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A chicken embryo gene expression database

	Anatomical Location
	Stage
	Gene Name
	GEISHA ID
	Multiple Parameters

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HDAC1
histone deacetylase 1

Gene

Official Symbol	HDAC1
Official Full Name	histone deacetylase 1
BirdBase ID	BB-GG4466
CGNC ID	2394
also known as	histone deacetylase 1\|HD1
gene type	protein-coding

Genomic Map

	Ensembl
	NCBI
	UCSC
	Gallus-Browse

Sequence Information

Genomic
RNA	NM_204156
Polypeptide	NP_989487
Sequence Clusters/ESTs	Unigene

Gene Expression

In Situ Hybridization	GEISHA
EST Profile	Gga.10603

Orthology

	Entrez Gene	Ensembl Gene	Genetic Phenotypes	MOD
Fruit Fly	38565			FBgn0015805
Human	3065	ENSG00000116478		MIM:601241
Mouse	433759	ENSMUSG00000028800	All phenotypic alleles (9):Chemically induced(1) Targeted, knock-out(2) Targeted, other(6)	MGI:108086
Xenopus	594953, 397868, 379083			479582
Zebrafish	192302	ENSDARG00000015427	ZDB-GENE-020419-32	ZFIN:ZDB-GENE-020419-32

Gene Ontology

Molecular Function	activating transcription factor binding, core promoter binding, histone deacetylase activity, more...
Biological Process	chromatin modification, negative regulation by host of viral transcription, more...
Cellular Component	cytoplasm, cytosol, histone deacetylase complex, nucleus, NuRD complex, Sin3 complex

Links to other databases

Entrez Gene	373961
Ensembl Gene	ENSGALG00000003297
KEGG	gga:373961

Entry 1

GEISHA Id	HDAC1.UApcr	Data Source	GEISHA ISH Analysis
Forward cDNA Template Primer	AAAGCAAAAGAGGAGAAAGCCG
Reverse cDNA Template Primer	ATTAACCCTCACTAAAGGGCTAATGAGGTCTGCCACATCC	cDNA Template Length	819
Forward cDNA Template Probe	show GGGAACGTTCCCACCACATCAGGGNTGGATTTTCACTTGGGCATTTTCCAGATCTATACCTGGCAGGGCTCTTGGGCAG ATTGGACTCGAGCGATTTTCTGATCTGCTTGTAAGCTGCTTCATCTCTTTCCACCAGTTTGCTGCAGGAAGGTAGCCAA CTCTGTTCAAGAACTGCACTATTTGACCCTGAGAAGCGGCACCAGCTTGCAGTTACTTGCCATGGTGGAATCAGACTGA AGACCAAAGGAACACTCAGTCTCTCACAGGCTTAATTTGGGAATTCATATCTCCCACAAAAAAAGATAAAATAAAATAA AATAAAAGAGAAAGGAAAAGAAGAAAAAAAAAAGTTTCANGGCCATCTTTCCNCCTAACCTGAAATGCANACNCTACTT CTACTTAAATTATTCATTTTCAAGGGNGGTTACTTCANAGGAGAGCAAAGAAAGGAAGTGATTCTTTTTAAAGACNCNC TAAGGAGGCAGNGGAAGGCAAANAGTGAAACTTCCCAGGCNCCAATCCNGGGCAGNGCGGGTCTCTCTACTCTGCANAG TCCNCCCNGTCNGCTCCCAGCGGAGTGCANCAAGGAATAATTTACAGTTCNCAAGTCATTTATATNTTTATATAGAAAT ATATACCGAAACTTATATAAAATATAAATCCTGNGGAATGGGAGGCAACCAGANAAGCTAACCTACGATAACTATGCNC TGACAGGTACTGTCCAGCTGCAGCCATCTTAGGTGGATTTTGTCTCTTCCTTCNCCCCCTTGGGTTCGGCTTTCNCCCT TTTNGCTTTAAA

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

1-3

stage 3

Area Pellucida
Primitive Streak

4-6

stage 4

Area Pellucida
Primitive Streak

7-12

stage 7

stage 10

Anterior Intestinal Portal
Extraembryonic Mesoderm
Forebrain
Head Mesenchyme
Headfold
Heart
Hindbrain
Intermediate Mesoderm
Lateral Plate Mesoderm
Midbrain
Neural Plate/Tube
Notochord
Primitive Streak
Somites

dorsal

13-18

stage 14

stage 15

Forebrain
Foregut
Gut
Hindbrain
Midbrain
Neural Plate/Tube
Spinal Cord
Widespread Expression

19-24

stage 22

Widespread Expression

25-26

stage 26

Widespread Expression

Entry 2

GEISHA Id	HDAC1.Murko.2010	Data Source	Publication
Complete cDNA Template Probe	show `GAAGAAGAAGAAGATCCTGAGAAGCGCATTTCAATCCGCAATTCTGATAAGAGAATATCCTGTGATGAAGAATTCTCTG ACTCTGAAGATGAAGGGGAAGGAGGGCGCAAAAATGTTGCCAACTTTAAGAAGGCCAAGCGTGTGAAAACAGAGGAGGA AAAGGAGGAGGAGGAGAAGAAGGATGAGAAAGAAGAGGAAAAAGCAAAAGAGGAGAAAGCCGAACCCAAGGGGGTGAAG GAAGAGACAAAATCCACCTAAGATGGCTGCAGCTGGACAGTACCTGTCAGTGCATAGTTATC`
Citation	Murko C, Lagger S, Steiner M, Seiser C, Schoefer C, Pusch O. Expression of class I histone deacetylases during chick and mouse development. Int J Dev Biol. 2010;54(10):1527-37.
Copyright	Reprinted from Int. J. Dev. Biol., 55(1), Copyright (2010), with permission from the authors and IJDB
Comments	Primer sequences used are: chHDAC1 f: GGATGAAGAAGAAGAAGATCC, r: GATAACTATGCACTGACAGG (AF_039751, bp1239- 1541);

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

7-12

stage 11

stage 12

Forebrain
Neural Plate/Tube
Notochord

13-18

stage 15

stage 17

Ear/Otic Placode
Eye
Forebrain
Neural Plate/Tube
Pharyngeal Arches and Clefts

Labels indicate otic and optic placodes, limb buds, and branchial arches, which are not available in the checklist below.

stage 25

Ear/Otic Placode
Face Mesenchyme
Limb Buds
Wing

Entry 3

GEISHA Id	Hdac1.Zwane.2015	Data Source	GEISHA ISH Analysis
Complete cDNA Template Probe	show GAGTCAATCTGCCCAAGAGCCCTGCAGGTATAGATCTGGAAAATGCCAAGTGAAAATCACCCTGATGTGGTGGTGAACG TTTTCCAGGATGTGGCAGACCTCATTAGCGGGGCAGCGCTGTGCATCGCCCATAGGAGAAGGGATGGAATCTTTATGCA CTTGTTTCCTATACCTGTGCCCCTCTTTGCAGGGAGGAGGTGAGTTACTGCCCATCTGGCTGCCTGCTTCACTCTGCTT CTGCCCACAGCTTCGTGTGCTGTAATTGCTTCTCAGTACTGATCTGTGTCCTTGCTGAAACCGTAGCAGAGCAGGACAG ACAGACGGAGCCCAGCTGATGCCTCTGCTCCACGTGTCACTCGCTGAGAAACTCTTTCTGAAGCAGACATGTTTTCAAG TGGAACCTTTCCTGTCTTTGCTCTCAAGGCCAGTAAATGCGGAGAGCCTTTTTATCAGCAGTCTGAGCTGTTATCTGTA CGAGGGAACAGCAGATGGGGCTCTGTACGTTTTTATAACTGCTCCTCTTCCTCCTCCCACACGTTATCTCACACCCAAA GGTCTTTTGTGATCAGAGCTGGCCTTTCTCACACCTTGCTTTGTACAGCTGAGCGTGAGATGAGCGCTCCGTGGGATGC TTTGCTGAGCTCCGACTTTGCAGAAGTTCTGCAGGCAGTTCTGACTCGCTGCTCTCCTTCCTCCGGGGGATTCCTCTGT CCATAAGAGGATCTGTACCTCCCCCGGGGTGCTGCTGGTGGTTTCAACTCTAATAATGCTGCTAACTTAACACAGGTTA TTTTTAAAATGTTTTATTTTTTTAAATGCTTTTTTCCCCCCTTTTCCACCGTAAGTTTTGTAGTCTCTTGGAACCTGAG TGGCGTCTCACT
Citation	Zwane TB, Nikitina NV. Spatiotemporal expression analysis of Prdm1 and Prdm1 binding partners in early chick embryo. Gene Expr Patterns. 2015 Jan;17(1):56-68. Epub 2015 Feb 17. DOI: 10.1016/j.gep.2014.12.003.
Copyright	Copyright © 2014 Elsevier B.V.
Comments	Authors indicated the probe was amplified by PCR using the following primers: 5'-GAGTCAATCTGCCCAAGAGC-3' and 5'-AGTGAGACGCCACTCAGGTT-3'. Above sequence was extracted from NCBI accession number NM_204156.1.

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

4-6

stage 4

stage 5

stage 6

Ectoderm
Epiblast
Neural Plate/Tube
Primitive Streak

7-10

stage 7

stage 8

stage 10

Anterior Intestinal Portal
Blood Islands
Ectoderm
Epiblast
Eye
Foregut
Headfold
Lateral Plate Mesoderm
Neural Crest
Neural Plate/Tube
Paraxial Mesoderm
Primitive Streak
Somites
Surface Ectoderm

double ISH, Hdc1 in purple, Snail2 in brown
stage 10-
stage 8-

all

Entry 4

GEISHA Id	HDAC1.Olivera-Martinez.2014	Data Source	Publication
Complete cDNA Template Probe	show GGTGGGGCGGGTTGCGTTGCGCTGCGCGGCGGTAGGGTCTGCGGCCGTGGGGAGGCAGGAAAATGGCGCTGACGCAGGG GACCAAGCGGAAAGTCTGCTACTACTACGACGGTGATGTTGGAAACTATTACTATGGCCAGGGGCACCCCATGAAGCCC CACAGGATCCGGATGACCCACAACCTACTGCTGAACTACGGCCTTTACAGGAAGATGGAGATATATCGCCCTCACAAGG CGAACGCGGAGGAGATGACCAAGTACCACAGTGATGACTACATCAAATTCCTGAGATCCATCCGCCCAGACAACATGTC TGAGTACAGCAAGCAGATGCAAAGATTTAACGTCGGGGAGGACTGCCCTGTGTTCGATGGGCTGTTTGAGTTCTGTCAG CTCTCTGCTGGAGGCTCCGTTGCCAGCGCTGTGAAGCTGAACAAGCAACAGACAGATATTGCTGTGAATTGGGCAGGAG GCCTTCACCACGCTAAGAAGTCGGAGGCTTCTGGCTTCTGTTATGTCAACGATATTGTCCTGGCTATCTTGGAGCTCTT AAAGTATCACCAGAGGGTCCTGTATATTGACATTGATATTCACCATGGAGATGGTGTGGAGGAAGCCTTCTATACCACA GACCGTGTGATGACCGTGTCCTTTCATAAGTATGGAGAGTACTTCCCAGGAACAGGGGACCTGCGGGACATTGGTGCAG GCAAAGGCAAATACTATGCTGTCAACTATCCCCTCCGGGATGGGATTGATGATGAGTCCTACGAGGCAATATTCAAGCC GGTGATATCTAAAGTGATGGAGACATTCCAGCCTAGTGCAGTTGTCCTGCAGTGCGGGTCGGATTCTCTGTCCGGGGAC AGGCTGGGTTGTTTTAATCTGACCATCAAAGGTCATGCCAAGTGTGTGGAGTTTGTCAAAAGTTTTAATTTGCCTATGC TGATGCTGGGAGGAGGTGGCTATACGATCCGCAACGTGGCCAGATGCTGGACCTATGAGACTGCTGTGGCTTTGGACAC TGAGATCCCAAATGAGCTCCCATATAATGACTATTTTGAGTACTTCGGACCAGACTTTAAGCTGCACATCAGTCCCTCA AACATGACCAACCAGAATACCAATGAGTATCTCGAGAAGATCAAGCAGCGTCTCTTTGAGAATCTGCGCATGCTGCCTC ATGCCCCTGGCGTCCAGATGCAGCCAATTCCTGAGGATGCTGTTCAGGAAGACAGTGGGGATGAAGAAGAAGAAGATCC TGAGAAGCGCATTTCAATCCGCAATTCTGATAAGAGAATATCCTGTGATGAAGAATTCTCTGACTCTGAAGATGAAGGG GAAGGAGGGCGCAAAAATGTTGCCAACTTTAAGAAGGCCAAGCGTGTGAAAACAGAGGAGGAAAAGGAGGAGGAGGAGA AGAAGGATGAGAAAGAAGAGGAAAAAGCAAAAGAGGAGAAAGCCGAACCCAAGGGGGTGAAGGAAGAGACAAAATCCAC CTAAGATGGCTGCAGCTGGACAGTACCTGTCAGTGCATAGTTATCGTAGGTTAGCTTCTCTGGTTGCCTCCCATTCCAC AGGATTTATATTTTATATATGTTTCTGTATATATTTCTATATAAATATATAAATGACTTGAGAACTGTAAATTATTCCT TGCTGCACTCCGCTGGGAGCAGACAGGGAGGACTCTGCAGAGTAGAGAGACCCGCACTGCCCAGGATTGGTGCCTGGGA AGTTTCACTCTTTGCCTTCCACTGCCTCCTTAGTGTGTCTTTAAAAAGAATCACTTCCTTTCTTTGCTCTCCTCTGAAG TAACCACCCTTGAAAATGAATAATTTAAGTAGAAGTAGTGTCTGCATTTCAGGTTAGGTGGAAAGATGGCCATGAAACT TTTTTTTTTCTTCTTTTCCTTTCTCTTTTATTTTATTTTATTTTATCTTTTTTTGTGGGAGATATGAATTCCCAAATTA AGCCTGTGAGAGACTGAGTGTTCCTTTGGTCTTCAGTCTGATTCCACCATGGCAAGTAACTGCAAGCTGGTGCCGCTTC TCAGGGTCAAATAGTGCAGTTCTTGAACAGAGTTGGCTACCTTCCTGCAGCAAACTGGTGGAAAGAGATGAAGCAGCTT ACAAGCAGATCAGAAAATCACTCGAGTCAATCTGCCCAAGAGCCCTGCAGGTATAGATCTGGAAAATGCCAAGTGAAAA TCACCCTGATGTGGTGGTGAACGTTTTCCAGGATGTGGCAGACCTCATTAGCGGGGCAGCGCTGTGCATCGCCCATAGG AGAAGGGATGGAATCTTTATGCACTTGTTTCCTATACCTGTGCCCCTCTTTGCAGGGAGGAGGTGAGTTACTGCCCACC TGGCTGCCTGCTTCACTCTGCTTCTGCCCACAGCTTCGTGTGCTGTAATTGCTTCTCAGTACTGATCTGTGTCCTTGCT GAAACCATAGCAGAGCAGGACAGACAGACGGAGCCCAGCTGATGCCTCTGCTCCACGTGTCACTCGCTAAGAAACTCTT TCTGAAGCAGACATGTTTTCAAGTGGAACCTTTCCTGTCTTTGCTCTCAAGGCCAGTAAATGCGGAGAGCCTTTTTATC AGCAGTCTGAGCTGTTATCTGTACGAGGGAACAGCAGATGGGGCTCTGTACGTTTTTATAACTGCTCCTCTTCCTCCTC CCACACGTTATCTCACACCCAAAGGTCTTTTGTGATCAGAGCTGGCCTTTCTCACACCTTGCTTTGTACAGCTGAGCGT GAGATGAGCGCTCCGTGGGATGCTTTGCTGAGCTCCGACTTTGCAGAAGTTCTGCAGGCAGTTCTGACTCGCTGCTCTC CTTCCTCCGGGGGATTCCTCTGTCCATAAGAGGATCTGTACCTCCCCCGGGGTGCTGCTGGTGGTTTCAACTCTAATAA TGCTGCTAACTTAACACAGGTTATTTTTAAAATGTTTTATTTTTTTAAATGCTTTTTTCCCCCCTTTTCCACCGTAAGT TTTGTAGTCTCTTGGAACCTGAGTGGCGTCTCACTCCTGCTCTTCAGTGTTTGTATGTGAAGCGAGAGAGATCAGTGTA TCTTTGTGTCTTGGGGAGGGGGGGGGAAATATATTGTGGTTTTTTAAAGATGCTTTTATTTTAAATTTTGAGAATCTTT GTAATAAAACGTACATTTCTATGGT
Citation	Isabel Olivera-Martinez, Nick Schurch, Roman A Li, Junfang Song, Pamela A Halley, Raman M Das, Dave W Burt, Geoffrey J Barton, Kate G Storey. Major transcriptome re-organisation and abrupt changes in signalling, cell cycle and chromatin regulation at neural differentiation in vivo. Development 2014 Aug;141(16):3266-76. Epub 2014 Jul 25. DOI: 10.1242/dev.112623.
Copyright	Copyright © 2014. 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 above was obtained from NCBI (accession number NM_204156.2 ).