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A chicken embryo gene expression database

	Anatomical Location
	Stage
	Gene Name
	GEISHA ID
	Multiple Parameters

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CDX1
caudal type homeobox 1

Gene

Official Symbol	CDX1
Official Full Name	caudal type homeobox 1
CGNC ID	4232
also known as	CDX-A, CDXA, CHOX-CAD1, CHox-cad, homeobox protein CDX-1\|caudal type homeo box transcription factor 1\|caudal type homeobox transcription factor 1\|caudal-type homeodomain protein A\|caudal-type homeodomain protein, CdxA\|homeobox protein CHOX-CAD, Homeobox protein CHOX-CAD, CHOX-CAD, CdxA
gene type	protein-coding

Genomic Map

	Ensembl
	NCBI
	UCSC
	Gallus-Browse

Sequence Information

Genomic
RNA	NM_204676
Polypeptide	NP_990007
Sequence Clusters/ESTs	Unigene

Gene Expression

In Situ Hybridization	GEISHA
EST Profile	Gga.210

Orthology

	Entrez Gene	Ensembl Gene	Genetic Phenotypes	MOD
Fruit Fly
Human	1044	ENSG00000113722		MIM:600746
Mouse	12590	ENSMUSG00000024619	All phenotypic alleles (6):Targeted, knock-out(3) Targeted, other(3)	MGI:88360
Xenopus	395055, 397695			485395
Zebrafish	100004956, 405762		ZDB-GENE-070615-29, ZDB-GENE-050510-1	ZFIN:ZDB-GENE-070615-29, ZFIN:ZDB-GENE-050510-1

Gene Ontology

Molecular Function	RNA polymerase II distal enhancer sequence-specific DNA binding, more...
Biological Process	anterior/posterior pattern specification, bone morphogenesis, multicellular organismal development
Cellular Component	nucleus

Links to other databases

Entrez Gene	395397
Ensembl Gene	ENSGALG00000005679
KEGG	gga:395397

Entry 1

GEISHA Id	ChEST637p4	Data Source	GEISHA ISH Analysis
Forward cDNA Template Probe	show `AGAATGAGCCGGTGGGATGCTTCCTGCACGGTCTTCCTGGTGATCCAGCTGCCTGCTGCTTTGGAGCAGCTTTAGTGAG GCTGAACTAGGGGAAAGGCTTGGCTGGACTCGAAGCAGAATAAATCTCAGCTGAGATTGTCTGCAGGATCTGCCATACC TGGAGCGAGTTGGACAACAGGAGCTGGGTAGGACCCTCAGCAGTGGGGCTGGAGGGGGAATGG`

Stage

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Location (click to highlight)

Comments (click to highlight)

1-3

stage 3

Epiblast
Primitive Streak

4-6

stage 4

stage 5

stage 6

Early Mesoderm
Epiblast
Primitive Streak

7-12

stage 7

stage 8

stage 9

stage 10

stage 12

Early Mesoderm
Extraembryonic
Forebrain
Heart
Hindbrain
Intermediate Mesoderm
Lateral Plate Mesoderm
Midbrain
Neural Plate/Tube
Notochord
Primitive Streak

13-18

stage 13

stage 17

stage 18

Extraembryonic
Gut
Head Mesenchyme
Heart
Lateral Plate Mesoderm
Spinal Cord

19-24

stage 20

stage 21

Gut

stage 25

Gut

Entry 2

GEISHA Id	CdxA.Matsushita.2002	Data Source	Publication
Complete cDNA Template Probe	show CCCCCTCCACCAGCCATAGACACTGAGAGATAAGCACTACACGGCAGAGCTTGTTGCTGAGCGCCCAAAGACACCACGT CCCCTGGGGCATGGTGGCTCTGTTGCCTTCCCAAGAGGCTGATGAGCTCTGTCCTACACAAAGCCCATACGTTAGGTAG TGCTGTTCTCCTGTAGGAAACGTGCGCTGGTCTTCGGTATTGGTAGCCCAAAACCAGTGGGATGAGTCTTTAAGTGGTG CTGGAGGACCCTTTCTGTGGCACATCAGAATGAGCCGGTGGGATGCTTCCTGCACGGTCTTCCTGGTGATCCAGCTGCC TGCTGCTTTGGAGCAGCTTTAGTGAGGCTGAACTAGGGGAAAGGCTTGGCTGGACTCGAAGCAGAATAAATCTCAGCTG AGATTGTCTGCAGGATCTGCCATACCTGGAGCGAGTTGGACAACAGGAGCTGGGTAGGACCCTCAGCAGTGGGGCTGGA GGGGGAATGGGGGCTCCTTAAACTGAGACAATGACAGTGAGTGTCCCCCATGTCCCCCAGCCACCATCCCCAGCTCCAT CCCTGCAGCAACTCAGGGCCATCGCGAGACCTGCAGACATCTGTCTCACAGATGGACCATCTGCGGAGGTTTTGAGACC ACCTTCCAGCATGGAGGAACAAGAACAAGGTTTGCAGTTAGGACACTGGACAGCTCTAGGTTGCCCAGAGGGGCCACTC ATCTACCGATGGCATTGCAGAACCTGCACAGCTCCATGCTGCACCAAGGCACTGCCAGCTGCCAGGACCATCATGGTGA TGGGACATGTCCTGGCACAAGATGATGGATAGCTGGCTTCCATAGAGAGGGATGGGTGGATTTGTGCTGTTTTCTCTGA AACACAAAAGGCTCTGGGTTTTGCCCACTTTGTACTCCTCCATGTGCTGCACATTGGTAACCAATGGCTTTTTTTTCCT GCTGGAAATCCACAGTTAAAATTCCCCTTAATCCTGCTGACTCCTGGGATCTCTACTGGCCCAGCTACCTTACAGCCCA GTTTTGGATGCCCCAAAGGGCGTGCTGGGACACAGGAGGGTTTGAGGCTCCTGCTTGGTTCTGTGGCTTCCCAAGACCA AGGTGAGGGTGCAGAGGCTCTGATGGTTCTCTCCTAGCACCATCATGCTGAGCCCCAGCAGGAACAAGAAGTGGAGGTG TCCCTGTTGCCTGCAGAGCCCCTCACCCATTCCCAGCCCATTCTGGCCCAGAACTCACAGTGTTAGGGGTTTTAAATAC TGGGATTTAAGCTCCTTGACACCCACTGCACCTACAGCCCCTTAATAGGGTCTGCATCCCCCACCATGGCGACCAGTGA CACCTCCCTGGGGCCACCACTGCTACTTTGCAGCAAAGGCAGACACCGGTGTTGGCTTGGGACTTCAGCTCAGGGCTTG TGTACAGAAGGCAGAACGTTTTATTTTCTAGGCTTTGGTCAAAATAAAAGCGAGCAGGAGCCCTGT
Citation	Matsushita S, Ishii Y, Scotting PJ, Kuroiwa A, Yasugi S. Pre-gut endoderm of chick embryos is regionalized by 1.5 days of development. Dev Dyn. 2002 Jan;223(1):33-47.
Copyright	Copyright © 2002 Wiley-Liss., Inc.
Comments	Insufficient information provided to identify probe sequence. Matsushita et al indicate that probe was generated using a 711 nt fragment of the 3' UTR. Entire UTR is mapped above.

Stage

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7-10

stage 10

Endoderm
Endoderm, early
Extraembryonic

extraembryonic junctional endoderm

Entry 3

GEISHA Id	CdxA.Hiramatsu.2004	Data Source	Publication
Complete cDNA Template Probe	show GCTGCGTGACACCCGGCCGCTTCGGCACGGAGCGGCGCAGCGCGGTGCATCGGCACAGCATGAGCACAGAGCCAGGTGG AGAAGATGTATGTAGGCTATCTTTTGGATAAGGACACCAACATGTATCCCAGTCCCGTCCGGCATCCCAGCCTCAACCT CAACCCCCAGAACTACGTGCCGGGGCCACCCCAGTACTCGGACTTCGCCAGCTACCACCATGTGCCAGGGATTAACAAC GACCCGCACCATGGGCAGCCCGCAGCTGCCTGGGGCTCACCCTACACCCCTGCCAAGGAGGACTGGCACTCATACGGCA CCGCTGCCGCCTCCGCCGCCACCAACCCGGGGCAGTTTGGATTTAGCCCCCCGGATTTTAACCCCATGCAGCCCCATGC GGGCTCTGGACTCCTGCCTCCAGCCATCAGCAGCTCGGTGCCACAGCTGTCCCCTAATGCACAGAGGCGCACCCCGTAC GAATGGATGAGGCGCAGTATTCCCAGCACCAGCAGCAGCGGCAAGACGAGGACAAAGGACAAGTACCGGGTGGTGTACA CGGACCACCAACGCCTGGAGCTGGAGAAGGAATTTCACTACAGCCGCTACATCACCATCCGCCGTAAGGCCGAGCTGGC TGCTGCCCTGGGGCTCACTGAACGGCAGGTGAAAATCTGGTTTCAGAACCGGAGGGCGAAAGAGAGGAAGGTGAATAAA AAGAAGCTGCAGCAGCAGAGCCAGCCCACCAGCACCACCACGCCAACCCCCCCAGCCGTGGGCACGCCAGGGCCCATGG GGACCCTCTGCAGTGGCAGTGCCCCAAGCCTTGTCTCCTCATCTCCGCTCACCATCAAGGAGGAGTTCATGCCTTAGCC CCCTCCACCAGCCATAGACACTGAGAGATAAGCACTACACGGCAGAGCTTGTTGCTGAGCGCCCAAAGACACCACGTCC CCTGGGGCATGGTGGCTCTGTTGCCTTCCCAAGAGGCTGATGAGCTCTGTCCTACACAAAGCCCATACGTTAGGTAGTG CTGTTCTCCTGTAGGAAACGTGCGCTGGTCTTCGGTATTGGTAGCCCAAAACCAGTGGGATGAGTCTTTAAGTGGTGCT GGAGGACCCTTTCTGTGGCACATCAGAATGAGCCGGTGGGATGCTTCCTGCACGGTCTTCCTGGTGATCCAGCTGCCTG CTGCTTTGGAGCAGCTTTAGTGAGGCTGAACTAGGGGAAAGGCTTGGCTGGACTCGAAGCAGAATAAATCTCAGCTGAG ATTGTCTGCAGGATCTGCCATACCTGGAGCGAGTTGGACAACAGGAGCTGGGTAGGACCCTCAGCAGTGGGGCTGGAGG GGGAATGGGGGCTCCTTAAACTGAGACAATGACAGTGAGTGTCCCCCATGTCCCCCAGCCACCATCCCCAGCTCCATCC CTGCAGCAACTCAGGGCCATCGCGAGACCTGCAGACATCTGTCTCACAGATGGACCATCTGCGGAGGTTTTGAGACCAC CTTCCAGCATGGAGGAACAAGAACAAGGTTTGCAGTTAGGACACTGGACAGCTCTAGGTTGCCCAGAGGGGCCACTCAT CTACCGATGGCATTGCAGAACCTGCACAGCTCCATGCTGCACCAAGGCACTGCCAGCTGCCAGGACCATCATGGTGATG GGACATGTCCTGGCACAAGATGATGGATAGCTGGCTTCCATAGAGAGGGATGGGTGGATTTGTGCTGTTTTCTCTGAAA CACAAAAGGCTCTGGGTTTTGCCCACTTTGTACTCCTCCATGTGCTGCACATTGGTAACCAATGGCTTTTTTTTCCTGC TGGAAATCCACAGTTAAAATTCCCCTTAATCCTGCTGACTCCTGGGATCTCTACTGGCCCAGCTACCTTACAGCCCAGT TTTGGATGCCCCAAAGGGCGTGCTGGGACACAGGAGGGTTTGAGGCTCCTGCTTGGTTCTGTGGCTTCCCAAGACCAAG GTGAGGGTGCAGAGGCTCTGATGGTTCTCTCCTAGCACCATCATGCTGAGCCCCAGCAGGAACAAGAAGTGGAGGTGTC CCTGTTGCCTGCAGAGCCCCTCACCCATTCCCAGCCCATTCTGGCCCAGAACTCACAGTGTTAGGGGTTTTAAATACTG GGATTTAAGCTCCTTGACACCCACTGCACCTACAGCCCCTTAATAGGGTCTGCATCCCCCACCATGGCGACCAGTGACA CCTCCCTGGGGCCACCACTGCTACTTTGCAGCAAAGGCAGACACCGGTGTTGGCTTGGGACTTCAGCTCAGGGCTTGTG TACAGAAGGCAGAACGTTTTATTTTCTAGGCTTTGGTCAAAATAAAAGCGAGCAGGAGCCCTGTGAAAAAAAAAAAAAA AAAAAAA
Citation	Hiramatsu H, Yasugi S. Molecular analysis of the determination of developmental fate in the small intestinal epithelium in the chicken embryo. Int J Dev Biol. 2004 Dec;48(10):1141-8.
Copyright	"Reprinted from Int. J. Dev. Biol., 48,Hiramatsu H, Yasugi S , Molecular analysis of the determination of developmental fate in the small intestinal epithelium in the chicken embryo, 1141-8, Copyright (2004), with permission from Copyright © 2004 UBC Press". All rights reserved.
Comments	Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (acc # AB046532 ).

Stage

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Location (click to highlight)

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4-6

stage 6

Midgut

Small intestine

7-12

stage 9

stage 12

Midgut

Small intestine

31-44

stage 44

Midgut

Comparison with other molecules
Small intestine

Entry 4

GEISHA Id	CdxA.Chapman.2008	Data Source	Direct Submission
Complete cDNA Template Probe	show AAGCTTTTCCAGCCACAGGCCCCTCTGGCAATACATAGGCCAAAGAGGAGGAAAAGAAGGAAGTTATCACTGGTGGATC TTTATGGCCCAATTATCGTCCCCTGTCCACCCTGGAGCTGGTGGCACGCTGCTAGAAGGCACCTGGCCGTGCTGCTCCG TGCTGAGCCCTTCACCTGCTGCAGGAGGGTGCAGGTAGGGTGCTCATGGACCCATGGAGCCCTGCACCCCCAGCCCAGA CATGGCTGGGACATGCCCAGTAGCAGCAGGGAAGCTCTTGTGTGTTGCATGCGCTGAGCTCCTACAACACAGCAGCTTT GCTGGCTTTGTTACCATTTTCCTTTTAACCCCATGAATCTGAAAAGCAATCCCACCTTCAAACCTCTTCACGGATTCAT AGCTACAATTGCAAAAAATGGTGAAAGTCTGCTGTTTTATCCTCTTCTCTCAATTGCATCTTAAACCCTTCCCTTCCCT TCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCCACACACTGTGACTG CAGAAGGGACCAGCGATGTGCTGCAATGGCACAGAGGTGATCTCAGTCCCTCATCCCCTCCAGAGCACAGGTGTGCCTG GCCTTCCTGGTGATGAGTGGATGGCCTCTGCTTGGGGACAGACGTGATTTTGGGGCATGCATCCACAAAATCATAGAAT ATCCCAATGGATTGGACCCATAAGGATAATTGTGTCCAGCTCTGTCTGTGCATCCTGTTCTCTGTGGCTGGGCTGAACT TGGCTATGGGGCTCGAGGGATGAGTTTGCCCCCAGATGCTATAAATGGAGGGGGACCCAGAGTGACCTCTTCCCACCAA TCCCATTTCCAAAACTGGCAGATGCATTGCTGGGGTTCGGTGTCCCCATCAAAAGTGCTGGGGCAATTCCATTGGGCAG TTCATGGGTGATTCAGTCCTTCAGCCAGGATTTGATGTGAGCTCTCACCCCAAGCTGCCCTTCTCCTGGCGCACAAATG GCTTTAGGGACAGGGTGACCTCCTTTGGGGCATCTTCAAACACAAAGCCAGCTGTGCCACACTGTCCCCAAAACCAGCT GCCACAAAGGGACCGTGGCCGGTGGCATGGGGACAGCCCGTGCTGGTGACCACAGAGGGAACGCGGGGCGGTGGGAGGT TCGGATTGCCCCGCACGGCTGGGGTTCCTGCACTTTGAAATGCAACCCTGCCTTTCAATGCAAATGCTGCGAGAGGTTG GGCCCAATAAAAGCCTGTGGGCAGGGAGGTGCCTGGCCCCGGGACACAGCTCCCCAAGGCGCCCAGGTGAGCGCGGTGA AGGAGGGGCGGCCGCTGCGTGACACCCGGCCGCTTCGGCACGGAGCGGCGCAGCGCGGTGCATCGGCACAGCATGAGCA CAGAGCCAGGTGGAGAGGATGTATGTAGGCTATCTTTTGGATAAGGACACCAACATGTATCCCAGTCCCGTCCGGCATC CCAGCCTCAACCTCAACCCCCAGAACTACGTGCCGGGGCCACCCCAGTACTCGGACTTCGCCAGCTACCACCATGTGCC AGGGATTAACAACGACCCGCACCATGGGCAGCCCGCAGCCGCCTGGGGCTCACCCTACACCCCTGCCAAGGAGGACTGG CACTCATACGGCACCGCTGCCGCCTCCGCCGCCACCAACCCGGGGCAGTTTGGATTTAGCCCCCCGGATTTTAACCCCA TGCAGCCCCATGCGGGCTCTGGACTCCTGCCTCCAGCCATCAGCAGCTCGGTGCCACAGCTGTCCCCTAATGCACAGAG GCGCACCCCGTACGAATGGATGAGGCGCAGTATTCCCAGCACCAGCAGCAGCGGTAAGGAAACCCCCAGCCCTACACCT GGGCTCCTTCCTCCACCTGGGAGCCCTCAGCTTGGAGTCCTGCAGGGCCGGATCCTGCTCTGGGACCTACCCCAATGGG GAGAGCTGTGGGGCTGGCGAGGTGGCATGGATTGAGGATGGGCATGGAGAGCATTGGTGTGCGGGTGACCCCGTTCTGC TGGCAGTCAGAATGAGAGCTCTGCTCTGCGTATGGGAAGTCCTTGTCATGGCCAGTCCAGGGTAGTTCATGCTCATCGT CATGGTGGTGGGGTGCTCCTGTTGGCGCAGTGCTGTGCTGTGTGTGCAGGGTGCTGCAAGCACTGCATGTGCACGGCAC TCACTGCACAGAATCGGCGAGCACATACAGGCAATACTGAGTGCTCAAAGTGCATGCAAGGTGCAATGTGTTGGGGACC GTGCCACATGCAATGTGTGTGTGGGTGCTCTGGGTGTTGCACGGCACACAAACGTATGCACAGCTCCTGTGTCTGGCAC TGGGCAGCCATACTGTTCCCGTGCCCTATCTCCTGTCCCCATGTCCCATCCCCTGTTCCTCTGCCTTATCCCCCGTCCC TTGTCCCTGTATCCTGTCCCCGACCCCGGGGTCTTGTCCTGCTGAACTCCTGACCCCGGCGGGGTGGGTGGGTGAAAGT GTCCGTGCCCTGCAGCCCTCCGCCCGTGGACGCCCCACTGCCCACTTCAAAGGCGGTGGGCAGTCCCCCCTTGGGGCCA GCCCAAATTGACACGGGCTTCTCTTTGTCATGGAGATGCCGCCGGCTCCTTTGGCATTGAGGCGAGGTTGGGGAGGGCC TTTGCCCTTTCATGTTCCCCTCCAGGGTTTCCAGCCCGACCGCCGTCCTCTCCGTCTCCCCCTTGTGCGGGGGCTCCCT GTTTGAAAATGGTGTAAAATGCCTCATTTGTTGGCTTGCTTCTGGTTTCCTGGCATCGCTGCGTTGGGTTTTCCCCATG CATGGCGCTGGGGATGTGACAGCCAAGAGCTGCACGGAGACTGAGTGGTGCTGAAGGGTCTGGGCACGGCGATGCGCTG CGGTGCCCACATCCTCACTGTCCTACCCCCTGCTCCTCTGCCCCATCCCCAGGCCCCATGCTCTGGAAATTGCATGGAA ATTGCTGTGAGACTGTGCTGGATGCTGGGGTTGGGGTCATCCCGGTGGGAGCGGGGGTTGCGGTGGGGCTGAGCATCCC AGGAGGTGGAAAGCAGCGAGCTCTGCTCTGCAAGAAGGAGGGAGAGGCAGGATGGTATTTCCTGGTCCATTTTAAGCAC TGAATATAACTCTTTAGGAAAATTGCCCCCCTCTCCTCATACGTGTTGAATGGGAGCCCACAGCTTCTGTGGGATTTGT AGGTCCAAACAGTTCGGTGTCTTCTGGGAAAGGTGGGAGGGAAAATGAAGGAGGGGGGGGAAACCATAAGAACACCTCT GGATGAAGGGAGTGAGACATAGCGAGGGCAGGAAGGTTCCCCTGCCTGAGTCACACAGCAATGGAGTGATTGAATTCTG GAAAAATCAGCCGTTGCGCAGTTTGTATCTCTTAGATTGGACGCACACAAAGGGACAAATGAGCCAGCTGTTGTCCCCT GCACGTGAAGCAGAGAGGGTGGCAGGAGCAAAACCCCCTTGGTTATATGGGACGCCTCTCTACAAACCCCCCCAGCCTT GAGGTTTCTGTCCATGGGACCGTGCAGTTGAATTCAAACCCACGGCGCCTGCCCAGGCTGCCTTTACATAAACCAGGAG GTGGGTTTGACACAGATAAGGGTGAAATGTTTTATTGGAATCAATAAACTGTACATTAATCAGGCTGGATGGGTTATAC CCCTCTCCACGCTGTGGGAGTAGGAAATGAATGCGCGGGCTATAAATACGGAGAGCTCCATTGCGAGCGCTGTAAATCA TCCGAGGGCTGTAAATTAAGGTTCCCTCTGTCTTCCCTTGTATAAACAGCCATCGGCCGCGGCGTGAAGGCGCTCGGAA GGAGCCTTGCCATGCTCAGAGGCAATGCAAGGCAGGGACGGAGCGTGCCGGGGGGTTCTGCCGGCGTGATGGAGAGCTG GGAGAAATCGATGAGAAATCTCCCAGTGACTCAGTGCGGAGTCAGACCTCATGGGGCGATGAGCTGATATAGCTGCTGC TAAGAACGTGCGTGCCTCACCCAGCAGAGCCAGCCACGGCACAGGGCAAAGCTCAGCCCAGGTAACGGATGCTCAAGTG CCCTAAATTGGGAAACAGGAGGAACAAGATGTCCCCGTGCCTCCTTTCTTCCCGAGCATCAGCCCTTTTTCTGCTCATA AAATCTTCACGAGCACAGTGTCAGACCCTCACGCTTCTCCTTACTCGTAATTATTTGCAAACTTCCTTGTGAATGGCAC CCCTGCTCTATAAAAAGCTCAAGAAGGCGCTGGAAACGGCAGCGCGCTGAACTTTGAAGTTCACCCCCCTTCC
Comments	Probe apparently genomic fragment overlapping with coding exons. Images Provided by Susan Chapman.

Stage

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Location (click to highlight)

Comments (click to highlight)

stage 4

Primitive Streak

Entry 5

GEISHA Id	CdxA.Kumar.2003	Data Source	Publication
Complete cDNA Template Probe	show GCTGCGTGACACCCAGCCGCTTCGGCACGGAGCGGCGCAGCGCGGTGCATCGGCACAGCATGAGCACAGAGCCAGGTGG AGAAGATGTATGTAGGCTATCTTTTGGATAAGGACACCAACATGTATCCCAGTCCCGTCCGGCATCCCAGCCTCAACCT CAACCCCCAGAACTACGTGCCGGGGCCACCCCAGTACTCGGACTTCGCCAGCTACCACCATGTGCCAGGGATTAACAAC GACCCTCACCATGGGCAGCCCGCAGCCGCCTGGGGCTCACCCTACACCCCTGCCAAGGAGGACTGGCACTCATATGGCA CCGCTGCCGCCTCCGCCGCCACCAACCCAGGGCAGTTTGGATTTAGCCCCCCGGATTTTAACCCCATGCAGCCCCATGC GGGCTCTGGACTCCTGCCTCCAGCCATCAGCAGCTCGGTGCCACAGCTGTCCCCTAATGCACAGAGGCGCACCCCGTAC GAATGGATGAGGCGCAGTATTCCCAGCACCAGCAGCAGCGGCAAGACGAGGACAAAGGACAAGTACCGGGTGGTGTACA CGGACCACCAACGCCTGGAGCTGGAGAAGGAATTTCACTACAGCCGCTACATCACCATCCGCCGTAAGGCCGAGCTGGC TGCTGCCCTGGGGCTCACTGAACGGCAGGTGAAAATCTGGTTTCAGAACCGGAGGGCGAAAGAGAGGAAGGTGAATAAA AAGAAGCTGCAGCAGCAGAGCCAGCCCACCAGCACCACCACGCCAACCCCCCCAGCCGTGGGCACGCCAGGGCCCATGG GGACCCTCTGCAGTGGCAGTGCCCCAAGCCTTGTCTCCTCATCTCCGCTCACCATCAAGGAGGAGTTCATGCCTTAGCC CCCTCCACCAGCCATAGACACTGAGAGATAAGCACTACACGGCAGAGCTTGTTGCTGAGCGCCCAAAGACACCACGTCC TCTGGGGCATGGTGGCTCTGTTGCCTTCCCAAGAGGCTGATGAGCTCTGTCCTACACAAAGCCCATACGTTAGGTAGTG CTGTTCTCCTGTAGGAAACGTGCGCTGGTCTCCGGTATTGGTAGCCCAAAACCAGTGGGATGAGTCTTTAAGTGGTGCT GGAGGACCCTTTCTGTGGCACATCAGAATGAGCCGGTGGGATGCTTCCTGCACGGTCTTCCTGGTGATCCAGCTGCCTG CTGCTTTGGAGCAGCTTTAGTGAGGCTGGACTAGGGGAAAGGCTTGGCTGGACTCGAGGCAGAATAAATCTCAGCTGAG ATTGTCTGCAGGATCTGCCACACCTGGAGCGAGTTGGACAACAGGAGCTGGGTAGGACCCTCAGCAGTGGGGCTGGAGG GGGAATGGGGGCTCCTTAAACTGAGACAATGACAGTGAGTGTCCCCCATGTCCCCCAGCCACCATCCCCAGCTCCATCC CTGCAGCAACTCAGGGCCATCGCGAGACCTGCAGACATCTGTCCCACAGGTGGACCACCCTGCGGAGGTTTTGAGACCA CCTTCCAGCATGGAGGAACAAGAACAAGGTTTGCAGTTAGGACACTGGACAGCTCTAGGTTGCCCAGAGGGGCCGCTCA CCTACCCATGGCACTGCAGAACCTGCACAGCTCCATGCTGCACCAGGGCACTGCCAGCTGCCGGGACCATCATGGTGAT GGGACATGTCCTGGCACAAGATGATGGATAGCTGGCTTCCATAGAGAGGGATGGGTGGATTTGTGCTGTTTTCTCTGAA ACACAAAAGGCTCTGGGTTTTGCCCACTTTGTACTCCTCCATGTGCTGCACCATTGGTAACCAATGGCTTTTTTTTCCT GCTGGAAATCCACAGTTAAAATTCCCCTTAATCCTGCTGACTCCTGGGATCTCTACTGGCCCAGCTACCTTACAGCCCA GTTTTGGATGCCCCAAAGGGCGTGCTGGGACACAGGAGGGTTTGAGGCTCCTGCTTGGGTCTGTGGCTTCCCAAGACCA AGGTGAGGGTGTAGAGGCTCTGATGGTTCTCTCCTAGCACCATCATGCTGAGCCCCAGCAGGAACAAGAAGTGGAGGTG TCCCTGTTGCCTGCAGAGCCCCTCACCCATTCCCAGCCCATTCTGGCCCAGAACTCACAGTGTTAGGGGTTTAATACTG GGATTTAAGCTCCTTGACACCCACTGCACCTACAGCCCCTTAATAGGGTCTGCATCCCCCACCATGGGGACCAGTGACA CCTCCCTGGGGCCACCACTGCTACTTTGCAGCAAAGGCAGACACCGGTGTTGGCTTGGGACTTCAGCTCAGGGCTTGTG TACAGAAGGCAGAACGTTTTATTTTCTAGGCTTTGGTCAAAATAAAAGCGAGCAGGAGCCCTGTGA
Citation	Kumar M, Jordan N, Melton D, Grapin-Botton A. Signals from lateral plate mesoderm instruct endoderm toward a pancreatic fate. Dev Biol. 2003 Jul 1;259(1):109-22.
Copyright	Copyright © 2003 Elsevier Science (USA). All rights reserved.
Comments	Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (NM_204676).

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

19-23

stage 23

Gut

Small Intestine

Entry 6

GEISHA Id	CDX1.Alev.2010	Data Source	Publication
Complete cDNA Template Probe	show ATGTGCTGCACCATTGGTAACCAATGGCTTTTTTTTCCTGCTGGAAATCCACAGTTAAAATTCCCCTTAATCCTGCTGA CTCCTGGGATCTCTACTGGCCCAGCTACCTTACAGCCCAGTTTTGGATGCCCCAAAGGGCGTGCTGGGACACAGGAGGG TTTGAGGCTCCTGCTTGGGTCTGTGGCTTCCCAAGACCAAGGTGAGGGTGTAGAGGCTCTGATGGTTCTCTCCTAGCAC CATCATGCTGAGCCCCAGCAGGAACAAGAAGTGGAGGTGTCCCTGTTGCCTGCAGAGCCCCTCACCCATTCCCAGCCCA TTCTGGCCCAGAACTCACAGTGTTAGGGGTTTAATACTGGGATTTAAGCTCCTTGACACCCACTGCACCTACAGCCCCT TAATAGGGTCTGCATCCCCCACCATGGGGACCAGTGACACCTCCCTGGGGCCACCACTGCTACTTTGCAGCAAAGGCAG ACACCGGTGTTGGCTTGGGACTTCAGCTCAGGGCTTGTGTACA
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	The probe for CDX1 was amplified by PCR using the following primers: forward (5' to 3'): ATGTGCTGCACCATTGGTAA reverse (3' to 5'): TGTACACAAGCCCTGAGCTG

Stage

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Location (click to highlight)

Comments (click to highlight)

stage 4

Early Mesoderm
Primitive Streak

Entry 7

GEISHA Id	cdxA.Bel-Vialar.2002	Data Source	GEISHA ISH Analysis
Complete cDNA Template Probe	show GCTGCGTGACACCCAGCCGCTTCGGCACGGAGCGGCGCAGCGCGGTGCATCGGCACAGCATGAGCACAGAGCCAGGTGG AGAAGATGTATGTAGGCTATCTTTTGGATAAGGACACCAACATGTATCCCAGTCCCGTCCGGCATCCCAGCCTCAACCT CAACCCCCAGAACTACGTGCCGGGGCCACCCCAGTACTCGGACTTCGCCAGCTACCACCATGTGCCAGGGATTAACAAC GACCCTCACCATGGGCAGCCCGCAGCCGCCTGGGGCTCACCCTACACCCCTGCCAAGGAGGACTGGCACTCATATGGCA CCGCTGCCGCCTCCGCCGCCACCAACCCAGGGCAGTTTGGATTTAGCCCCCCGGATTTTAACCCCATGCAGCCCCATGC GGGCTCTGGACTCCTGCCTCCAGCCATCAGCAGCTCGGTGCCACAGCTGTCCCCTAATGCACAGAGGCGCACCCCGTAC GAATGGATGAGGCGCAGTATTCCCAGCACCAGCAGCAGCGGCAAGACGAGGACAAAGGACAAGTACCGGGTGGTGTACA CGGACCACCAACGCCTGGAGCTGGAGAAGGAATTTCACTACAGCCGCTACATCACCATCCGCCGTAAGGCCGAGCTGGC TGCTGCCCTGGGGCTCACTGAACGGCAGGTGAAAATCTGGTTTCAGAACCGGAGGGCGAAAGAGAGGAAGGTGAATAAA AAGAAGCTGCAGCAGCAGAGCCAGCCCACCAGCACCACCACGCCAACCCCCCCAGCCGTGGGCACGCCAGGGCCCATGG GGACCCTCTGCAGTGGCAGTGCCCCAAGCCTTGTCTCCTCATCTCCGCTCACCATCAAGGAGGAGTTCATGCCTTAGCC CCCTCCACCAGCCATAGACACTGAGAGATAAGCACTACACGGCAGAGCTTGTTGCTGAGCGCCCAAAGACACCACGTCC TCTGGGGCATGGTGGCTCTGTTGCCTTCCCAAGAGGCTGATGAGCTCTGTCCTACACAAAGCCCATACGTTAGGTAGTG CTGTTCTCCTGTAGGAAACGTGCGCTGGTCTCCGGTATTGGTAGCCCAAAACCAGTGGGATGAGTCTTTAAGTGGTGCT GGAGGACCCTTTCTGTGGCACATCAGAATGAGCCGGTGGGATGCTTCCTGCACGGTCTTCCTGGTGATCCAGCTGCCTG CTGCTTTGGAGCAGCTTTAGTGAGGCTGGACTAGGGGAAAGGCTTGGCTGGACTCGAGGCAGAATAAATCTCAGCTGAG ATTGTCTGCAGGATCTGCCACACCTGGAGCGAGTTGGACAACAGGAGCTGGGTAGGACCCTCAGCAGTGGGGCTGGAGG GGGAATGGGGGCTCCTTAAACTGAGACAATGACAGTGAGTGTCCCCCATGTCCCCCAGCCACCATCCCCAGCTCCATCC CTGCAGCAACTCAGGGCCATCGCGAGACCTGCAGACATCTGTCCCACAGGTGGACCACCCTGCGGAGGTTTTGAGACCA CCTTCCAGCATGGAGGAACAAGAACAAGGTTTGCAGTTAGGACACTGGACAGCTCTAGGTTGCCCAGAGGGGCCGCTCA CCTACCCATGGCACTGCAGAACCTGCACAGCTCCATGCTGCACCAGGGCACTGCCAGCTGCCGGGACCATCATGGTGAT GGGACATGTCCTGGCACAAGATGATGGATAGCTGGCTTCCATAGAGAGGGATGGGTGGATTTGTGCTGTTTTCTCTGAA ACACAAAAGGCTCTGGGTTTTGCCCACTTTGTACTCCTCCATGTGCTGCACCATTGGTAACCAATGGCTTTTTTTTCCT GCTGGAAATCCACAGTTAAAATTCCCCTTAATCCTGCTGACTCCTGGGATCTCTACTGGCCCAGCTACCTTACAGCCCA GTTTTGGATGCCCCAAAGGGCGTGCTGGGACACAGGAGGGTTTGAGGCTCCTGCTTGGGTCTGTGGCTTCCCAAGACCA AGGTGAGGGTGTAGAGGCTCTGATGGTTCTCTCCTAGCACCATCATGCTGAGCCCCAGCAGGAACAAGAAGTGGAGGTG TCCCTGTTGCCTGCAGAGCCCCTCACCCATTCCCAGCCCATTCTGGCCCAGAACTCACAGTGTTAGGGGTTTAATACTG GGATTTAAGCTCCTTGACACCCACTGCACCTACAGCCCCTTAATAGGGTCTGCATCCCCCACCATGGGGACCAGTGACA CCTCCCTGGGGCCACCACTGCTACTTTGCAGCAAAGGCAGACACCGGTGTTGGCTTGGGACTTCAGCTCAGGGCTTGTG TACAGAAGGCAGAACGTTTTATTTTCTAGGCTTTGGTCAAAATAAAAGCGAGCAGGAGCCCTGTGA
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_204676.2).