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A chicken embryo gene expression database

	Anatomical Location
	Stage
	Gene Name
	GEISHA ID
	Multiple Parameters

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HOXA1
homeobox A1

Gene

Official Symbol	HOXA1
Official Full Name	homeobox A1
BirdBase ID	BB-GG4619
CGNC ID	49021
also known as	HOXA2, homeobox protein Hox-A1\|homeo box A1\|homeobox A2
gene type	protein-coding

Genomic Map

	Ensembl
	NCBI
	UCSC
	Gallus-Browse

Sequence Information

Genomic
RNA	XM_003640697
Polypeptide	XP_003640745
Sequence Clusters/ESTs	Unigene

Gene Expression

In Situ Hybridization	GEISHA
EST Profile	Gga.55802

Orthology

	Entrez Gene	Ensembl Gene	Genetic Phenotypes	MOD
Fruit Fly
Human
Mouse
Xenopus
Zebrafish

Gene Ontology

Molecular Function
Biological Process
Cellular Component

Links to other databases

Entrez Gene	374051
Ensembl Gene	ENSGALG00000028095
KEGG	gga:374051

Entry 1

GEISHA Id	NKX2.3.Smith.2000	Data Source	Publication
Complete cDNA Template Probe	show GTTGCTGTCGGCGCCGGGCTAATGGAGGCAACTTAGACAGGAGCAGGCGCGCCCCTCGTCTCTCGGCGCTGCCGCTCCC CCCGCACCGGGCGCGGCGCTCCCCGCCGAGCGCAGCCCGAGCGCCGCCGCGCCCCGGGACTCCCCGGCCTCGCGCTGCC CCGATGATGTTACCGAGCCCCGTCACCTCCACCCCTTCCTCTGTCAAAGACATCCTCAACCTGGAGCAGCAGCAGCAGG ACCCGCACTATGGGGCCCACGTCCCGCACCACCTGGAGCACCACTTTCACCCCGCCGCCTGCCTGCTCGCCGCGACGGC GCCCCGGTTCTCCGACGGCGAGGAGGAAGAGGAGGAGGAGAAGCTGTCCTACCTGAGCTCCGTGGAACGCCCGGCGGCC AGGCCGACGCGCGGCTCTGCCGACAGCTACGTGCATGCCGTGCTGCGCGGCTCCTGCGAGGCTCCCGGCCCGGGAGAGG AGCTGGACCCCACGGCTCGCGACCCGAAGAGCTGCGCCCTGAAGAAACCGCTGGACGCCGCGGAGAAGCCGGAGGAGGC GGAGAGGCCGAAGCAGCGGAGTCGGAGGAAGCCGCGCGTCCTCTTCTCGCAGGCGCAGGTCTTCGAGCTGGAGCGGCGG TTCAAGCAGCAGCGTTACCTGTCGGCTCCCGAGCGGGAGCACCTGGCCAGCAGCCTGAAGCTCACCTCCACGCAGGTGA AGATCTGGTTCCAGAACCGGCGCTACAAGTGCAAGCGGCAGCGGCAGGACAAGTCGCTGGAGCTGGGCGCCCCGCGGCC CCGCGCGCCGCGCAGAGTGGCCGTGCCCGTGCTGGTCCGCGACGGCAAGCCGTGCCTGGGCGGCTCGCAGGGCTACAGC TCGGTGTACAACGGGCCCTACTCCTACAACAGCTTCCTTACGGCTAGCCAACGCCGCCTCCTACAACCCCGGCTACGGC TGCACCTACCCGGCGGGCAGCGGCGGGGCCTCGGTGCAAGCCGCCTGCAGCCCGGCGGCGGCCGCCGGCCCCTTCGTGA ACGTGGGCGGCCTGGGGGGCTTCGGCGGCGGCGGGCAGGCGCTGCACCAGGCGGCGGCGGGGCCCTCCTGCAGCCAGGG CGACTCGAGGGCATTCGGGCCTGGTAGCCCGCACGCACTTAGGGCCGGGAGCGGACCGGCACGACGGCCCCGCGGCCCC GCAGCGCCCTTACGCCCCGCGGACTGAAGGCGGAGGGGCGGTGCGGCAGGACCCCGGCTCTCTCCCAGGGCCGCGGGGC GGAGCGGAGCGCGGAACGGAAGGGAACGGGACTGGACGGGACAGGACGGGCCGAGCCCGCGGCGGAGGCCGCCGCCCCG AGGTGCCGCCGCGACGGCGGCGGAGCTGACCGCGCCGACGGAGCAGCTCGTTGTAAGAAGCCGACGGGGACCCGGGGTC CCGCGCCCTGCTCTCTATCTACGCTGTATCGGTTTCTCTGGGCTCCAACTGCGCGGAGTCAGTCAATAAACCAGGTGCC ATATCCAAAAAAAAAA
Citation	Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM. Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evol Dev. 2000 Nov-Dec;2(6):348-59.
Copyright	Copyright © 2000-2011 by John Wiley & Sons, Inc., or related companies. All rights reserved.

Stage

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Location (click to highlight)

Comments (click to highlight)

19-24

stage 24

Foregut
Midgut

E4.5
group photo

Entry 2

GEISHA Id	HOXA1.Barak.2012	Data Source	Publication
Complete cDNA Template Probe	show ATGAGCTCCTTCCTCGAGTACCCCGTCCTCGGCGGCGAGGCGGGGGCCTGCGCCGCCCGCTCCTACCACCCCGAGCACG GGATTACAACTTTTCAGCCCTGCGCCGTCAGCGCCGGCAGCTGCAGCGGGGAGGACCGCTTCCTCGTGGGCCGCGGGGT GTCCCTCAGCCCCCACCGGCACCACCACCCCCCGGCCCAGCCCGCCGCCTACCAGCACCACGGCGGCCTGGGGGTGTCC TACGCGCACCCCGGCTGCCCCCCGACGTACGGCGCGCAGGGCTTCGGCGCCGCCTACGGCCCCTACGCTCTGGGGCAGG ACGCGGAGCTGGGCGGCGGCTTCCCCCCCTGCGCGCCCGCCGTCTACTCGGGCAGCCTCTCCTCCGCCGCAGCGCAGCA CCCGCACCAGGGCTACGCGGGGGGGCCCGCGCAGTACGTGCCCTCCCCGTACGGGCAGGAGCAGCAGAGCCTGCCCCTG GGCACCTACAACCATGCCCTGTCTCCCCTCCACGCCGGCCACCAGGACAACTCCCGCTCCCCCTCCGCCGACACCTCGC CGCCGGCGCAGACCTTCGACTGGATGAAAGTTAAAAGGAACCCCCCTAAAACAGGCAAGGCCGGCGAGTACGGCTTCGT GGGGCAGCCCAACACCGTCCGGACCAACTTCACCACCAAGCAGCTCACCGAGCTGGAGAAGGAGTTCCACTTCAACAAG TACCTGACCCGGGCCAGGCGGGTGGAAATCGCCGCCTCCCTCCAGCTCAACGAGACGCAGGTGAAGATCTGGTTCCAGA ACCGGCGGATGAAGCAGAAGAAGAGGGAGAAAGAGGGGCTGCTGCCCATCTCCCCCGCCACCCCCACGGGCTGCGAGGA GAAGGCGGACGACCCGTCGGAGAAGTGCTGCCCGTCGCCCTGCAGCGCCTCTCCCGCATCCTGCGCCTCGGACCCGGGA CCCGCCGCCAACTGAGCTCCCCCGAGCCGCGGTGCGCTCCGTCGGTCCGTCCCGTCGGTCGGGCCCGGGGGCGCCGGCC CGGCCGCTCCCGGCCCCTGCCGCCAAGAGGTTTTCTTTCGGTCCCCCCCTCCTCACCTCCTTGCCGGAGGAGTCGCGTT GGCACGCGCGTGGGTTCTCCCTCCTCCCCGCAAGGACGTTCCTCTGAGTTTCCCTGGGTGACAGACAGGTCACGGAGGG TACATAACCTCACGAAGAGATGCACTATGGCAAGTGTTTACACGACTTCTAGGACTTTCATCCTTTAATTTAATGTATA CTTTGTTCGTGTCTATGAGTTCGTTGCTTGTAAATACTTTGTCCGAGAGATTTATCTTTTTACAGATTTT
Citation	Barak H, Preger-Ben Noon E, Reshef R. Comparative spatiotemporal analysis of Hox gene expression in early stages of intermediate mesoderm formation. Dev Dyn. 2012 Oct;241(10):1637-49.
Copyright	Copyright © 2012 Wiley Periodicals, Inc.
Comments	As insufficient information is provided in publication to verify exact sequence used to synthesize probe, the sequence below was obtained from NCBI (acc # XM_003640697.1).

Stage

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Location (click to highlight)

Comments (click to highlight)

4-6

stage 4

stage 6

Epiblast
Primitive Streak

7-11

stage 7

stage 8

stage 9

stage 10

stage 11

Anterior Intestinal Portal
Intermediate Mesoderm
Lateral Plate Mesoderm
Neural Plate/Tube
Paraxial Mesoderm
Somatic Mesoderm
Somites
Tail
Veins

Entry 3

GEISHA Id	HOXA1.Anderson.2021	Data Source	Direct Submission
Complete cDNA Template Probe	show GACTTCTAGGACTTTCATCCTTTAATTTAATGTATACTTGTTCGTGTCTATGAGTTCGTTGCTTGTAAATACTTGTCCG AGAGATTTATCTTTTTACAGATTTTTTCTAGAGATGACGTTTAGATGATCAGGTGAAGCAGGGTGAGTGCATTCGCCAA ACCGGACCCACTTTTCGATCGGTCAGGCTGACGGCAGCATCAAGCAGACGTGTTAAGCTCCAGCAGATACCTCAAAGCG TAGCGCTATTTCCCAAAACGTGACAAACAAGGCTTCAATTGCACTAGGTTTGTAAACCTTACCCCGTGTGCTGTCCCCC CCCTCCCCCATCAGCTGTGCTGGGCTGGCCGGACAGAGGGACACCGCGCCCCACGGACCTCACCCTCTCCCCGTTTCCG TACTCCCCCTCCTTTAGCCTCGATGTCTTTTCGACCCGCTCGTGAATGTGTCGGATGGCCAAATGAATGTATAACTTCT GTGGTTGGTGTCCGGGCCGCTGCATGCCGCCCCGTGTGTGCTGTACTCGGGACACGGAGCTCTGTTCGGGCGGGAGCCG GGTCCCCGGAGTTGCGTACACTCACCAGGGCTCTGCGGTCCCAGCGCTGGACCC
Comments	Images and probe sequence provided by Claire Anderson. The probe was synthesized from cDNA clone ChEST1010d14. Related paper: Anderson C, Hill B, Lu HC, Moverley A, Yang Y, Oliveira NMM, Baldock RA, Stern CD. A 3D molecular atlas of the chick embryonic heart. Dev Biol. 2019 Dec 1;456(1):40-46. doi: 10.1016/j.ydbio.2019.07.003. Epub 2019 Jul 5.

Stage

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Location (click to highlight)

Comments (click to highlight)

7-12

stage 12

Amnion
Anterior Intestinal Portal
Blood Vessels
Dermomyotome
Endoderm
Extraembryonic Blood Vessels
Intermediate Mesoderm
Lateral Plate Mesoderm
Neural Plate/Tube
Notochord
Pharynx
Sclerotome
Sinus Venosus
Somatic Mesoderm
Splanchnic Mesoderm
Yolk Sack or Stalk
extraembryonic ectoderm
extraembryonic endoderm
extraembryonic mesoderm

section 14
section 25
section 38
section 48
section 5
section 65

Entry 4

GEISHA Id	HOXA1.Anderson.2019	Data Source	Publication
Complete cDNA Template Probe	show ACTTTCATCCTTTAATTTAATGTATACTTGTTCGTGTCTATGAGTTCGTTGCTTGTAAATACTTGTCCGAGAGATTTAT CTTTTTACAGATTTTTTCTAGAGATGACGTTTAGATGATCAGGTGAAGCAGGGTGAGTGCATTCGCCAAACCGGACCCA CTTTTCGATCGGTCAGGCTGACGGCAGCATCAAGCAGACGTGTTAAGCTCCAGCAGATACCTCAAAGCGTAGCGCTATT TCCCAAAACGTGACAAACAAGGCTTCAATTGCACTAGGTTTGTAAACCTTACCCCGTGTGCTGTCCCCCCCCTCCCCCA TCAGCTGTGCTGGGCTGGCCGGACAGAGGGACACCGCGCCCCACGGACCTCACCCTCTCCCCGTTTCCGTACTCCCCCT CCTTTAGCCTCGATGTCTTTTCGACCCGCTCGTGAATGTGTCGGATGGCCAAATGAATGTATAACTTCTGTGGTTGGTG TCCGGGCCGCTGCATGCCGCCCCGTGTGTGCTGTACTCGGGACACGGAGCTCTGTTCGGGCGGGAG
Citation	Anderson C, Hill B, Lu HC, Moverley A, Yang Y, Oliveira NMM, Baldock RA, Stern CD. A 3D molecular atlas of the chick embryonic heart. Dev Biol. 2019 Dec 1;456(1):40-46. doi: 10.1016/j.ydbio.2019.07.003. Epub 2019 Jul 5.
Copyright	Copyright © 2019 Elsevier Inc. All rights reserved.
Comments	The complete cDNA template sequence was obtained from the information from the publication as described in Anderson et al. 2019.

Stage

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Location (click to highlight)

Comments (click to highlight)

7-12

stage 12

Unlabeled

Data from NCBI Unigene EST Profile
Unigene ID: Gga.55802

Mouse

Emage
Eurexpress
MGI GXD

Frog

Xenbase

Fruit Fly

BDGP

Zebra Finch

ZEBrA

Zebrafish

ZFIN

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HOXA1homeobox A1

Entry 1

Entry 2

Entry 3

Entry 4

Mouse

Frog

Fruit Fly

Zebra Finch

Zebrafish

HOXA1
homeobox A1