GEISHA 2.0

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A chicken embryo gene expression database

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	Gene Name
	GEISHA ID
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Gene Expression Report

Probe 1

GEISHA Id Pax6.Jensen.2005

NCBI Ensembl

Gene Name PAX6 PAX6_CHICK

Aliases PAX-6

Gene Description paired box gene 6 Paired box protein Pax-6 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P47237]

Gene Ontology

show

NCBI Nucleotide Hit

NM_205066 show details

Ensembl Genome Map contig view

Citation Jensen A. Potential Roles for BMP and Pax Genes in the Development of Iris Smooth Muscle. Dev Dyn. 2005 Feb;232(2):385-92.

Comments Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (acc #NM_205066)

Complete Sequence

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Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

31-39

stage 31

stage 36

stage 39

lens epithelial cells,

pigmented epithelium

Probe 2

GEISHA Id PAX6.Gimeno.2007

NCBI Ensembl

Gene Name PAX6 PAX6_CHICK

Aliases PAX-6

Gene Description paired box gene 6 Paired box protein Pax-6 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P47237]

Gene Ontology

show

NCBI Nucleotide Hit

NM_205066 show details

Ensembl Genome Map contig view

Citation Gimeno L, Martinez S. Expression of chick Fgf19 and mouse Fgf15 orthologs is regulated in the developing brain by Fgf8 and Shh. Dev Dyn. 2007 Aug;236(8):2285-97.

Comments According to the authors, "Digoxigenin and fluorescein RNA antisense probes for chick Pax6 gene was prepared according to the instructions of the manufacturer (Roche)." As information provided was insufficient to verify exact sequence used to synthesize probe, the sequence below was obtained from NCBI (NM_205066).

Complete Sequence

show

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

19-20

stage 20

Probe 3

GEISHA Id PAX6.Ohuchi.2007

NCBI Ensembl

Gene Name PAX6 PAX6_CHICK

Aliases PAX-6

Gene Description paired box gene 6 Paired box protein Pax-6 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P47237]

Gene Ontology

show

NCBI Nucleotide Hit

NM_205066 show details

Ensembl Genome Map contig view

Citation Ohuchi H, Hayashibara Y, Matsuda H, Onoi M, Mitsumori M, Tanaka M, Aoki J, Arai H, Noji S. Diversified expression patterns of autotaxin, a gene for phospholipid-generating enzyme during mouse and chicken development. Dev Dyn. 2007 Apr;236(4):1134-43.

Comments Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (NM_205066).

Complete Sequence

show

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

7-12

stage 9

stage 11

Presumptive Pretectum

Sinus Rhomboidalis

13-15

stage 13

stage 15

Presumptive Pretectum

Probe 4

GEISHA Id PAX6.Garcia-Calero.2006

NCBI Ensembl

Gene Name PAX6 PAX6_CHICK

Aliases PAX-6

Gene Description paired box gene 6 Paired box protein Pax-6 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P47237]

Gene Ontology

show

NCBI Nucleotide Hit

NM_205066 show details

Ensembl Genome Map contig view

Citation García-Calero E, Garda AL, Marín F, Puelles L. Expression of Lrrn1 marks the prospective site of the zona limitans thalami in the early embryonic chicken diencephalon. Gene Expr Patterns. 2006 Oct;6(8):879-85. Epub 2006 Feb 28.

Comments According to the authors, "Digoxigenin-labeled RNA probes were prepared from plasmids kindly provided by J.L.R. Rubenstein (Pax6)..." As information provided was insufficient to verify exact sequence used to synthesize probe, the sequence below was obtained from NCBI (NM_205066).

Complete Sequence

show

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

13-18

stage 17

Diencephalon

Hindbrain

Telencephalon

19-24

stage 24

Diencephalon

Hindbrain

Telencephalon

Probe 5

GEISHA Id	Pax6.Bhattacharyya.2004
	NCBI	Ensembl
Gene Name		PAX6_CHICK
Gene Description		Paired box protein Pax-6 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P47237]
Gene Ontology		show GO:0001709 cell fate determination IEA GO:0001764 neuron migration IEA GO:0003677 DNA binding IEA GO:0003700 transcription factor activity IEA GO:0005515 protein binding IPI GO:0005634 nucleus IEA GO:0006350 transcription IEA GO:0006355 regulation of transcription, DNA-dependent IEA GO:0007275 multicellular organismal development IEA GO:0007411 axon guidance IEA GO:0007435 salivary gland morphogenesis IEA GO:0008285 negative regulation of cell proliferation IEA GO:0009950 dorsal/ventral axis specification IEA GO:0009952 anterior/posterior pattern formation IEA GO:0021543 pallium development IEA GO:0021798 forebrain dorsal/ventral pattern formation IEA GO:0021902 commitment of a neuronal cell to a specific type of neuron in the forebrain IEA GO:0021983 pituitary gland development IEA GO:0030334 regulation of cell migration IEA GO:0030900 forebrain development IEA GO:0042462 eye photoreceptor cell development IEA GO:0043010 camera-type eye development IEA GO:0043565 sequence-specific DNA binding IEA GO:0045449 regulation of transcription IEA GO:0045665 negative regulation of neuron differentiation IEA GO:0045944 positive regulation of transcription from RNA polymerase II promoter IEA GO:0050767 regulation of neurogenesis IEA
Ensembl Genome Map	contig view
Citation	Bhattacharyya S, Bailey AP, Bronner-Fraser M, Streit A. Segregation of lens and olfactory precursors from a common territory: cell sorting and reciprocity of Dlx5 and Pax6 expression. Dev Biol. 2004 Jul 15;271(2):403-14.
Copyright	Reprinted from Developmental Biology, Volume 271, Issue 2, Sujata Bhattacharyya, Andrew P. Bailey, Marianne Bronner-Fraser, and Andrea Streit, Segregation of lens and olfactory precursors from a common territory: cell sorting and reciprocity of Dlx5 and Pax6 expression, Pages 403-414, Copyright 2004, with permission from Elsevier. Copyright © 2004 Elsevier B.V. All rights reserved.
Comments	Authors indicate that the cDNAs for Pax6 came from Goulding et al., 1993), and they said:a 520 bp fragment spanning both the homeobox and paired box was used for Pax-6. As information provided is insufficient to verify exact sequence used to synthesize the probe, the sequence below was obtained from NCBI (Acc# NM_205066.1)
Complete Sequence	show TTCCGGCGTAGGAATCGCCGAGCGGAGCCGCCAGGTGCCTCCTCGGGCCGCCGCGCCGCCGGACAGGACCTCGGCATCG CACCGCCGCCGCAGCCTCAGTGGAGACAAACTATTCTGCGGGCAACTCTTTGGGAGCGCGTCAGTGCCCGGCGGTGCGC CCCGTCCTGCTGACAGCAGCGGTGCCGCGGACGGGATATGCCTCTGCGAGAGGGCCGCCGGGAGTAGAGGCACGCAGAT GTGCGAGCCCCCACGCTGCAGGAGAGGACAGCGCGCCCGGCTTCCAGACCGCTCCAGGCGAGCCCCGCGGGACCCCGCT GCCCCGGCCCACCATGCAGAACAGTCACAGCGGCGTGAACCAGCTCGGCGGGGTGTTCGTCAACGGGAGGCCGCTGCCC GACTCCACGCGGCAGAAGATCGTGGAACTCGCGCACAGCGGCGCGCGGCCGTGCGACATCTCCCGAATCCTGCAGACCC ATGCAGATGCAAAAGTCCAAGTGCTGGACAATCAAAACGTGTCGAATGGATGTGTGAGTAAAATTTTGGGCAGGTATTA CGAAACTGGCTCCATCAGGCCCAGGGCGATCGGAGGTAGTAAGCCGAGAGTAGCGACTCCCGAAGTTGTAAGCAAAATA GCGCAGTATAAACGAGAGTGCCCCTCCATCTTTGCGTGGGAGATTCGAGACAGATTACTCTCGGAGGGGGTCTGTACCA ACGATAACATACCCAGTGTGTCGTCGATAAACAGAGTCCTCCGCAACCTGGCTAGCGAAAAGCAACAGATGGGTGCCGA CGGGATGTACGACAAGCTAAGGATGCTGAACGGGCAGACGGGGACATGGGGCACCCGGCCCGGCTGGTATCCCGGCACC TCGGTACCCGGGCAGCCCGCACAAGACGGCTGCCCGCAGCAGGAGGGAGGAGGGGAGAACACCAACTCCATCAGCTCCA ATGGGGAAGATTCCGATGAGGCCCAGATGAGACTTCAGCTGAAAAGGAAGCTGCAGAGAAATAGGACATCCTTTACCCA AGAGCAAATCGAAGCCCTTGAGAAAGAGTTTGAGAGAACCCACTATCCTGATGTGTTTGCGAGAGAGCGACTAGCTGCT AAAATAGACTTGCCTGAAGCAAGGATACAGGTGTGGTTTTCTAACAGAAGGGCCAAGTGGAGAAGGGAGGAGAAGCTGC GGAACCAGCGGAGACAAGCCAGCAACACTCCCAGCCACATCCCCATCAGCAGTAGTTTCAGCACAAGCGTTTACCAGCC GATCCCACAGCCGACCACCCCCGTTTCCTCTTTCACATCAGGTTCCATGTTGGGCAGGACAGACACAGCGCTCACGAAC ACGTACAGCGCACTGCCGCCCATGCCCAGCTTCACCATGGCCAACAACCTGCCTATGCAACCCCCGGTACCCAGCCAGA CCTCCTCCTACTCTTGCATGCTGCCCACCAGCCCGTCGGTGAATGGCCGGAGCTATGACACCTACACCCCTCCGCACAT GCAGACACACATGAATAGCCAGCCCATGGGCACCTCTGGCACCACTTCCACAGGTCTCATTTCCCCTGGAGTGTCAGTT CCAGTTCAAGTTCCTGGCAGTGAACCTGACATGTCTCAGTATTGGCCAAGATTACAGTAAAACATGTGTTAATTCTGTA AATGACTATATGGACAACAGTTGGATGTTCAGCAGTATTTTCTAAAGGAAGAATGGCTCTCAGAGTACTTCTGTACTGC AACTGTGCCCTACGCTGTAACACATGGAAAAGACTCTAACATGGACCTTTGTACACTGAAGGCATTATATCGGTTCGGC ACGAAATCTTGCATTTTGGTATCCAAACTTTTATTCATTTTGGTGTATTATTTGTAAATGGGCATTTGTATGTTATAAT GAAAAAAAAAAAGAACAATGTAGACTGGATGGATGTTTGATCTGTGTTGGTCATGAAGTTGTTTTAAG

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

7-10

stage 7

stage 8

stage 10

Neural Plate/Tube

Surface Ectoderm

Probe 6

GEISHA Id PAX6.Agarwala.2005

NCBI Ensembl

Gene Name PAX6 PAX6_CHICK

Aliases PAX-6

Gene Description paired box gene 6 Paired box protein Pax-6 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P47237]

Gene Ontology

show

NCBI Nucleotide Hit

NM_205066 show details

Ensembl Genome Map contig view

Citation Agarwala S, Aglyamova GV, Marma AK, Fallon JF, Ragsdale CW. Differential susceptibility of midbrain and spinal cord patterning to floor plate defects in the talpid2 mutant. Dev Biol. 2005 Dec 1;288(1):206-20. Epub 2005 Oct 21.

Comments According to the authors, "Digoxigenin (DIG)- and fluorescein-labeled riboprobes were synthesized from chick cDNA plasmids..." As information provided was insufficient to verify exact sequence used to synthesize probe,the sequence below was obtained from NCBI (NM_205066).

Complete Sequence

show

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

25-28

stage 26

stage 28

Probe 7

GEISHA Id	Pax6.Maden.2007
	NCBI	Ensembl
Gene Name		PAX6_CHICK
Gene Description		Paired box protein Pax-6 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P47237]
Gene Ontology		show GO:0001709 cell fate determination IEA GO:0001764 neuron migration IEA GO:0003677 DNA binding IEA GO:0003700 transcription factor activity IEA GO:0005515 protein binding IPI GO:0005634 nucleus IEA GO:0006350 transcription IEA GO:0006355 regulation of transcription, DNA-dependent IEA GO:0007275 multicellular organismal development IEA GO:0007411 axon guidance IEA GO:0007435 salivary gland morphogenesis IEA GO:0008285 negative regulation of cell proliferation IEA GO:0009950 dorsal/ventral axis specification IEA GO:0009952 anterior/posterior pattern formation IEA GO:0021543 pallium development IEA GO:0021798 forebrain dorsal/ventral pattern formation IEA GO:0021902 commitment of a neuronal cell to a specific type of neuron in the forebrain IEA GO:0021983 pituitary gland development IEA GO:0030334 regulation of cell migration IEA GO:0030900 forebrain development IEA GO:0042462 eye photoreceptor cell development IEA GO:0043010 camera-type eye development IEA GO:0043565 sequence-specific DNA binding IEA GO:0045449 regulation of transcription IEA GO:0045665 negative regulation of neuron differentiation IEA GO:0045944 positive regulation of transcription from RNA polymerase II promoter IEA GO:0050767 regulation of neurogenesis IEA
Ensembl Genome Map	contig view
Citation	Maden M, Blentic A, Reijntjes S, Seguin S, Gale E, Graham A. (2007). Retinoic acid is required for specification of the ventral eye field and for Rathke's pouch in the avian embryo. Int J Dev Biol. 2007;51(3):191-200.
Copyright	"Reprinted from Int. J. Dev. Biol., 51, Maden M, Blentic A, Reijntjes S, Seguin S, Gale E, Graham A, Retinoic acid is required for specification of the ventral eye field and for Rathke's pouch in the avian embryo, 191-200, Copyright (2007), with permission from Copyright © 2007 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 #NM_205066). Thus images are from Quail, but sequence shown and map are the chick homolog.
Complete Sequence	show TTCCGGCGTAGGAATCGCCGAGCGGAGCCGCCAGGTGCCTCCTCGGGCCGCCGCGCCGCCGGACAGGACCTCGGCATCG CACCGCCGCCGCAGCCTCAGTGGAGACAAACTATTCTGCGGGCAACTCTTTGGGAGCGCGTCAGTGCCCGGCGGTGCGC CCCGTCCTGCTGACAGCAGCGGTGCCGCGGACGGGATATGCCTCTGCGAGAGGGCCGCCGGGAGTAGAGGCACGCAGAT GTGCGAGCCCCCACGCTGCAGGAGAGGACAGCGCGCCCGGCTTCCAGACCGCTCCAGGCGAGCCCCGCGGGACCCCGCT GCCCCGGCCCACCATGCAGAACAGTCACAGCGGCGTGAACCAGCTCGGCGGGGTGTTCGTCAACGGGAGGCCGCTGCCC GACTCCACGCGGCAGAAGATCGTGGAACTCGCGCACAGCGGCGCGCGGCCGTGCGACATCTCCCGAATCCTGCAGACCC ATGCAGATGCAAAAGTCCAAGTGCTGGACAATCAAAACGTGTCGAATGGATGTGTGAGTAAAATTTTGGGCAGGTATTA CGAAACTGGCTCCATCAGGCCCAGGGCGATCGGAGGTAGTAAGCCGAGAGTAGCGACTCCCGAAGTTGTAAGCAAAATA GCGCAGTATAAACGAGAGTGCCCCTCCATCTTTGCGTGGGAGATTCGAGACAGATTACTCTCGGAGGGGGTCTGTACCA ACGATAACATACCCAGTGTGTCGTCGATAAACAGAGTCCTCCGCAACCTGGCTAGCGAAAAGCAACAGATGGGTGCCGA CGGGATGTACGACAAGCTAAGGATGCTGAACGGGCAGACGGGGACATGGGGCACCCGGCCCGGCTGGTATCCCGGCACC TCGGTACCCGGGCAGCCCGCACAAGACGGCTGCCCGCAGCAGGAGGGAGGAGGGGAGAACACCAACTCCATCAGCTCCA ATGGGGAAGATTCCGATGAGGCCCAGATGAGACTTCAGCTGAAAAGGAAGCTGCAGAGAAATAGGACATCCTTTACCCA AGAGCAAATCGAAGCCCTTGAGAAAGAGTTTGAGAGAACCCACTATCCTGATGTGTTTGCGAGAGAGCGACTAGCTGCT AAAATAGACTTGCCTGAAGCAAGGATACAGGTGTGGTTTTCTAACAGAAGGGCCAAGTGGAGAAGGGAGGAGAAGCTGC GGAACCAGCGGAGACAAGCCAGCAACACTCCCAGCCACATCCCCATCAGCAGTAGTTTCAGCACAAGCGTTTACCAGCC GATCCCACAGCCGACCACCCCCGTTTCCTCTTTCACATCAGGTTCCATGTTGGGCAGGACAGACACAGCGCTCACGAAC ACGTACAGCGCACTGCCGCCCATGCCCAGCTTCACCATGGCCAACAACCTGCCTATGCAACCCCCGGTACCCAGCCAGA CCTCCTCCTACTCTTGCATGCTGCCCACCAGCCCGTCGGTGAATGGCCGGAGCTATGACACCTACACCCCTCCGCACAT GCAGACACACATGAATAGCCAGCCCATGGGCACCTCTGGCACCACTTCCACAGGTCTCATTTCCCCTGGAGTGTCAGTT CCAGTTCAAGTTCCTGGCAGTGAACCTGACATGTCTCAGTATTGGCCAAGATTACAGTAAAACATGTGTTAATTCTGTA AATGACTATATGGACAACAGTTGGATGTTCAGCAGTATTTTCTAAAGGAAGAATGGCTCTCAGAGTACTTCTGTACTGC AACTGTGCCCTACGCTGTAACACATGGAAAAGACTCTAACATGGACCTTTGTACACTGAAGGCATTATATCGGTTCGGC ACGAAATCTTGCATTTTGGTATCCAAACTTTTATTCATTTTGGTGTATTATTTGTAAATGGGCATTTGTATGTTATAAT GAAAAAAAAAAAGAACAATGTAGACTGGATGGATGTTTGATCTGTGTTGGTCATGAAGTTGTTTTAAG

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

13-14

stage 14

Eye

Quail

Probe 8

GEISHA Id PAX6.Vieira.2005

NCBI Ensembl

Gene Name PAX6 PAX6_CHICK

Aliases PAX-6

Gene Description paired box gene 6 Paired box protein Pax-6 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P47237]

Gene Ontology

show

NCBI Nucleotide Hit

NM_205066 show details

Ensembl Genome Map contig view

Citation Vieira C, Garda AL, Shimamura K, Martinez S. Thalamic development induced by Shh in the chick embryo. Dev Biol. 2005 Aug 15;284(2):351-63.

Comments According to the authors, "Digoxigenin and fluorescein-labeled RNA probes were prepared from plasmids kindly provided by J.L.R. Rubenstein." As information provided was insufficient to verify exact sequence used to synthesize probe,the sequence below was obtained from NCBI (NM_205066).

Complete Sequence

show

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

19-23

stage 23

Diencephalon

Midbrain

di-mesencephelon

Probe 9

GEISHA Id PAX6.Bell.2001

NCBI Ensembl

Gene Name PAX6 PAX6_CHICK

Aliases PAX-6

Gene Description paired box gene 6 Paired box protein Pax-6 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P47237]

Gene Ontology

show

NCBI Nucleotide Hit

NM_205066 show details

Ensembl Genome Map contig view

Citation Bell E, Ensini M, Gulisano M, Lumsden A. Dynamic domains of gene expression in the early avian forebrain. Dev Biol. 2001 Aug 1;236(1):76-88.

Comments Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (NM_205066).

Complete Sequence

show

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

7-12

stage 8

stage 9

stage 10

stage 11

stage 12

13-18

stage 13

Expression patterns of qin, Emx1, Emx2, and Pax6 along the A-P axis of the prosencephalon during early development.

19-20

stage 20

Telencephalon

Dorsal and Intermediate Telencephalon (pallium and dorsal ventricular ridge)

Expression of dorsal-expressed genes, Emx1, Emx2, Pax6 in relation to a ventral-expressed gene, Dlx2.

Probe 10

GEISHA Id PAX6.Zhang.2001

NCBI Ensembl

Gene Name PAX6 PAX6_CHICK

Aliases PAX-6

Gene Description paired box gene 6 Paired box protein Pax-6 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P47237]

Gene Ontology

show

NCBI Nucleotide Hit

NM_205066 show details

Ensembl Genome Map contig view

Citation Zhang XM, Yang XJ (2001). Temporal and spatial effects of Sonic hedgehog signaling in chick eye morphogenesis. Dev Biol. 2001 May 15;233(2):271-90.

Comments Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (NM_205066).

Complete Sequence

show

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

19-24

stage 22

stage 24

Probe 11

GEISHA Id PAX6.Spieler.2004

NCBI Ensembl

Gene Name PAX6 PAX6_CHICK

Aliases PAX-6

Gene Description paired box gene 6 Paired box protein Pax-6 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P47237]

Gene Ontology

show

NCBI Nucleotide Hit

NM_205066 show details

Ensembl Genome Map contig view

Citation Spieler D, Bäumer N, Stebler J, Köprunner M, Reichman-Fried M, Teichmann U, Raz E, Kessel M, Wittler L (2004). Involvement of Pax6 and Otx2 in the forebrain-specific regulation of the vertebrate homeobox gene ANF/Hesx1. Dev Biol. 2004 May 15;269(2):567-79.

Comments Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (NM_205066).

Complete Sequence

show

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

7-8

stage 8

Neural Plate/Tube

Posterior Neural Folds

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