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A chicken embryo gene expression database

	Anatomical Location
	Stage
	Gene Name
	GEISHA ID
	Multiple Parameters

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CDX4
caudal type homeobox 4

Gene

Official Symbol	CDX4
Official Full Name	caudal type homeobox 4
CGNC ID
also known as	CDXB, CHOX-CAD2, ox-cad2, homeobox protein CHOX-CAD2\|Homeobox protein CHOX-CAD2\|caudal type homeo box transcription factor 4\|caudal type homeobox transcription factor 4\|caudal-type homeobox protein CDXB
gene type	protein-coding

Genomic Map

	Ensembl
	NCBI
	UCSC

Sequence Information

Genomic
RNA	NM_204614
Polypeptide	NP_989945

Gene Expression

In Situ Hybridization

GEISHA

Orthology

	Entrez Gene	Ensembl Gene	Genetic Phenotypes	MOD
Fruit Fly
Human	1046			MIM:300025
Mouse	12592	ENSMUSG00000031326	All phenotypic alleles (5):Targeted, knock-out(1) Targeted, other(4)	MGI:88362
Xenopus	395056, 380412			482786
Zebrafish	798281	ENSDARG00000036292	ZDB-GENE-980526-330	ZFIN:ZDB-GENE-980526-330

Gene Ontology

Molecular Function
Biological Process
Cellular Component

Links to other databases

Entrez Gene	395320
Ensembl Gene	ENSGALG00000007657
KEGG	gga:395320

Entry 1

GEISHA Id	ChEST433k20	Data Source	GEISHA ISH Analysis
Forward cDNA Template Probe	show AAAGGGACATGAGGGCTAGCATGAGTCATTTATAGAGCCAGTCAGAGCTAGAAAAGAGAGAGAAAGAAAGAGGAGGGGA AGAGATCAAACAAACACCGTGAGGAGCAGGATGCCCCAGCAAGACAAAGCCAGGCTGTGAGCATCATGTATGTGAGTTA CCTTTTGGATAAAGAGACCAGCATGTATCCAGGACCTGCAAGGTGCAGCAACAACAACCTGCCAGTGCAGAACTTTGTG CCTGCTCCCCCCTACTCAGACTACATGGGGTATCACCACGTGCCAGCTCCAGACAGCCACGGACAGCCCGCGGGAACCT GGGGACCCCACTACGGCCCCCAGAGGGAGGACTGGAACGCTTACGGCCCGTGCCCAGGGCCCTCCGGCACGGCTGCTGC CGCACAGCTCAGCGGCTCCTCTCCTGGGCAGGGCTCCTACAGTCCAGCTGAGTACAGCTCCCTCCATCCCGCTGCACCC GGGGGGTTACCTCCTGCAGGCACCGTTGGCACACAGCAGGTCTCACCCACCAACCAAAGGCACAGCTCTTACGAATGGA TGAGGAAAACGGTGCAATCCACTTCTACAGGTAAAACAAGAACAAGAGAGAAGTACCGAGTGGTTTACACAGATCATCA GAGATTAGAATTAGAGAAGGAATTTCATTACAACAGATACATTACAATCAGGAGGAAGTCTGAACTTGCTGCAAACCTA AGACTTTCCGAGAGACAGGTG
Comments	potenetially enough overlap in homology to also bind to paralog HMD2_CHICK (Homeobox protein CHOX-CAD2)

Stage

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Location (click to highlight)

Comments (click to highlight)

4-6

stage 4

stage 5

stage 6

Early Mesoderm
Epiblast
Lateral Plate Mesoderm
Mesoderm, early
Paraxial Mesoderm
Primitive Streak

7-12

stage 7

stage 8

stage 9

stage 10

stage 12

Lateral Plate Mesoderm
Neural Plate/Tube
Notochord
Primitive Streak
Spinal Cord

13-18

stage 13

stage 14

stage 17

stage 18

Extraembryonic
Lateral Plate Mesoderm
Paraxial Mesoderm
Primitive Streak
Spinal Cord
Tail

19-24

stage 20

stage 21

stage 22

stage 24

Amnion
Extraembryonic
Hindgut
Tail

stage 25

Hindgut
Tail

Entry 2

GEISHA Id	CDX4.Alev.2010	Data Source	Publication
Complete cDNA Template Probe	show ACGAATGGATGAGGAAAACGGTGCCAACTAACACTACTGGTAAAACAAGAACAAAAGAGAAGTACCGGGTTGTTTACAC AGACCATCAGAGACTAGAATTAGAGAAGGAATTTCACTGCAACAGATACATTACAATAAGGAGAAAGTCAGAACTTGCA GCAAACCTTGGACTATCTGAAAGACAGGTAAAAATCTGGTTCCAGAATCGCCGAGCCAAAGAAAGAAAAATAATCAAGA AGAAAATCTCTCAGTTTGATGGCAGCGGGGGCTCAGTTCAGAGTGACTCTGGTTCACTCAGCCCTAATGAAATAACAAG TTCCCTGTTCCCACCACCACACGGAATAAATGTATTACAGTCTGCTGACATCCATCAGGTCATAGTTTCAGAATGAACA GTGGGGGAAAAAGAAAAACAGAAAAAAAGAGTTGTATGGATTTTTTGTTTTTGTTTTTAACTCCCTCTATTGAAAACTC AATTTTGCAAAGCACCATTCTTGTTTAACTACCTTCAGAGTACTTATTTCCACATAGAGGATCTGGAACTATTACCAAA ATATTTCAATTAAAAAAATCTCAGGGAGTTCGTGCTGCTGCTAATACTCATCACTCAAAATCTTTTGAATAGAAGATAA TTTACTTCAGATACCGAAGCAGAAAAAGATACTGCTGAAGATTCAAGCAAACCTAATTCTAGTCTGCTCATGTATACAA AGAAAACTGTCAGTGAATTGATTATAGAGTAATACTGCATAAAATGTAAGATGCTGGATGTATTTAGTTTGTTACATTT TATATAATTAAACAGTAGATTTTATAAATATTCACATTTAATGTGTACTGAAAATTAAGTCATTTTTTGAAAACAACTT TTTAAACACTTAAACACTCAAGAGACATAACAATGTTACGCCTGGTGACACA
Citation	Alev C, Wu Y, Kasukawa T, Jakt LM, Ueda HR, Sheng G. Transcriptomic landscape of the primitive streak. Development. 2010 Sep 1;137(17):2863-74. Epub 2010 Jul 28.
Copyright	Published by The Company of Biologists 2010. This material is protected by a copyright retained by the authors. Permission granted by Dr. G Sheng.

Stage

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Location (click to highlight)

Comments (click to highlight)

stage 4

Primitive Streak

Entry 3

GEISHA Id	CDX4.Joshi.2019	Data Source	Publication
Complete cDNA Template Probe	show CATGTATGTGAGTTCTCTCTTGGATAAAGAGACCAGCATGTATCCAGGACCTGCAAGGTGCAGCAACAACAACCTGCCA GTGCAGAACTTTGTGCCTGCTCCCCCCTACTCAGACTACATGGGGTATCACCACGTGCCAGCTCCAGACAGCCACGGAC AGCCCGCGGGAGCCTGGGGACCCCACTACGGCCCCCAGAGGGAGGACTGGAACGCTTACGGCCCGTGCCCAGGGCCCTC CGGCACGGCTGCTGCCGCACAGCTCAGCGGCTCCTCTCCTGGGCAGGGCTCCTACAGTCCAGCTGAGTACAGCTCCCTC CATCCCGCTGCACCCGGGGGGTTACCTCCTGCAGGCACCGTTGGCACACAGCAGGTCTCACCCACCAACCAAAGGCACA GCTCTTACGAATGGATGAGGAAAACGGTGCCAACTAACACTACTGGTAAAACAAGAACAAAAGAGAAGTACCGGGTTGT TTACACAGACCATCAGAGACTAGAATTAGAGAAGGAATTTCACTGCAACAGATACATTACAATAAGGAGAAAGTCAGAA CTTGCAGCAAACCTTGGACTATCTGAAAGACAGGTAAAAATCTGGTTCCAGAATCGCCGAGCCAAAGAAAGAAAAATAA TCAAGAAGAAAATCTCTCAGTTTGATGGCAGCGGGGGCTCAGTTCAGAGTGACTCTGGTTCACTCAGCCCTAATGAAAT AACAAGTTCCCTGTTCCCACCACCACACGGAATAAATGTATTACAGTCTGCTGACATCCATCAGGTCATAGTTTCAGAA TGAACA
Citation	Piyush Joshi, Andrew J Darr, Isaac Skromne. CDX4 regulates the progression of neural maturation in the spinal cord. Dev Biol. 2019 May 15;449(2):132-142. Epub 2019 Feb 28. DOI: 10.1016/j.ydbio.2019.02.014.
Copyright	Copyright © 2019 Elsevier Inc.
Comments	Authors indicated that the probe was amplified by PCR using the following primers: 5'-ACATGTATGTGAGTTCTCTCTTGG-3' and 5'-TGATCATTCTGAAACTATGAC-3' and was extracted from NCBI accession number NM_204614.1

Stage

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Location (click to highlight)

Comments (click to highlight)

7-11

stage 11

Lateral Plate Mesoderm
Neural Plate/Tube
Primitive Streak

all

Entry 4

GEISHA Id	cdxB.Bel-Vialar.2002	Data Source	GEISHA ISH Analysis
Complete cDNA Template Probe	show AAAATCAAGCTACTATTTTTTAAGCAGCAAAAGAAAATACAGAAGAGCAAGATGTTGTGACAACATTTACAATCTGCAA GCATCATGTATGTGAGTTCTCTCTTGGATAAAGAGACCAGCATGTATCCAGGACCTGCAAGGTGCAGCAACAACAACCT GCCAGTGCAGAACTTTGTGCCTGCTCCCCCCTACTCAGACTACATGGGGTATCACCACGTGCCAGCTCCAGACAGCCAC GGACAGCCCGCGGGAGCCTGGGGACCCCACTACGGCCCCCAGAGGGAGGACTGGAACGCTTACGGCCCGTGCCCAGGGC CCTCCGGCACGGCTGCTGCCGCACAGCTCAGCGGCTCCTCTCCTGGGCAGGGCTCCTACAGTCCAGCTGAGTACAGCTC CCTCCATCCCGCTGCACCCGGGGGGTTACCTCCTGCAGGCACCGTTGGCACACAGCAGGTCTCACCCACCAACCAAAGG CACAGCTCTTACGAATGGATGAGGAAAACGGTGCCAACTAACACTACTGGTAAAACAAGAACAAAAGAGAAGTACCGGG TTGTTTACACAGACCATCAGAGACTAGAATTAGAGAAGGAATTTCACTGCAACAGATACATTACAATAAGGAGAAAGTC AGAACTTGCAGCAAACCTTGGACTATCTGAAAGACAGGTAAAAATCTGGTTCCAGAATCGCCGAGCCAAAGAAAGAAAA ATAATCAAGAAGAAAATCTCTCAGTTTGATGGCAGCGGGGGCTCAGTTCAGAGTGACTCTGGTTCACTCAGCCCTAATG AAATAACAAGTTCCCTGTTCCCACCACCACACGGAATAAATGTATTACAGTCTGCTGACATCCATCAGGTCATAGTTTC AGAATGAACAGTGGGGGAAAAAGAAAAACAGAAAAAAAGAGTTGTATGGATTTTTTGTTTTTGTTTTTAACTCCCTCTA TTGAAAACTCAATTTTGCAAAGCACCATTCTTGTTTAACTACCTTCAGAGTACTTATTTCCACATAGAGGATCTGGAAC TATTACCAAAATATTTCAATTAAAAAAATCTCAGGGAGTTCGTGCTGCTGCTAATACTCATCACTCAAAATCTTTTGAA TAGAAGATAATTTACTTCAGATACCGAAGCAGAAAAAGATACTGCTGAAGATTCAAGCAAACCTAATTCTAGTCTGCTC ATGTATACAAAGAAAACTGTCAGTGAATTGATTATAGAGTAATACTGCATAAAATGTAAGATGCTGGATGTATTTAGTT TGTTACATTTTATATAATTAAACAGTAGATTTTATAAATATTCACATTTAATGTGTACTGAAAATTAAGTCATTTTTTG AAAACAACTTTTTAAACACTTAAACACTCAAGAGACATAACAATGTTACGCCTGGTGACACATTGCGTCCCATTAAATA AAATGAATAGTCTTTGTATTCTAAAAAAAAA
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_204614.1).