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A chicken embryo gene expression database

	Anatomical Location
	Stage
	Gene Name
	GEISHA ID
	Multiple Parameters

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HOXB5
homeobox B5

Gene

Official Symbol	HOXB5
Official Full Name	homeobox B5
CGNC ID	52343
also known as	Ghox-2.1, Hoxb-5, homeobox protein Hox-B5\|homeo box B5\|homeobox protein Hox-2.1, Homeobox protein Hox-B5, Ghox-2.1
gene type	protein-coding

Genomic Map

	Ensembl
	NCBI
	UCSC
	Gallus-Browse

Sequence Information

Genomic
RNA	NM_001025355
Polypeptide	NP_001020526
Sequence Clusters/ESTs	Unigene

Gene Expression

In Situ Hybridization	GEISHA
EST Profile	Gga.22931

Orthology

	Entrez Gene	Ensembl Gene	Genetic Phenotypes	MOD
Fruit Fly	40833			FBgn0003339
Human	3215	ENSG00000120075		MIM:142960
Mouse	15413		All phenotypic alleles (2):Targeted, knock-out(1) Targeted, other(1)	MGI:96186
Xenopus	100113366, 378578			1005990
Zebrafish	30317, 58052	ENSDARG00000013057, ENSDARG00000054030	ZDB-GENE-980526-70, ZDB-GENE-000823-6	ZFIN:ZDB-GENE-980526-70, ZFIN:ZDB-GENE-000823-6

Gene Ontology

Molecular Function	RNA polymerase II distal enhancer sequence-specific DNA binding, more...
Biological Process	anterior/posterior pattern specification, embryonic skeletal system morphogenesis, more...endothelial cell differentiation
Cellular Component	nucleus

Links to other databases

Entrez Gene	425096
Ensembl Gene	ENSGALG00000027903
KEGG	gga:425096

Entry 1

GEISHA Id	HOXB5.UApcr	Data Source	GEISHA ISH Analysis
Forward cDNA Template Primer	ATAAGCAGCAGCATCCCCCG
Reverse cDNA Template Primer	AATTAACCCTCACTAAAGGCAGAGAAAAACTCACCCCCAAAG	cDNA Template Length	822
Forward cDNA Template Probe	show NNNNNAGGACATCTCAGCAGTAACTCAGGAAGGGGAAAAGCAACAAATAAACAAACAATCGTTATCTGTTACCATCTCA TAAATAAGTTATAACATTTATAGGGCTCACATAAAACATGCTGGCTTTCCAGAAAGCATCAAGATAGCACGGACACGTA CATTTATAAGAACAACGAGAGCATGGGGAGCATCTGGAAATAAAATTTAATAATAATTAAAAAAAATTATTGGGAAAAA AATTTTATATCTCCCCCCAAAAAAGAAAAACCCCCCACGTGAACCCTCCCCGGGGAAAAGGGTCCCACACGCCTGGGTT TCAAATAACCACCACGTCCCAAAAAAAGGGGGCCTCAGTGTACAGTACCCCAAAACAAAAATCCGGTGCGCTTTATTTT TTTAGGGATTTATTAAATGTTCCCTCCTCTTTCCCCGATATTCCCCCCCCTAAAATTTAGGGGAAAAAGGCTCCCCCCA CAAAACCAAACCACACGCTTTACCGTTTAATACCCCTCCCCCATTTCCCCCCCCTGTTCGGGAACCAAATTTTGATCCC CCTCTCAGAAAGGCACAGAGCGTGAGAAATCTCTTTTCCCCCCCCGGGGGAGAAATATCTTGTGAAGTGAAATTCTTTT TCCCACCCCGGGGTCTGGGAGCGAGTGTACCCTCTCCCCCCCCTTTTCCGGTGGGGTCCAGATGTGTTGTGGCTAATGA AAAGTTCCCCCCCCCAGGGGAATATCTAGAAGTGCCCCCCCTTTTTTTCCCTCCGTGGATTTCCCTATGGGCTCCCTCT TCTC

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

1-3

stage 3

Unlabeled

4-6

stage 4

stage 5

stage 6

Extraembryonic Mesoderm
Kohler's Sickle
Lateral Plate Mesoderm
Primitive Streak

7-12

stage 7

stage 8

Extraembryonic Mesoderm
Lateral Plate Mesoderm
Primitive Streak

13-18

stage 13

stage 14

stage 15

stage 17

Intermediate Mesoderm
Lateral Plate Mesoderm
Paraxial Mesoderm
Somatic Mesoderm
Somites
Spinal Cord
Tail

19-24

stage 22

stage 24

Somatic Mesoderm
Somites
Spinal Cord
Tail

25-29

stage 25

stage 29

Gizzard
Somatic Mesoderm
Somites
Spinal Cord
Tail

Entry 2

GEISHA Id	HOXB5.Sakiyama.2000	Data Source	Publication
Complete cDNA Template Probe	show CGTCAAGCACAGGGTTATAACGACCACGAGCCACAAATCAAGCCCTCCAAAATAACCCAAATGAGCTCTTACTTTGTAA ACTCGTTCTCAGGGCGCTACCCAAATGGCCCCGACTATCAGTTACTAAATTATGGGACCAGCAGTTCCATGAACGGTTC TTACAGAGATTCAAGCACCATGCATTCCAGCTCTTATGGCTACAACTACAATGGGATGGACCTTAGCATCAACCGCTCA GCCTCCTCTAGTCACTTTGGGGCTGTGGGGGAGAGCTCCCGCGGTTTCCCTTCTCCAGCTCAGGAGAGCAGGTTTAGAC AGGCGTCTAGCTGCTCCTTATCTTCTCCCGACTCCCTTCCCTGCTCCAACAGCGAGAGCCATGGAGGCAAGCCCGCCCC GTCCCCCTCCGACCAAGCTACTTCTGCCAGCACCAACACAAATTTCACAGAACTAGACGAGACCAGCGCGTCCTCGGGA GCCGACGAGGGCACTCCAATAAGCAGCAGCATCCCCCGAGCGCAGGCAGAGCCCATCGCAACCTCCACGGCAGCAACAG AAGGGCAGGCACCTCAGATATTCCCTTGGATGAGGAAACTTCACATTAGTCATGACATGACTGGACCAGACGGGAAGAG GGCGAGGACAGCGTACACTCGCTACCAGACCCTGGAGTTGGAAAAGGAATTCCACTTCAATAGATATCTCACCCGCAGG AGGAGAATAGAGATCGCTCACGCTCTGTGCCTCTCCGAGAGGCAGATCAAAATCTGGTTCCAGAACAGGAGGATGAAAT GGAAGAAGGATAATAAACTGAAAAGCATGAGCTTAGCTTCTGCGGGCAGCGCCTTTCAGCCATAAATTATAGAGGAAGG AATATCGAGGAAAGAAGAGGAAACATTAAATAAATCCGTAAATAAATAAAGCGCAGCAGATCTTAGTTTTGGAGTACTG TACAGTGAGGCACCTTCTTTTCGGCATGTTGTTGCTATTCGAAACCGACGCGTATGGTACCTTTATCCCAGGACTGAGT TCATGTCGTGGTTTTTTCTTTTTTGGGTTGATTTATTAATTTTTTTCCTATTATTTTTTTTTAATTATTATTAAATTTT ATTTCCAGATGCTCCCCATGCTCTCGTTGTTTTTATAAATGTACGTGTCCGTGCTATCTTGATGCTTTCTGGAAAGCCA GCATGTTTTATGTGAGCCCTATAAATGTTATAACTTATTTATGAGATGGTAACAGATAACGATTGTTTGTTTATTTGTT GCTTTTTCCCCTTCCTGAGTTTACTGCTTTGGGGGTGAGTTTTTCTCTGCCTGAGCTAAAATCGGGGGTTCCTGCACTA CAGTCGCAGTAAAAAATAATAATAAGCAAGAAAAAAAAACATAAAAAAGAGGGGGAAAAAAGAGAAAAAAAAGGGGGAA AAAGATTAAAAAAATTTAAAAAGGGGAAAAA
Citation	Sakiyama J, Yokouchi Y, Kuroiwa A. Coordinated expression of Hoxb genes and signaling molecules during development of the chick respiratory tract. Dev Biol. 2000 Nov 1;227(1):12-27.
Copyright	Reprinted with permission from Elsevier. Copyright © 2000 Elsevier B.V. All rights reserved.
Comments	Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI (NM_001025355).

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

19-24

stage 24

Lung

25-30

stage 27

stage 29

Lung

31-34

stage 34

Figure 2 compares expression of the Hoxb genes in the developing chick respiratory tract at HH stages 24, 27, 29 and 34.

Entry 3

GEISHA Id	HOXB5.Barak.2012	Data Source	Publication
Complete cDNA Template Probe	show CGTCAAGCACAGGGTTATAACGACCACGAGCCACAAATCAAGCCCTCCAAAATAACCCAAATGAGCTCTTACTTTGTAA ACTCGTTCTCAGGGCGCTACCCAAATGGCCCCGACTATCAGTTACTAAATTATGGGACCAGCAGTTCCATGAACGGTTC TTACAGAGATTCAAGCACCATGCATTCCAGCTCTTATGGCTACAACTACAATGGGATGGACCTTAGCATCAACCGCTCA GCCTCCTCTAGTCACTTTGGGGCTGTGGGGGAGAGCTCCCGCGGTTTCCCTTCTCCAGCTCAGGAGAGCAGGTTTAGAC AGGCGTCTAGCTGCTCCTTATCTTCTCCCGACTCCCTTCCCTGCTCCAACAGCGAGAGCCATGGAGGCAAGCCCGCCCC GTCCCCCTCCGACCAAGCTACTTCTGCCAGCACCAACACAAATTTCACAGAACTAGACGAGACCAGCGCGTCCTCGGGA GCCGACGAGGGCACTCCAATAAGCAGCAGCATCCCCCGAGCGCAGGCAGAGCCCATCGCAACCTCCACGGCAGCAACAG AAGGGCAGGCACCTCAGATATTCCCTTGGATGAGGAAACTTCACATTAGTCATGACATGACTGGACCAGACGGGAAGAG GGCGAGGACAGCGTACACTCGCTACCAGACCCTGGAGTTGGAAAAGGAATTCCACTTCAATAGATATCTCACCCGCAGG AGGAGAATAGAGATCGCTCACGCTCTGTGCCTCTCCGAGAGGCAGATCAAAATCTGGTTCCAGAACAGGAGGATGAAAT GGAAGAAGGATAATAAACTGAAAAGCATGAGCTTAGCTTCTGCGGGCAGCGCCTTTCAGCCATAAATTATAGAGGAAGG AATATCGAGGAAAGAAGAGGAAACATTAAATAAATCCGTAAATAAATAAAGCGCAGCAGATCTTAGTTTTGGAGTACTG TACAGTGAGGCACCTTCTTTTCGGCATGTTGTTGCTATTCGAAACCGACGCGTATGGTACCTTTATCCCAGGACTGAGT TCATGTCGTGGTTTTTTCTTTTTTGGGTTGATTTATTAATTTTTTTCCTATTATTTTTTTTTAATTATTATTAAATTTT ATTTCCAGATGCTCCCCATGCTCTCGTTGTTTTTATAAATGTACGTGTCCGTGCTATCTTGATGCTTTCTGGAAAGCCA GCATGTTTTATGTGAGCCCTATAAATGTTATAACTTATTTATGAGATGGTAACAGATAACGATTGTTTGTTTATTTGTT GCTTTTTCCCCTTCCTGAGTTTACTGCTTTGGGGGTGAGTTTTTCTCTGCCTGAGCTAAAATCGGGGGTTCCTGCACTA CAGTCGCAGTAAAAAATAATAATAAGCAAGAAAAAAAAACATAAAAAAGAGGGGGAAAAAAGAGAAAAAAAAGGGGGAA AAAGATTAAAAAAATTTAAAAAGGGGAAAAA
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 #NM_001025355.1).

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

4-6

stage 4

stage 6

Kohler's Sickle
Lateral Plate Mesoderm
Primitive Streak

7-11

stage 7

stage 8

stage 9

stage 10

stage 11

Area Opaca
Blood Vessels
Central Nervous System
Extraembryonic Mesoderm
Lateral Plate Mesoderm
Paraxial Mesoderm
Primitive Streak
Somites
Tail

Entry 4

GEISHA Id	Hoxb5.Bel-Vialar.2002	Data Source	GEISHA ISH Analysis
Complete cDNA Template Probe	show CGTCAAGCACAGGGTTATAACGACCACGAGCCACAAATCAAGCCCTCCAAAATAACCCAAATGAGCTCTTACTTTGTAA ACTCGTTCTCAGGGCGCTACCCAAATGGCCCCGACTATCAGTTACTAAATTATGGGACCAGCAGTTCCATGAACGGTTC TTACAGAGATTCAAGCACCATGCATTCCAGCTCTTATGGCTACAACTACAATGGGATGGACCTTAGCATCAACCGCTCA GCCTCCTCTAGTCACTTTGGGGCTGTGGGGGAGAGCTCCCGCGGTTTCCCTTCTCCAGCTCAGGAGAGCAGGTTTAGAC AGGCGTCTAGCTGCTCCTTATCTTCTCCCGACTCCCTTCCCTGCTCCAACAGCGAGAGCCATGGAGGCAAGCCCGCCCC GTCCCCCTCCGACCAAGCTACTTCTGCCAGCACCAACACAAATTTCACAGAACTAGACGAGACCAGCGCGTCCTCGGGA GCCGACGAGGGCACTCCAATAAGCAGCAGCATCCCCCGAGCGCAGGCAGAGCCCATCGCAACCTCCACGGCAGCAACAG AAGGGCAGGCACCTCAGATATTCCCTTGGATGAGGAAACTTCACATTAGTCATGACATGACTGGACCAGACGGGAAGAG GGCGAGGACAGCGTACACTCGCTACCAGACCCTGGAGTTGGAAAAGGAATTCCACTTCAATAGATATCTCACCCGCAGG AGGAGAATAGAGATCGCTCACGCTCTGTGCCTCTCCGAGAGGCAGATCAAAATCTGGTTCCAGAACAGGAGGATGAAAT GGAAGAAGGATAATAAACTGAAAAGCATGAGCTTAGCTTCTGCGGGCAGCGCCTTTCAGCCATAAATTATAGAGGAAGG AATATCGAGGAAAGAAGAGGAAACATTAAATAAATCCGTAAATAAATAAAGCGCAGCAGATCTTAGTTTTGGAGTACTG TACAGTGAGGCACCTTCTTTTCGGCATGTTGTTGCTATTCGAAACCGACGCGTATGGTACCTTTATCCCAGGACTGAGT TCATGTCGTGGTTTTTTCTTTTTTGGGTTGATTTATTAATTTTTTTCCTATTATTTTTTTTTAATTATTATTAAATTTT ATTTCCAGATGCTCCCCATGCTCTCGTTGTTTTTATAAATGTACGTGTCCGTGCTATCTTGATGCTTTCTGGAAAGCCA GCATGTTTTATGTGAGCCCTATAAATGTTATAACTTATTTATGAGATGGTAACAGATAACGATTGTTTGTTTATTTGTT GCTTTTTCCCCTTCCTGAGTTTACTGCTTTGGGGGTGAGTTTTTCTCTGCCTGAGCTAAAATCGGGGGTTCCTGCACTA CAGTCGCAGTAAAAAATAATAATAAGCAAGAAAAAAAAACATAAAAAAGAGGGGGAAAAAAGAGAAAAAAAAGGGGGAA AAAGATTAAAAAAATTTAAAAAGGGGAAAAA
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_001025355.1).

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

7-11

stage 11

Lateral Plate Mesoderm
Somites
Spinal Cord

in between HH stage 11-13

Entry 5

GEISHA Id	HOXB5.Anderson.2021	Data Source	Direct Submission
Complete cDNA Template Probe	show ATGAGCTCTTACTTTGTAAACTCGTTCTCAGGGCGCTACCCAAATGGCCCCGACTATCAGTTACTAAATTATGGGACCA GCAGTTCCATGAACGGTTCTTACAGAGATTCAAGCACCATGCATTCCAGCTCTTATGGCTACAACTACAATGGGATGGA CCTTAGCATCAACCGCTCAGCCTCCTCTAGTCACTTTGGGGCTGTGGGGGAGAGCTCCCGCGGTTTCCCTTCTCCAGCT CAGGAGAGCAGGTTTAGACAGGCGTCTAGCTGCTCCTTATCTTCTCCCGACTCCCTTCCCTGCTCCAACAGCGAGAGCC ATGGAGGCAAGCCCGCCCCGTCCCCCTCCGACCAAGCTACTTCTGCCAGCACCAACACAAATTTCACAGAACTAGACGA GACCAGCGCGTCCTCGGGAGCCGACGAGGGCACTCCAATAAGCAGCAGCATCCCCCGAGCGCAGGCAGAGCCCATCGCA ACCTCCACGGCAGCAACAGAAGGGCAGGCACCTCAGATATTCCCTTGGATGAGGAAACTTCACATTAGCCATGACATGA CTGGACCAGACGGGAAGAGGGCGAGGACAGCGTACACTCGCTACCAGACCCTGGAGTTGGAAAAGGAATTCCACTTCAA TAGATATCTCACCCGCAGGAGGAGAATAGAGATCGCTCACGCTCTGTGCCTCTCCGAGAGGCAGATCAAAATCTGGTTC CAGAACAGGAGGATGAAATGGAAGAAGGATAATAAACTGAAAAGCATGAGCTTAGCTTC
Comments	Images and probe sequence provided by Claire Anderson. 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

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

7-12

stage 12

Allantois
Extraembryonic Blood Vessels
Intermediate Mesoderm
Lateral Plate Mesoderm
Neural Plate/Tube
Somites
Tail

Entry 6

GEISHA Id	HOXB5.Anderson.2019	Data Source	Publication
Complete cDNA Template Probe	show CGTCAAGCACAGGGTTATAACGACCACGAGCCACAAATCAAGCCCTCCAAAATAACCCAAATGAGCTCTTACTTTGTAA ACTCGTTCTCAGGGCGCTACCCAAATGGCCCCGACTATCAGTTACTAAATTATGGGACCAGCAGTTCCATGAACGGTTC TTACAGAGATTCAAGCACCATGCATTCCAGCTCTTATGGCTACAACTACAATGGGATGGACCTTAGCATCAACCGCTCA GCCTCCTCTAGTCACTTTGGGGCTGTGGGGGAGAGCTCCCGCGGTTTCCCTTCTCCAGCTCAGGAGAGCAGGTTTAGAC AGGCGTCTAGCTGCTCCTTATCTTCTCCCGACTCCCTTCCCTGCTCCAACAGCGAGAGCCATGGAGGCAAGCCCGCCCC GTCCCCCTCCGACCAAGCTACTTCTGCCAGCACCAACACAAATTTCACAGAACTAGACGAGACCAGCGCGTCCTCGGGA GCCGACGAGGGCACTCCAATAAGCAGCAGCATCCCCCGAGCGCAGGCAGAGCCCATCGCAACCTCCACGGCAGCAACAG AAGGGCAGGCACCTCAGATATTCCCTTGGATGAGGAAACTTCACATTAGTCATGACATGACTGGACCAGACGGGAAGAG GGCGAGGACAGCGTACACTCGCTACCAGACCCTGGAGTTGGAAAAGGAATTCCACTTCAATAGATATCTCACCCGCAGG AGGAGAATAGAGATCGCTCACGCTCTGTGCCTCTCCGAGAGGCAGATCAAAATCTGGTTCCAGAACAGGAGGATGAAAT GGAAGAAGGATAATAAACTGAAAAGCATGAGCTTAGCTTCTGCGGGCAGCGCCTTTCAGCCATAAATTATAGAGGAAGG AATATCGAGGAAAGAAGAGGAAACATTAAATAAATCCGTAAATAAATAAAGCGCAGCAGATCTTAGTTTTGGAGTACTG TACAGTGAGGCACCTTCTTTTCGGCATGTTGTTGCTATTCGAAACCGACGCGTATGGTACCTTTATCCCAGGACTGAGT TCATGTCGTGGTTTTTTCTTTTTTGGGTTGATTTATTAATTTTTTTCCTATTATTTTTTTTTAATTATTATTAAATTTT ATTTCCAGATGCTCCCCATGCTCTCGTTGTTTTTATAAATGTACGTGTCCGTGCTATCTTGATGCTTTCTGGAAAGCCA GCATGTTTTATGTGAGCCCTATAAATGTTATAACTTATTTATGAGATGGTAACAGATAACGATTGTTTGTTTATTTGTT GCTTTTTCCCCTTCCTGAGTTTACTGCTTTGGGGGTGAGTTTTTCTCTGCCTGAGCTAAAATCGGGGGTTCCTGCACTA CAGTCGCAGTAAAAAATAATAATAAGCAAGAAAAAAAAACATAAAAAAGAGGGGGAAAAAAGAGAAAAAAAAGGGGGAA AAAGATTAAAAAAATTTAAAAAGGGGAAAAA
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	Insufficient information provided in publication to verify exact sequence used to synthesize probe. Sequence below was obtained from NCBI ( NM_001025355).