCGAGCGCCGGGTACCCAACCCAAAACTGCAGCCCCGGCTACGGCACCACCAGCTCTACCTCGGCC AGCAGGACGCGGACGCGGTGTACTTCCAGGCGGCCGGGTACTCCTCCAGCACCGGACCCCACCTCGGCTCCCTGGCAGA GGGCTATTGTGGGGCCGTAGGGCAGTACCAGCAGCAGCAGCACCTTTACGGGCAGGAGCAGCCCAGCTACTTGCCCGGG GTTTACGGCAACCTCTCGCCTTCCCTAAATGAGGACAAAGACCCCGCGTGCCCCTCCGAGCCGTGCCCCAATGCCAGCC GGGCGCGGACCTTCGATTGGATGAAAGTGAAGAGGAACCCCCCCAAGACAGCCAAAGTGTCGGAATACGGGCTGCTGGG ACAGCCCAACACCATTCGCACCAACTTCACCACCAAGCAGCTGACGGAGCTGGAGAAGGAGTTTCACTTTAACAAGTAC CTCACCCGGGCCCGGAGGGTGGAGATCGCCGCTACACTGGAGCTCAACGAAACCCAAGTCAAGATCTGGTTCCAGAACA GGCGGATGAAACAGAAGAAGAGGGAAAAGGAAGGTCTCGCCCCTCCTGCTGCCTCCAGGTCCGCGAAGGAAGCGAGTGA AGCCTCGGATCAGTCCAACTGCACCTCACCTGAGGCCTCCCCCAGCTCCGTGTCCTCCTGA
Citation	Paxton CN, Bleyl SB, Chapman SC, Schoenwolf GC. Identification of differentially expressed genes in early inner ear development. Gene Expr Patterns. 2010 Jan;10(1):31-43. Epub 2009 Nov 11.
Copyright	2009 Elsevier B.V. All rights reserved.
Comments	Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (acc # NM_001080859.1).

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

4-6

stage 5

stage 6

Mesoderm
Primitive Streak

7-11

stage 9

stage 11

Ear/Otic Placode
Endoderm
Mesoderm
Neural Plate/Tube
Primitive Streak
Somites

Entry 5

GEISHA Id	HOXB1.Alev.2010	Data Source	Publication
Complete cDNA Template Probe	show CCTCGAGACGGCTAAAACAGAAAAGTTTGGGGTGCTTTTTTTTTGTTTCCCTTTTACATTTACTCTGTGTATCTCGGAA AGAGCCCAAGGCGCTGAAGGCCTCTGGGAAGACCCGAAAAAGAAAAGAAACGAAGCAAAAACGCAACTCCTCTGCTGCC ATTTTGCACTATCGTCGCTTTACAGGGTTTCCTACACGCTCTCCGCCTGTATTACCGATCCTGGGGGTGGGAGCGTTGT CCTATCAGATAAAACGAGATAAGGGGAAGGCTGAGCCGGGGTGCTTGGGCAACGGTCATTGCCGCACCGAGTGTGAACG TGCATGGGACGAAGGCGGGGGGGTCCGCACTGGCCTCCCCCAACCGCGATGCACTGACTGCTATTTATTGTACGTCTCG ATAGCCTCACTTCTTGGGGCGAACTGGCACGGCTCCTCGTATCCCCACCCCCTCAGGCTTATCGGAGTCGAGAAAAACA TAATAGGCACGGCCAGTTGCTACCCTTTACCACCAGAAGCTTTAGCGCAGGGCGAAGTGAAAACCACGGCGAGTTTCGT TAAAGGTTGTTTTAAAGAGATAAAGGGTCATCCTGAAAAGCCTGTGGT
Citation	Alev C, Wu Y, Kasukawa T, Jakt LM, Ueda HR, Sheng G. Transcriptomic landscape of the primitive streak. Development. 2010 Sep 1;137(17):2863-74. Epub 2010 Jul 28.
Copyright	Published by The Company of Biologists 2010. This material is protected by a copyright retained by the authors. Permission granted by Dr. G Sheng.
Comments	FORWARD PRIMER CCTCGAGACGGCTAAAACAG REVERSE PRIMER ACCACAGGCTTTTCAGGATG

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

stage 4

Early Mesoderm
Primitive Streak

Entry 6

GEISHA Id	HOXB1.Bothe.2011	Data Source	Publication
Complete cDNA Template Probe	show ATGGACAATACTAGGATGAACTCCTTCTTAGAGTATGCAATTTGTAACCGTGGGACGGGCGCCTACCACCATTTAGAGC AAAGCTCCCCTTCCTTCCCCTCTTGCTCAGGTAGCCCCTCCAGTGACACTTTTCATGGAGAAGGGCGCTACGGTGCGGG GGGCAGCGCGGTCGCGGCCGCCCATCTCCCCCCGCAGAGCCCCGGCTTCTTCCCCGCCGCCTCCGGGCGCTCCGTGCCC TTCGCGGCCGCTGCCCCGAGCGCCGGGTACCCAACCCAAAATTGCAGCCCCGGCTACGGGCACCACCAGCTCTACCTCG GCCAGCAGGACGCGGACGGCGTGTACTTCCAGGCGGCCGGGTACTCCTCCAGCACCGGACCCCACCTCGGCTCCCTGGC AGAGGGCTATTGTGGGGCCGTAGGGCAGTACCAGCAGCAGCAGCACCTTTACGGGCAGGAGCAGCCCGGTTACTTGCCC GGGGTTTACGGCAACCTCTCGCCTTCCCTAAATGAGGACAAAGACCCCGCGTGCCCCTCCGAGCCGTGCCCCAATGCCA GCGCGGCGCGGACCTTCGATTGGATGAAAGTGAAGAGGAACCCCCCCAAGACAGCCAAAGTGTCGGAATACGGGCTGCT GGGACAGCCCAACACCATTCGCACCAACTTCACCACCAAGCAGCTGACGGAGCTGGAGAAGGAGTTTCACTTTAACAAG TACCTCACCCGGGCCCGGAGGGTGGAGATCGCCGCTACACTGGAGCTCAACGAAACCCAAGTCAAGATCTGGTTCCAGA ACAGGCGGATGAAACAGAAGAAGAGGGAAAAGGAAGGTCTCGCCCCTCCTGCTGCCTCCAGGTCCGCGAAGGAAGCGAG TGAAGCCTCGGATCAGTCCAACTGCACCTCACCTGAGGCCTCCCCCAGCTCCGTGTCCTCCTGA
Citation	Bothe I, Tenin G, Oseni A, Dietrich S., Dynamic control of head mesoderm patterning., Development. 2011 Jul;138(13):2807-21.
Copyright	Permission from the authors and the Company of Biologists Ltd. Copyright held by the authors.
Comments	Insufficient information provided in publication to verify exact sequence used to synthesize probe. The sequence below was obtained from NCBI (acc #XM_003642793.1)

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

4-6

stage 5

Early Endoderm
Early Mesoderm
Epiblast
Hensen's Node
Primitive Streak

7-12

stage 7

stage 10

Neural Plate/Tube
Rhombomeres
Sinus Venosus
Spinal Cord

stage 13

Rhombomeres
Spinal Cord
Trunk Mesenchyme

Entry 7

GEISHA Id	HOXB1.Chambers.2007	Data Source	Publication
Complete cDNA Template Probe	show ATGGACAATACTAGGATGAACTCCTTCTTAGAGTATGCAATTTGTAACCGTGGGACGGGCGCCTACCACCATTTAGAGC AAAGCTCCCCTTCCTTCCCCTCTTGCTCAGGTAGCCCCTCCAGTGACACTTTTCATGGAGAAGGGCGCTACGGTGCGGG GGGCAGCGCGGTCGCGGCCGCCCATCTCCCCCCGCAGAGCCCCGGCTTCTTCCCCGCCGCCTCCGGGCGCTCCGTGCCC TTCGCGGCCGCTGCCCCGAGCGCCGGGTACCCAACCCAAAATTGCAGCCCCGGCTACGGGCACCACCAGCTCTACCTCG GCCAGCAGGACGCGGACGGCGTGTACTTCCAGGCGGCCGGGTACTCCTCCAGCACCGGACCCCACCTCGGCTCCCTGGC AGAGGGCTATTGTGGGGCCGTAGGGCAGTACCAGCAGCAGCAGCACCTTTACGGGCAGGAGCAGCCCGGTTACTTGCCC GGGGTTTACGGCAACCTCTCGCCTTCCCTAAATGAGGACAAAGACCCCGCGTGCCCCTCCGAGCCGTGCCCCAATGCCA GCGCGGCGCGGACCTTCGATTGGATGAAAGTGAAGAGGAACCCCCCCAAGACAGCCAAAGTGTCGGAATACGGGCTGCT GGGACAGCCCAACACCATTCGCACCAACTTCACCACCAAGCAGCTGACGGAGCTGGAGAAGGAGTTTCACTTTAACAAG TACCTCACCCGGGCCCGGAGGGTGGAGATCGCCGCTACACTGGAGCTCAACGAAACCCAAGTCAAGATCTGGTTCCAGA ACAGGCGGATGAAACAGAAGAAGAGGGAAAAGGAAGGTCTCGCCCCTCCTGCTGCCTCCAGGTCCGCGAAGGAAGCGAG TGAAGCCTCGGATCAGTCCAACTGCACCTCACCTGAGGCCTCCCCCAGCTCCGTGTCCTCCTGA
Citation	Chambers D, Wilson L, Maden M, Lumsden A. RALDH-independent generation of retinoic acid during vertebrate embryogenesis by CYP1B1. Development. 2007 Apr;134(7):1369-83.
Copyright	© 2007
Comments	Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (acc # XM_003642793.1).

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

13-17

stage 17

Hindbrain
Neural Plate/Tube
Pharyngeal Arches and Clefts
Rhombomeres

Entry 8

GEISHA Id	HOXB1.Garcia-Dominguez.200	Data Source	Publication
Complete cDNA Template Probe	show ATGGACAATACTAGGATGAACTCCTTCTTAGAGTATGCAATTTGTAACCGTGGGACGGGCGCCTACCACCATTTAGAGC AAAGCTCCCCTTCCTTCCCCTCTTGCTCAGGTAGCCCCTCCAGTGACACTTTTCATGGAGAAGGGCGCTACGGTGCGGG GGGCAGCGCGGTCGCGGCCGCCCATCTCCCCCCGCAGAGCCCCGGCTTCTTCCCCGCCGCCTCCGGGCGCTCCGTGCCC TTCGCGGCCGCTGCCCCGAGCGCCGGGTACCCAACCCAAAATTGCAGCCCCGGCTACGGGCACCACCAGCTCTACCTCG GCCAGCAGGACGCGGACGGCGTGTACTTCCAGGCGGCCGGGTACTCCTCCAGCACCGGACCCCACCTCGGCTCCCTGGC AGAGGGCTATTGTGGGGCCGTAGGGCAGTACCAGCAGCAGCAGCACCTTTACGGGCAGGAGCAGCCCGGTTACTTGCCC GGGGTTTACGGCAACCTCTCGCCTTCCCTAAATGAGGACAAAGACCCCGCGTGCCCCTCCGAGCCGTGCCCCAATGCCA GCGCGGCGCGGACCTTCGATTGGATGAAAGTGAAGAGGAACCCCCCCAAGACAGCCAAAGTGTCGGAATACGGGCTGCT GGGACAGCCCAACACCATTCGCACCAACTTCACCACCAAGCAGCTGACGGAGCTGGAGAAGGAGTTTCACTTTAACAAG TACCTCACCCGGGCCCGGAGGGTGGAGATCGCCGCTACACTGGAGCTCAACGAAACCCAAGTCAAGATCTGGTTCCAGA ACAGGCGGATGAAACAGAAGAAGAGGGAAAAGGAAGGTCTCGCCCCTCCTGCTGCCTCCAGGTCCGCGAAGGAAGCGAG TGAAGCCTCGGATCAGTCCAACTGCACCTCACCTGAGGCCTCCCCCAGCTCCGTGTCCTCCTGA
Citation	Garcia-Dominguez M, Poquet C, Garel S, Charnay P. PIASxβ acts as an activator of Hoxb1 and is antagonized by Krox20 during hindbrain segmentation. EMBO J. 2006 June 7; 25(11): 24322442. Published online 2006 May 4.
Copyright	Copyright © 2006, European Molecular Biology Organization
Comments	Fig4C

no images

Entry 9

GEISHA Id	GHOXLAB.Bell.2004	Data Source	Publication
Forward cDNA Template Probe	show GAGCAGCAGCACCTTTACGGGCAGGAGCAGCCCGGTTACTTGCCCGGGGTTTACGGCAACCTCTCGCCTTCCCTAAATG AGGACAAAGACCCCGCGTGCCCCTCCGAGCCGTGCCCCAATGCCAGCGCGGCGCGGACCTTCGATTGGATGAAAGTGAA GAGGAACCCCCCCAAGACAGCCAAAGTGTCGGAATACGGGCTGCTGGGACAGCCCAACACCATTCGCACCAACTTCACC ACCAAGCAGCTGACGGAGCTGGAGAAGGAGTTTCACTTTAACAAGTACCTCACCCGGGCCCGGAGGGTGGAGATCGCCG CTACACTGGAGCTCAACGAAACCCAAGTCAAGATCTGGTTCCAGAACAGGCGGATGAAACAGAAGAAGAGGGAAAAGGA AGGTCTTGCTCCTCCTGCTGCCTCCAGGTCCGCGAAGGAAGCGAGTGAAGCCTCGGATCAGTCCAACTGCACCTCACCT GATGCCTCCCCCAACTCCGTGTCCTCCTGAGCCGCGGTCCCGCGGGGCACAACGACCGGATCGGGGCTGCCTTCGAAGG CCGCTGCATCCCCG
Reverse cDNA Template Probe	show GCCATTTTGCACTATCGTCGCTTTACAGGGTTTCCTACACGCTCTCCGCCTGTATTACCGATCCTGGGGGTGGGAGCGT TGTGCTATCAGATAAAACGAGATAAGGGGAAGGCTGAGCCCGGGGTGCTTTGGGCAACGGTCATTGCCGCACCGAGTGT GAACGTGCACGGGACGAAGGCCGGGGGGGTCCGCACTGCGCTCCCCCAACCGCGATGCACTGACTGCTATTTATTGTAC GTCTCGATAGCCTCACGTCTTGGGGCGAAGCTGCACGGCTCCTCGTATCCCCACCCCCTCAGGCTTATCGGAGTCCGAG AAAAACATAATTAACCACGGCCAGTTGCTACCCTTTACCACCAGAAGCTTTAGCGCAGGGCGAAGTGAAAACCACGGCG AGTTTCGTTAAAGGTTGTTTTAAAGAGATAAAGGGTCATCCTGAAAAGCCTGTGGTTTCTTAATCGGAATCTGTTTTCC CTCTACTCCCTTCCCTGTTTTTCGAAATGAAACTACCTCAGTCTAATAAAGTTTACTTTTTCCAAAAAAAAAAAAAAAA AA
Citation	Bell GW, Yatskievych TA, Antin PB. GEISHA, a whole-mount in situ hybridization gene expression screen in chicken embryos. Dev Dyn. 2004 Mar;229(3):677-87.
Copyright	Copyright © 2004 Wiley-Liss, Inc.
Comments	The probe sequence below was obtained from the GEISHA database using information provided in the publication, Geisha W24.

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

stage 4

Primitive Streak

Entry 10

GEISHA Id	Hoxb‐1.Gaunt.1996	Data Source	Publication
Complete cDNA Template Probe	show `TAGGGCAGTACCAGCAGCAGCAGCACCTTTACGGGCAGGAGCAGCCCAGCTACTTGCCCGGGGTTTACGGCAACCTCTC GCCTTCCCTAAATGAGGACAAAGACCCCGCGTGCCCCTCCGAGCCGTGCCCCAATGCCAGCCGGGCGCGGACCTTCGAT TGGATGAAAGTGAAGAGGAACCCCCCCAAGACAGGTGAGTTT`
Citation	Gaunt SJ, Strachan L. Temporal colinearity in expression of anterior Hox genes in developing chick embryos. Dev Dyn. 1996 Nov;207(3):270-80.
Copyright	Copyright © 1996 Wiley‐Liss, Inc.
Comments	The complete cDNA template sequence was obtained from the information from the publication as described in Gaunt et al. 1996.

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

4-6

stage 4

Primitive Streak

7-12

stage 7

stage 8

Headfold
Neural Plate/Tube
Paraxial Mesoderm
Primitive Streak
Somites

31-44

stage 44

Entry 11

GEISHA Id	Hoxb1.Iimura.2006	Data Source	GEISHA ISH Analysis
Complete cDNA Template Probe	show ATGGACAATACTAGGATGAACTCCTTCTTAGAGTATGCAATTTGTAACCGTGGGACGGGCGCCTACCACCATTTAGAGC AAAGCTCCCCTTCCTTCCCCTCTTGCTCAGGTAGCCCCTCCAGTGACACTTTTCATGGAGAAGGGCGCTACGGTGCGGG GGGCAGCGCGGTCGCGGCCGCCCATCTCCCCCCGCAGAGCCCCGGCTTCTTCCCCGCCGCCTCCGGGCGCTCCGTGCCC TTCGCGGCCGCTGCCCCGAGCGCCGGGTACCCAACCCAAAATTGCAGCCCCGGCTACGGGCACCACCAGCTCTACCTCG GCCAGCAGGACGCGGACGGCGTGTACTTCCAGGCGGCCGGGTACTCCTCCAGCACCGGACCCCACCTCGGCTCCCTGGC AGAGGGCTATTGTGGGGCCGTAGGGCAGTACCAGCAGCAGCAGCACCTTTACGGGCAGGAGCAGCCCGGTTACTTGCCC GGGGTTTACGGCAACCTCTCGCCTTCCCTAAATGAGGACAAAGACCCCGCGTGCCCCTCCGAGCCGTGCCCCAATGCCA GCGCGGCGCGGACCTTCGATTGGATGAAAGTGAAGAGGAACCCCCCCAAGACAGCCAAAGTGTCGGAATACGGGCTGCT GGGACAGCCCAACACCATTCGCACCAACTTCACCACCAAGCAGCTGACGGAGCTGGAGAAGGAGTTTCACTTTAACAAG TACCTCACCCGGGCCCGGAGGGTGGAGATCGCCGCTACACTGGAGCTCAACGAAACCCAAGTCAAGATCTGGTTCCAGA ACAGGCGGATGAAACAGAAGAAGAGGGAAAAGGAAGGTCTCGCCCCTCCTGCTGCCTCCAGGTCCGCGAAGGAAGCGAG TGAAGCCTCGGATCAGTCCAACTGCACCTCACCTGAGGCCTCCCCCAGCTCCGTGTCCTCCTGAGCCGCGGTCCCGCGG GGCACAACGACCGGATCGGGGCTGCCTTCGAGGGCCGCTGCTCCCCGCCGCTCCCCGCAGCCCGACCCGCACTGCCCCG CACAGCCCCGGCCGCACACGCTTCCCTCCGAGCCGCCCCTTCGGCTCCGGCCGCCTCCACGCGTGCGGTGCCCATTCCC CGTTTGCCTTCCTCTCTTAATTTATAGACCCTCCGTCAAACGTTGGACTCCAAAGGAGCGGCCGTGTCCTCGTTTATCC TTAGCAATAGGCGTTTGTCTCAGGGACGTTTCTCCCTTCTCCCCTCCCCCGATAGGAACTGCACTTTCAACTACAGAAA CTTGAAAACGAATTTAGTTCTCTCCCGCTTTAAAGATGTGCACAACGACTTTTGTCCGCACGCACCCTGAGTTTGCTGT GTTATTCCTCCCCTCGAGACGGCTAAAACAGAAAAGTTTGGGGTGCTTTTTTTTGTTTCCCTTTTACATTTACTCTGTG TATCTCGGAAAGAGCCCAAGGCGCTGAAGGCCTCTGGGAAGACCCGAAAAAGAAAAGAAACGAAGCAAAAACGCAACTC CTCTGCTGCCATTTTGCACTATCGTCGCTTTACAGGGTTTCCTACACGCTCTCCGCCTGTATTACCGATCCTGGGGGTG GGAGCGTTGTGCTATCAGATAAAACGAGATAAGGGGAAGGCTGAGCCCGGGGTGCTTTGGGCAACGGTCATTGCCGCAC CGAGTGTGAACGTGCATGGGACGAAGGCCGGGGGGGTCCGCACTGCGCTCCCCCAACCGCGATGCACTGACTGCTATTT ATTGTACGTCTCGATAGCCTCACTTCTTGGGGCGAAGCTGCACGGCTCCTCGTATCCCCACCCCCTCAGGCTTATCGGA GTCCGAGAAAAACATAATTAACCACGGCCAGTTGCTACCCTTTACCACCAGAAGCTTTAGCGCAGGGCGAAGTGAAAAC CACGGCGAGTTTCGTTAAAGGTTGTTTTAAAGAGATAAAGGGTCATCCTGAAAAGCCTGTGGTTTCTTAATCGGAATCT GTTTTCCCTCTACTCCCTTCCCTGTTTTTCGAAATGAAACTACCTCAGTCTAATAAAGTTTACTTTTTCCA
Citation	Tadahiro Iimura, Olivier Pourquié. Collinear activation of Hoxb genes during gastrulation is linked to mesoderm cell ingression. Nature. 2006 Aug 3;442(7102):568-71. Epub 2006 Jun 7. DOI: 10.1038/nature04838.
Copyright	Copyright © 2006 Nature Publishing Group.
Comments	As insufficient information is provided in publication to verify exact sequence used to synthesize probe, the sequence above was obtained from NCBI (accession number NM_001080859.2).

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

1-3

stage 3

Primitive Streak

HH3+

4-5

stage 4

stage 5

Early Mesoderm
Primitive Streak

Entry 12

GEISHA Id	Hoxb1.Bel-Vialar.2002	Data Source	GEISHA ISH Analysis
Complete cDNA Template Probe	show ATGGACAATACTAGGATGAACTCCTTCTTAGAGTATGCAATTTGTAACCGTGGGACGGGCGCCTACCACCATTTAGAGC AAAGCTCCCCTTCCTTCCCCTCTTGCTCAGGTAGCCCCTCCAGTGACACTTTTCATGGAGAAGGGCGCTACGGTGCGGG GGGCAGCGCGGTCGCGGCCGCCCATCTCCCCCCGCAGAGCCCCGGCTTCTTCCCCGCCGCCTCCGGGCGCTCCGTGCCC TTCGCGGCCGCTGCCCCGAGCGCCGGGTACCCAACCCAAAATTGCAGCCCCGGCTACGGGCACCACCAGCTCTACCTCG GCCAGCAGGACGCGGACGGCGTGTACTTCCAGGCGGCCGGGTACTCCTCCAGCACCGGACCCCACCTCGGCTCCCTGGC AGAGGGCTATTGTGGGGCCGTAGGGCAGTACCAGCAGCAGCAGCACCTTTACGGGCAGGAGCAGCCCGGTTACTTGCCC GGGGTTTACGGCAACCTCTCGCCTTCCCTAAATGAGGACAAAGACCCCGCGTGCCCCTCCGAGCCGTGCCCCAATGCCA GCGCGGCGCGGACCTTCGATTGGATGAAAGTGAAGAGGAACCCCCCCAAGACAGCCAAAGTGTCGGAATACGGGCTGCT GGGACAGCCCAACACCATTCGCACCAACTTCACCACCAAGCAGCTGACGGAGCTGGAGAAGGAGTTTCACTTTAACAAG TACCTCACCCGGGCCCGGAGGGTGGAGATCGCCGCTACACTGGAGCTCAACGAAACCCAAGTCAAGATCTGGTTCCAGA ACAGGCGGATGAAACAGAAGAAGAGGGAAAAGGAAGGTCTCGCCCCTCCTGCTGCCTCCAGGTCCGCGAAGGAAGCGAG TGAAGCCTCGGATCAGTCCAACTGCACCTCACCTGAGGCCTCCCCCAGCTCCGTGTCCTCCTGAGCCGCGGTCCCGCGG GGCACAACGACCGGATCGGGGCTGCCTTCGAGGGCCGCTGCTCCCCGCCGCTCCCCGCAGCCCGACCCGCACTGCCCCG CACAGCCCCGGCCGCACACGCTTCCCTCCGAGCCGCCCCTTCGGCTCCGGCCGCCTCCACGCGTGCGGTGCCCATTCCC CGTTTGCCTTCCTCTCTTAATTTATAGACCCTCCGTCAAACGTTGGACTCCAAAGGAGCGGCCGTGTCCTCGTTTATCC TTAGCAATAGGCGTTTGTCTCAGGGACGTTTCTCCCTTCTCCCCTCCCCCGATAGGAACTGCACTTTCAACTACAGAAA CTTGAAAACGAATTTAGTTCTCTCCCGCTTTAAAGATGTGCACAACGACTTTTGTCCGCACGCACCCTGAGTTTGCTGT GTTATTCCTCCCCTCGAGACGGCTAAAACAGAAAAGTTTGGGGTGCTTTTTTTTGTTTCCCTTTTACATTTACTCTGTG TATCTCGGAAAGAGCCCAAGGCGCTGAAGGCCTCTGGGAAGACCCGAAAAAGAAAAGAAACGAAGCAAAAACGCAACTC CTCTGCTGCCATTTTGCACTATCGTCGCTTTACAGGGTTTCCTACACGCTCTCCGCCTGTATTACCGATCCTGGGGGTG GGAGCGTTGTGCTATCAGATAAAACGAGATAAGGGGAAGGCTGAGCCCGGGGTGCTTTGGGCAACGGTCATTGCCGCAC CGAGTGTGAACGTGCATGGGACGAAGGCCGGGGGGGTCCGCACTGCGCTCCCCCAACCGCGATGCACTGACTGCTATTT ATTGTACGTCTCGATAGCCTCACTTCTTGGGGCGAAGCTGCACGGCTCCTCGTATCCCCACCCCCTCAGGCTTATCGGA GTCCGAGAAAAACATAATTAACCACGGCCAGTTGCTACCCTTTACCACCAGAAGCTTTAGCGCAGGGCGAAGTGAAAAC CACGGCGAGTTTCGTTAAAGGTTGTTTTAAAGAGATAAAGGGTCATCCTGAAAAGCCTGTGGTTTCTTAATCGGAATCT GTTTTCCCTCTACTCCCTTCCCTGTTTTTCGAAATGAAACTACCTCAGTCTAATAAAGTTTACTTTTTCCA
Citation	Sophie Bel-Vialar, Nobue Itasaki, Robb Krumlauf. Initiating Hox gene expression: in the early chick neural tube differential sensitivity to FGF and RA signaling subdivides the HoxB genes in two distinct groups. Development 2002 Nov;129(22):5103-15.
Copyright	Copyright © The Company of Biologists Limited 2002.
Comments	As insufficient information is provided in publication to verify exact sequence used to synthesize probe, the sequence above was obtained from NCBI (accession number NM_001080859.2).

Stage

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13-15

stage 15

Intermediate Mesoderm
Lateral Plate Mesoderm
Rhombomeres
Spinal Cord

Entry 13

GEISHA Id	HOXB1.Trevers.2023	Data Source	GEISHA ISH Analysis
Complete cDNA Template Probe	show GTTCGAGGGCCAGCGATGCATGGAAGGAAGTTTTACAGCTTTGACATACTATCTAAAGGTTGTAGGGCAGGCGGAATCC CCCCCAAAACAGGCTGACCCTCCTCCATCAGTGGCAGATGGACAATACTAGGATGAACTCCTTCTTAGAGTATGCAATT TGTAACCGTGGGACGGGCGCCTACCACCATTTAGAGCAAAGCTCCCCTTCCTTCCCCTCTTGCTCAGGTAGCCCCTCCA GTGACACTTTTCATGGAGAAGGGCGCTACGGTGCGGGGGGCAGCGCGGTCGCGGCCGCCCATCTCCCCCCGCAGAGCCC CGGCTTCTTCCCCGCCGCCTCCGGGCGCTCCGTGCCCTTCGCGGCCGCTGCCCCGAGCGCCGGGTACCCAACCCAAAAT TGCAGCCCCGGCTACGGGCACCACCAGCTCTACCTCGGCCAGCAGGACGCGGACGGCGTGTACTTCCAGGCGGCCGGGT ACTCCTCCAGCACCGGACCCCACCTCGGCTCCCTGGCAGAGGGCTATTGTGGGGCCGTAGGGCAGTACCAGCAGCAGCA GCACCTTTACGGGCAGGAGCAGCCCGGTTACTTGCCCGGGGTTTACGGCAACCTCTCGCCTTCCCTAAATGAGGACAAA GACCCCGCGTGTCCCTCCGAGCCGTGCCCCAATGCCAGCGCGGCGCGGACCTTCGATTGGATGAAAGTGAAGAGGAACC CTCCCAAGACAGCCAAAGTGTCGGAATACGGGCTGCTGGGCCAGCCCAACACCATTCGCACCAACTTCACCACCAAGCA GCTGACGGAGCTGGAGAAGGAGTTTCACTTTAACAAGTACCTCACCCGGGCCCGGAGGGTGGAGATCGCCGCTACACTG GAGCTCAACGAAACCCAAGTCAAGATCTGGTTCCAGAACAGGCGGATGAAACAGAAGAAGAGGGAAAAGGAAGGTCTCG CCCCTCCTGCTGCCTCCAGGTCCGCGAAGGAAGCGAGTGAAGCCTCGGATCAGTCCAACTGCACCTCACCTGAGGCCTC CCCCAGCTCCGTGTCCTCCTGAGCCGCGGTTCCGCGGGGCACAACGACCGGATCGGGGCTGCCTTCGAGGGCCGCTGCT CCCCGCCGCTCCCCGCAGCCCGACCCGCACTGCCCCGCACAGCCCCGGCCGCACACGCTTCCCTCCGAGCCGCCCCTTC GGCTCCGGCCGCCTCCACGCGTGCGGTGCCCATTCCCCGTTTGCCTTCCTCTCTTAATTTATAGACCCTCCGTCAAACG TTGGACTCCAAAGGAGCGGCCGTGTCCTCGTTTATCCTTAGCAATAGGCGTTTGTCTCAGGGACGTTTCTCCCTTCTCC CCTCCCCCGATAGGAACTGCACTTTCAACTACAGAAACTTGAAAACGAATTTAGTTCTCTCCCGCTTTAAAGATGTGCA CAACGACTTTTGTCCGCACGCACCCTGAGTTTGCTGTGTTATTCCTCCCCTCGAGACGGCTAAAACAGAAAAGTTTGGG GTGCTTTTTTTTTGTTTCCCTTTTACATTTACTCTGTGTATCTCGGAAAGAGCCCAAGGCGCTGAAGGCCTCTGGGAAG ACCCGAAAAAGAAAAGAAACGAAGCAAAAACGCAACTCCTCTGCTGCCATTTTGCACTATCGTCGCTTTACAGGGTTTC CTACACGCTCTCCGCCTGTATTACCGATCCTGGGGGTGGGAGCGTTGTGCTATCAGATAAAACGAGATAAGGGGAAGGC TGAGCCCGGGGTGCTTTGGGCAACGGTCATTGCCGCACCGAGTGTGAACGTGCATGGGACGAAGGCCGGGGGGGTCCGC ACTGCGCTCCCCCAACCGCGATGCACTGACTGCTATTTATTGTACGTCTCGATAGCCTCACGTCTTGGGGCGAAGCTGC ACGGCTCCTCGTATCCCCACCCCCTCAGGCTTATCGGAGTCCGAGAAAAACATAATTAACCACGGCCAGTTGCTACCCT TTACCACCAGAAGCTTTAGCGCAGGGCGAAGTGAAAACCACGGCGAGTTTCGTTAAAGGTTGTTTTAAAGAGATAAAGG GTCATCCTGAAAAGCCTGTGGTTTCTTAATCGGAATCTGTTTTCCCTCTACTCCCTTCCCTGTTTTTCGAAATGAAACT ACCTCAGTCTAATAAAGTTTACTTTTTCCA
Comments	Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (NM_001080859 ).