GEISHA 2.0

NCBI Nucleotide Hit

Ensembl Genome Map contig view

Citation Matsumata M, Uchikawa M, Kamachi Y, Kondoh H. Multiple N-cadherin enhancers identified by systematic functional screening indicate its Group B1 SOX-dependent regulation in neural and placodal development. Dev Biol. 2005 Oct 15;286(2):601-17. Epub 2005 Sep 16.

Comments Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (NM_204195).

Complete Sequence

Stage

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7-12

stage 12

Central Nervous System

Ear/Otic Placcode

Lens

Sensory Organs

Probe 2

GEISHA Id Sox3.Abu-Elmagd.2001

NCBI Ensembl

Gene Name SOX3 CH03_CHICK

Aliases CH3, transcription factor SOX-3

Gene Description SRY (sex determining region Y)-box 3 SRY-related protein CH3 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P40667]

Gene Ontology

NCBI Nucleotide Hit

Ensembl Genome Map contig view

Citation Abu-Elmagd M, Ishii Y, Cheung M, Rex M, Le Rouëdec D, Scotting PJ. cSox3 expression and neurogenesis in the epibranchial placodes. Dev Biol. 2001 Sep 15;237(2):258-69.

Comments Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (NM_204195).

Complete Sequence

Stage

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Location (click to highlight)

Comments (click to highlight)

7-12

stage 10

stage 12

Ectoderm

13-18

stage 13

stage 15

stage 17

stage 18

Ectoderm

Pharyngeal Arches and Clefts

Second Nodose Placode

Probe 3

GEISHA Id Sox3.Barembaum.2007

NCBI Ensembl

Gene Name SOX3 CH03_CHICK

Aliases CH3, transcription factor SOX-3

Gene Description SRY (sex determining region Y)-box 3 SRY-related protein CH3 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P40667]

Gene Ontology

NCBI Nucleotide Hit

Ensembl Genome Map contig view

Citation Barembaum M, Bronner-Fraser M. Spalt4 mediates invagination and otic placode gene expression in cranial ectoderm. Development. 2007 Nov;134(21):3805-14.

Comments Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (NM_204195).

Complete Sequence

Stage

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4-5

stage 5

Probe 4

GEISHA Id	Sox3.Chapman.2008
	NCBI	Ensembl
Gene Name		CH03_CHICK
Gene Description		SRY-related protein CH3 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P40667]
Gene Ontology		show GO:0003677 DNA binding IEA GO:0005634 nucleus IEA GO:0006355 regulation of transcription, DNA-dependent IEA GO:0009887 organ morphogenesis IEA GO:0030900 forebrain development IEA GO:0048515 spermatid differentiation IEA
Ensembl Genome Map	contig view
Comments	Images Provided by Susan Chapman.
Complete Sequence	show GGGCTCAGCGCTGCCCGCGGGGAACCTCCGCTGCACCTCGGGGAGCGGCACGGGAAAACTCCTTCCCCCTCCTGCGGCC GCCGCCCGGACCGGTTCTTTCTTTTACTCTTATTATTTTGAACTTCCTTTCCCCGAGCTGTGCCCGCCCGTCTGCCACC CTGGCGCATCTCTTACCGGCCCCGGCCATGTACAGCATGCTGGAGACCGAGATCAAGACGCCGCAGCCCACGCGGGCAG CGCGGGGGGAACCCGCCCGGGCGGCAACGGCAAAGGTCGGCGGGGCGGCCGCAGCGGACGGGTGCCGGTCGGACCAGGA CCGGGTGAAGCGCCCCATGAACGCCTTCATGGTGTGGTCCCGGGGCCAGCGCCGGAAGATGGCCCAGGAGAATCCAAAG ATGCACAACTCGGAGATCAGCAAGCGCCTCGGGGCCGATTGGAAGCTGCTGAGCGATGCCGAGAAGCGGCCCTTCATCG ACGAGGCCAAGAGGCTGCGGGCCGTGCACATGAAGGAGTACCCGGATTACAAATACCGGCCCCGGAGGAAGACCAAGAC CTTGCTGAAGAAGGACAAATACTCGCTGCCGGGCAACCTCTGGCCCCCGGGCAGCGCGGGAGCAGCCGCCGTCGGGGTG GGCCAGAGGATTGACACTTACGCCCATATGAACGGTTGGACCAACGGGGCTTACTCCCTGATGCAAGACCAGCTGGGTT ACGGGCAGCACCCGGGCATGAACAGCCCGCAGCTGCAGCAGATGCACCGCTACGACATGCCGGGCCTGCAGTACAGCCC CATGATGTCCACGGCGCAGACCTACATGAACGCCGGCCTCCACCTACAGCATGTCCCCCGCCCGTACGGCCAGCAGCCC TCCACGGCCATGAGCCTGGGCTCCATGGGCTCGGTGGTGAAGTCCGAGCCCAGCTCCGCTCCGCCGGCCATCACCTCGC ACTCGCAGAGGGCCTGCCTGGGAGAGCTGCGGGATATGATCAGCATGTACCTGGGCCCCGGGGGCGACGCCACACACCC TTCGGCCCTGCAGGGCAGCAGGTTGCACAGTGTGCACCAGCACTACCAGAGTGCCGGGACTCGCGTGAACGGCACCGTA CCACTAACTCACATATAAACAAACTGGCCTCCTCCGGACGGCTCCTCATCGCAACCCCAGCGCCGGGACGTGCGGCTCA GCAGACTCGATACTAACTTGGGTAGAAATTTTAAACAGAAAATCCGTTCGTTGTCTTCATTTTCTTTTTTCTTTTGTAC AAAAAAAAAAAACGATTTGGGCAATCTGTTCTTTTAACAGAGTGCAACCGCCTCCTAAAGCCCCGCGAAGTTCTTAAGC CACGGCGACTCTCCCCGGTCTCCGCGGGGTTGGGCGTAGTTTTGTTCGCTTCCGAGTCTTAAAGATGGTGCATCGCCCC GTTCCATTTTAGTCGTTGCAATGACAAAACGAAAAACCGACCCGGCGGGCGTTGTTTTCAAACTCAGTCGTTCCGTTGT TTACATTTTCGTTGTGGTTACTGAAAGTGTTGTTCTTCCCACCTTGCGAGCGCCGCTCGGTTCGTGTCCGCATTCGTAG AGTTTTTAACTTTAGGGTTTTGTTCCTACGGAAAGGGGGCGGTGGGAGAGAGCTGTGCGGGTCGCAAACCCTTTCTTTT ATTTATAGCAAGTTGTGTGTCTGGGTTTTTCTTAAGCTGTAAACTTATGTAAATCGGTTTGTAATTTTACTGTGAACGA TGTTTTGACATATCAGACGAAGAAAAGTTTTAATTTTTTGTTTGTTTGTTTTGTTTACCGGATTTCTTCC

Stage

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Location (click to highlight)

Comments (click to highlight)

stage 4

Probe 5

GEISHA Id	Sox3.Linker.2004.Oct
	NCBI	Ensembl
Gene Name		CH03_CHICK
Gene Description		SRY-related protein CH3 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P40667]
Gene Ontology		show GO:0003677 DNA binding IEA GO:0005634 nucleus IEA GO:0006355 regulation of transcription, DNA-dependent IEA GO:0009887 organ morphogenesis IEA GO:0030900 forebrain development IEA GO:0048515 spermatid differentiation IEA
Ensembl Genome Map	contig view
Citation	Linker C, Stern CD (2004). Neural induction requires BMP inhibition only as a late step, and involves signals other than FGF and Wnt antagonists. Development. 2004 Nov;131(22):5671-81.
Comments	Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (acc #NM_204195).
Complete Sequence	show TGCGCGTCGCTCAGCGCTGCCCGCGGGAACCTCCGCTGCACCTCGGGGAGCGGCACGGGAAAACTCCTTCCCCCTCCTG CGGCCGCCGCCCGGACCGGTTCTTTCTTTTACTCTTATTATTTTGAACTTCCTTTCCCCGAGCTGTGCCCGCCCGTCTG CCACCCTGGCGCATCTCTTACCGGCCCCGGCCATGTACAGCATGCTGGAGACCGAGATCAAGACGCCGCAGCCCACGCC GGGCAGCGCCGGGGGGAACCCGGCCCCGGGCGGCAACGGCAAAGGCGGCGGCGGGGCCGGCAGCGGAGCGGGTGCCGGG TCGGACCAGGACCGGGTGAAGCGCCCCATGAACGCCTTCATGGTGTGGTCCCGGGGCCAGCGGCGGAAGATGGCCCAGG AGAATCCCAAGATGCACAACTCGGAGATCAGCAAGCGCCTCGGGGCCGATTGGAAGCTGCTGAGCGATGCCGAGAAGCG GCCCTTCATCGACGAGGCCAAGAGGCTGCGGGCCGTGCACATGAAGGAGTACCCGGATTACAAATACCGGCCCCGGAGG AAGACCAAGACCTTGCTGAAGAAGGACAAATACTCGCTGCCGGGCAACCTGCTGGCCCCCGGAGGGGGCAACGCGGTGA GCAGCCCCGTCGGGGTGGGCCAGAGGATTGACACTTACGCCCATATGAACGGTTGGACCAACGGGGCTTACTCCCTGAT GCAAGACCAGCTGGGTTACGGGCAGCACCCGGGCATGAACAGCCCGCAGCTGCAGCAGATGCACCGCTACGACATGCCG GGCCTGCAGTACAGCCCCATGATGTCCACGGCGCAGACCTACATGAACGCCGCCTCCACCTACAGCATGTCCCCCGCCG CCTACGGCCAGCAGCCCTCCACGGCCATGAGCCTGGGCTCCATGGGCTCGGTGGTGAAGTCCGAGCCCAGCTCGCCTCC GCCGGCCATCACCTCGCACTCGCAGAGGGCCTGCCTGGGAGACCTGCGGGATATGATCAGCATGTACCTGCCCCCGGGG GGCGACGCCACAGACCCTTCGGCCCTGCAGGGCAGCAGGTTGCACAGTGTGCACCAGCACTACCAGAGTGCCGGGACTG CCGTGAACGGCACCGTACCACTAACTCACATATAAACGAACTGGCCTCCTCCGGACGGCTCCTCATCGCAACCCCAGCG CCGGGACGTGCGGCTCAGCAGACTCGATACTAACTTGGGAGAAATTTTAAACAGAAAATCCGTTCGTTGTCTTCATTTT CTTTTTTCTTTTGTACAAAAAAAAAAACGATTTGGGCAATCTGTTCTTTTAACAGAGCGCAACCGCCTCCTAAAGCCCC GCGAAGTTCTTAAGCCACGGCGACTCTCCCGGTCTCCGCGGGGTTGGGCGTAGTTTTGTTCGCTTCCGAGTCTTAAAGA TGGTGCATCGCCCCGTTCCATTTTAGCGTTGCAATGACAAAACGAAAAACCGACCCGGCGGGCGTTGTTTTCAAACTCA GTCGTTCCGTTGTTTACATTTTCGTTGTGGTTACTGAAAGTGTTGTTCTTCCCACCTTGCCGAGCGCCGCTCGGTTCGT GTCCGCAATTCGTAGAGTTTTTAACTTTAGGGTTTTGTTCCTACGGAAAGGGGGCGGTGGGAGAGAGCTGTGCGGGTCG CAAACCCTTTCTTTTATTTATAGCAAGTTGTGTGTCTGGGTTTTTCTTAAGCTGTAAACTTATGTAAATCGGTTTGTGA ATTTTACTGTGAACGATGTTTTGACATATCAGACCAAGAAAAGTTTTAATTTTTTGTTTGTTTGTTTTGTTTACCGGAT TTCTTCC

Stage

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1-3

stage 3

Stage 3+

Probe 6

GEISHA Id Sox3.Mikawa.2004

NCBI Ensembl

Gene Name SOX3 CH03_CHICK

Aliases CH3, transcription factor SOX-3

Gene Description SRY (sex determining region Y)-box 3 SRY-related protein CH3 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P40667]

Gene Ontology

NCBI Nucleotide Hit

Ensembl Genome Map contig view

Citation Mikawa, T, Poh, A, Kelly, K, Ishii, Y, Reese, D. Induction and Patterning of the Primitive Streak, an Organizing Center of Gastrulation in the Amniote. Dev Dyn. 2004 Mar;229(3):422-32.

Complete Sequence

Stage

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Location (click to highlight)

Comments (click to highlight)

1-3

stage 3

Epiblast

anterolateral epiblast

Probe 7

GEISHA Id Sox3.Rex.1997

NCBI Ensembl

Gene Name SOX3 CH03_CHICK

Aliases CH3, transcription factor SOX-3

Gene Description SRY (sex determining region Y)-box 3 SRY-related protein CH3 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P40667]

Gene Ontology

NCBI Nucleotide Hit

Ensembl Genome Map contig view

Citation Rex M, Orme A, Uwanogho D, Tointon K, Wigmore PM, Sharpe PT, Scotting PJ. Dynamic expression of chicken Sox2 and Sox3 genes in ectoderm induced to form neural tissue. Dev Dyn. 1997 Jul;209(3):323-32.

Comments Insufficient information in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (acc # U12467).

Complete Sequence

Stage

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Location (click to highlight)

Comments (click to highlight)

1-3

stage 2

stage 3

Epiblast

4-6

stage 4

stage 5

stage 6

7-8

stage 8

Probe 8

GEISHA Id Sox3.Streit.1999

NCBI Ensembl

Gene Name SOX3 CH03_CHICK

Aliases CH3, transcription factor SOX-3

Gene Description SRY (sex determining region Y)-box 3 SRY-related protein CH3 (Fragment). [Source:Uniprot/SWISSPROT;Acc:P40667]

Gene Ontology

NCBI Nucleotide Hit