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A chicken embryo gene expression database

	Anatomical Location
	Stage
	Gene Name
	GEISHA ID
	Multiple Parameters

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LHX3
LIM homeobox 3

The human orthologue of this gene is associated
with the following human disease:

Pituitary hormone deficiency, combined, 3

Gene

Official Symbol	LHX3
Official Full Name	LIM homeobox 3
CGNC ID	48967
also known as	lim-3, LIM/homeobox protein Lhx3\|LIM homeobox protein 3\|homeobox protein LIM-3, LIM/homeobox protein Lhx3, Homeobox protein LIM-3, LIM-3
gene type	protein-coding

Genomic Map

	Ensembl
	NCBI
	UCSC
	Gallus-Browse

Sequence Information

Genomic
RNA	NM_001030335
Polypeptide	NP_001025506
Sequence Clusters/ESTs	Unigene

Gene Expression

In Situ Hybridization	GEISHA
EST Profile	Gga.91

Orthology

	Entrez Gene	Ensembl Gene	Genetic Phenotypes	MOD
Fruit Fly	35184			FBgn0002023
Human	8022	ENSG00000107187	MIM:221750	MIM:600577
Mouse	16871	ENSMUSG00000026934	All phenotypic alleles (5):Targeted, knock-out(1) Targeted, other(4)	MGI:102673
Xenopus	100489308, 397959			490074
Zebrafish	30455		ZDB-GENE-980526-131	ZFIN:ZDB-GENE-980526-131

Gene Ontology

Molecular Function	sequence-specific DNA binding, sequence-specific DNA binding transcription factor activity, more...zinc ion binding
Biological Process	transcription, DNA-templated
Cellular Component	nucleus

Links to other databases

Entrez Gene	373940
Ensembl Gene	ENSGALG00000003928
KEGG	gga:373940

Entry 1

GEISHA Id	LHX3.UApcr	Data Source	GEISHA ISH Analysis
Reverse cDNA Template Probe	show GTGCTTGAAATGTTCCGACTGCCAGACGCAGCTGGCCGAGAAGTGCTTCAGCCGAGGGGACGGCGTGTACTGCAAGGAG GATTTCTTCAAACGCTTCGGGACGAAGTGCGCCGCCTGCCAGCAGGGCATCCCCCCGACCCAGGTGGTGCGCCGGGCCC AGGACTTCGTGTACCACCTGCACTGCTTCGCCTGCATCGTCTGCAAGCGGCAGCTGGCCACCGGAGATGAGTTCTACCT GATGGAGGACAGCAGGCTGGTGTGCAAGGCTGACTACGAGACGGCCAAGCAGAGAGAGGCCGAGTCCACGGCCAAGAGG CCCCGCACCACCATCACAGCCAAGCAGCTGGAGACCCTCAAAAACGCCTACAACAACTCGCCCAAGCCGGCGCGGCACG TCCGGGAGCAGCTCTCGTCGGAGACGGGGTTGGATATGCGGGTGGTGCAGGTCTGGTTCCAGAACCGCAGGGCCAAGGA GAAGCGGCTGAAGAAGGACGCGGGGAGGCAGCGCTGGGGGCAGTACTTCAGGAACATGAAGAGGTCCCGGGGGACCTCC AAGTCCGACAAGGACAGCATCCAGGAGGAGGGGCCCGACAGCGACGCCGAGGTCTCCTTCACAGACGAGCCCTCCATGT CCGAGATGAGCCACTCCAATGGCATTTACAGCAATCTCAGCGAGGCGTCCCCGGCCCTGGGGAGGCAGGCTGGGACCAA CGGGGGCTTCTCTCTGGATCACAGTGGCATCCCAGCTCAGGACCAGTACCACGACCTGCGATCCAACAGCCCCTATGGG ATTCCCCAGTCACCGGCTTCATTGCAAGCGCTGCCGGGCCACCAGCCTTTAGTGAGGNTTATTTTTTTTAAAAA

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

Primitive Streak

7-12

stage 10

Oral Pharynx

13-18

stage 13

stage 14

stage 15

stage 16

stage 18

Face Mesenchyme
Oral Pharynx
Spinal Cord

motor horns

19-22

stage 19

stage 20

stage 21

stage 22

Face Mesenchyme
Hindbrain
Oral Pharynx
Spinal Cord

Entry 2

GEISHA Id	LIM3.Hargrave.2000	Data Source	Publication
Complete cDNA Template Probe	show ATGCTGCTGGAGAGGGTCCGCGCCGGCTCGGAGAAGGCAGCGGAGCTCTGCCCCTTCCCTCGGAGCCCAGAGATCCCGC TGTGCGCCGGCTGCAATCAGCACATCGTGGACAGGTTCATCCTCAAGGTCCTGGACCGGCATTGGCACAGCAAGTGCTT GAAATGTTCCGACTGCCAGACGCAGCTGGCCGAGAAGTGCTTCAGCCGAGGGGACGGCGTGTACTGCAAGGAGGATTTC TTCAAACGCTTCGGGACGAAGTGCGCCGCCTGCCAGCAGGGCATCCCCCCGACCCAGGTGGTGCGCCGGGCCCAGGACT TCGTGTACCACCTGCACTGCTTCGCCTGCATCGTCTGCAAGCGGCAGCTGGCCACCGGAGATGAGTTCTACCTGATGGA GGACAGCAGGCTGGTGTGCAAGGCTGACTACGAGACGGCCAAGCAGAGAGAGGCCGAGTCCACGGCCAAGAGGCCCCGC ACCACCATCACAGCCAAGCAGCTGGAGACCCTCAAAAACGCCTACAACAACTCGCCCAAGCCGGCGCGGCACGTCCGGG AGCAGCTCTCGTCGGAGACGGGGTTGGATATGCGGGTGGTGCAGGTCTGGTTCCAGAACCGCAGGGCCAAGGAGAAGCG GCTGAAGAAGGACGCGGGGAGGCAGCGCTGGGGGCAGTACTTCAGGAACATGAAGAGGTCCCGGGGGACCTCCAAGTCC GACAAGGACAGCATCCAGGAGGAGGGGCCCGACAGCGACGCCGAGGTCTCCTTCACAGACGAGCCCTCCATGTCCGAGA TGAGCCACTCCAATGGCATTTACAGCAATCTCAGCGAGGCGTCCCCGGCCCTGGGGAGGCAGGCTGGGACCAACGGGGG CTTCTCTCTGGATCACAGTGGCATCCCAGCTCAGGACCAGTACCACGACCTGCGATCCAACAGCCCCTATGGGATTCCC CAGTCACCGGCTTCATTGCAAGCGCTGCCGGGCCACCAGCCTTTAATCTCCAGCTTGGTTTACCCTGACAGCGGTTTGG GCATCATGGGACAAGGTGGACAGGGGGTGCCCCAGTCCATGCGGGTCCTGGCCGGGAATGGGCCCAGCTCCGACCTCTC CACCGGCAGCAGTGGGGGATACCCGGATTTCCCTGCCAGCCCGGCCTCCTGGCTGGATGAAGTCGATCACGCTCAGTTT TGATAGAGG
Citation	Hargrave M, Karunaratne A, Cox L, Wood S, Koopman P, Yamada T. The HMG box transcription factor gene Sox14 marks a novel subset of ventral interneurons and is regulated by sonic hedgehog. Dev Biol. 2000 Mar 1;219(1):142-53.
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_001030335).

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

25-28

stage 25

stage 28

Spinal Cord

Figure 3 compares the expression patterns of Sox14, Islet1 and Lim3 in a population of ventral interneurons in chick spinal cord at HH18, HH24 and HH28.
Medial Interneurons
Medial Motor Column
Motor Neurons
Ventral Interneurons

Entry 3

GEISHA Id	LIM3.Parkinson.2010	Data Source	Publication
Complete cDNA Template Probe	show CGGACATCCCGTGCACCCGGCGCGCCCGCGATGCTGCTGGAGAGGGTCCGCGCCGGCTCGGAGAAGGCAGCGGAGCTCT GCCCCTTCCCTCGGAGCCCAGAGATCCCGCTGTGCGCCGGCTGCAATCAGCACATCGTGGACAGGTTCATCCTCAAGGT CCTGGACCGGCATTGGCACAGCAAGTGCTTGAAATGTTCCGACTGCCAGACGCAGCTGGCCGAGAAGTGCTTCAGCCGA GGGGACGGCGTGTACTGCAAGGAGGATTTCTTCAAACGCTTCGGGACGAAGTGCGCCGCCTGCCAGCAGGGCATCCCCC CGACCCAGGTGGTGCGCCGGGCCCAGGACTTCGTGTACCACCTGCACTGCTTCGCCTGCATCGTCTGCAAGCGGCAGCT GGCCACCGGAGATGAGTTCTACCTGATGGAGGACAGCAGGCTGGTGTGCAAGGCTGACTACGAGACGGCCAAGCAGAGA GAGGCCGAGTCCACGGCCAAGAGGCCCCGCACCACCATCACAGCCAAGCAGCTGGAGACCCTCAAAAACGCCTACAACA ACTCGCCCAAGCCGGCGCGGCACGTCCGGGAGCAGCTCTCGTCGGAGACGGGGTTGGATATGCGGGTGGTGCAGGTCTG GTTCCAGAACCGCAGGGCCAAGGAGAAGCGGCTGAAGAAGGA
Citation	Parkinson N, Collins MM, Dufresne L, Ryan AK. Expression patterns of hormones, signaling molecules, and transcription factors during adenohypophysis development in the chick embryo. Dev Dyn. 2010 Apr;239(4):1197-210.
Copyright	Copyright © 2010 Wiley-Liss, 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 #AF461699).

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

19-24

stage 21

Pituitary (Rudiment)

25-30

stage 27

Pituitary (Rudiment)

31-36

stage 32

stage 36

Pituitary (Rudiment)

Entry 4

GEISHA Id	LHX3.Inoue.2006	Data Source	Publication
Complete cDNA Template Probe	show ATGCTGCTGGAGAGGGTCCGCGCCGGCTCGGAGAAGGCAGCGGAGCTCTGCCCCTTCCCTCGGAGCCCAGAGATCCCGC TGTGCGCCGGCTGCAATCAGCACATCGTGGACAGGTTCATCCTCAAGGTCCTGGACCGGCATTGGCACAGCAAGTGCTT GAAATGTTCCGACTGCCAGACGCAGCTGGCCGAGAAGTGCTTCAGCCGAGGGGACGGCGTGTACTGCAAGGAGGATTTC TTCAAACGCTTCGGGACGAAGTGCGCCGCCTGCCAGCAGGGCATCCCCCCGACCCAGGTGGTGCGCCGGGCCCAGGACT TCGTGTACCACCTGCACTGCTTCGCCTGCATCGTCTGCAAGCGGCAGCTGGCCACCGGAGATGAGTTCTACCTGATGGA GGACAGCAGGCTGGTGTGCAAGGCTGACTACGAGACGGCCAAGCAGAGAGAGGCCGAGTCCACGGCCAAGAGGCCCCGC ACCACCATCACAGCCAAGCAGCTGGAGACCCTCAAAAACGCCTACAACAACTCGCCCAAGCCGGCGCGGCACGTCCGGG AGCAGCTCTCGTCGGAGACGGGGTTGGATATGCGGGTGGTGCAGGTCTGGTTCCAGAACCGCAGGGCCAAGGAGAAGCG GCTGAAGAAGGACGCGGGGAGGCAGCGCTGGGGGCAGTACTTCAGGAACATGAAGAGGTCCCGGGGGACCTCCAAGTCC GACAAGGACAGCATCCAGGAGGAGGGGCCCGACAGCGACGCCGAGGTCTCCTTCACAGACGAGCCCTCCATGTCCGAGA TGAGCCACTCCAATGGCATTTACAGCAATCTCAGCGAGGCGTCCCCGGCCCTGGGGAGGCAGGCTGGGACCAACGGGGG CTTCTCTCTGGATCACAGTGGCATCCCAGCTCAGGACCAGTACCACGACCTGCGATCCAACAGCCCCTATGGGATTCCC CAGTCACCGGCTTCATTGCAAGCGCTGCCGGGCCACCAGCCTTTAATCTCCAGCTTGGTTTACCCTGACAGCGGTTTGG GCATCATGGGACAAGGTGGACAGGGGGTGCCCCAGTCCATGCGGGTCCTGGCCGGGAATGGGCCCAGCTCCGACCTCTC CACCGGCAGCAGTGGGGGATACCCGGATTTCCCTGCCAGCCCGGCCTCCTGGCTGGATGAAGTCGATCACGCTCAGTTT TGATAGAGG
Citation	Inoue M, Kawakami M, Tatsumi K, Manabe T, Makinodan M, Matsuyoshi H, Kirita T, Wanaka A. Expression and regulation of the LIM homeodomain gene L3/Lhx8 suggests a role in upper lip development of the chick embryo. Anat Embryol (Berl). 2006 Jun;211(3):247-53. Epub 2006 Feb 3.
Copyright	© Springer-Verlag 2006
Comments	The cDNA template used to generate the probe was obtained from EST Clone ID: 604159366F1 using the information provided in the publication.

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

25-30

stage 25

stage 26

stage 27

stage 29

Eye
Head Mesenchyme
Nasal Placode/Nerve

Mn - mandible
Mx - maxilla
Mx - maxilla (arrows)

stage 31

Eye

Entry 5

GEISHA Id	LIM3.Davey.2006	Data Source	Publication
Complete cDNA Template Probe	show ATGCTGCTGGAGAGGGTCCGCGCCGGCTCGGAGAAGGCAGCGGAGCTCTGCCCCTTCCCTCGGAGCCCAGAGATCCCGC TGTGCGCCGGCTGCAATCAGCACATCGTGGACAGGTTCATCCTCAAGGTCCTGGACCGGCATTGGCACAGCAAGTGCTT GAAATGTTCCGACTGCCAGACGCAGCTGGCCGAGAAGTGCTTCAGCCGAGGGGACGGCGTGTACTGCAAGGAGGATTTC TTCAAACGCTTCGGGACGAAGTGCGCCGCCTGCCAGCAGGGCATCCCCCCGACCCAGGTGGTGCGCCGGGCCCAGGACT TCGTGTACCACCTGCACTGCTTCGCCTGCATCGTCTGCAAGCGGCAGCTGGCCACCGGAGATGAGTTCTACCTGATGGA GGACAGCAGGCTGGTGTGCAAGGCTGACTACGAGACGGCCAAGCAGAGAGAGGCCGAGTCCACGGCCAAGAGGCCCCGC ACCACCATCACAGCCAAGCAGCTGGAGACCCTCAAAAACGCCTACAACAACTCGCCCAAGCCGGCGCGGCACGTCCGGG AGCAGCTCTCGTCGGAGACGGGGTTGGATATGCGGGTGGTGCAGGTCTGGTTCCAGAACCGCAGGGCCAAGGAGAAGCG GCTGAAGAAGGACGCGGGGAGGCAGCGCTGGGGGCAGTACTTCAGGAACATGAAGAGGTCCCGGGGGACCTCCAAGTCC GACAAGGACAGCATCCAGGAGGAGGGGCCCGACAGCGACGCCGAGGTCTCCTTCACAGACGAGCCCTCCATGTCCGAGA TGAGCCACTCCAATGGCATTTACAGCAATCTCAGCGAGGCGTCCCCGGCCCTGGGGAGGCAGGCTGGGACCAACGGGGG CTTCTCTCTGGATCACAGTGGCATCCCAGCTCAGGACCAGTACCACGACCTGCGATCCAACAGCCCCTATGGGATTCCC CAGTCACCGGCTTCATTGCAAGCGCTGCCGGGCCACCAGCCTTTAATCTCCAGCTTGGTTTACCCTGACAGCGGTTTGG GCATCATGGGACAAGGTGGACAGGGGGTGCCCCAGTCCATGCGGGTCCTGGCCGGGAATGGGCCCAGCTCCGACCTCTC CACCGGCAGCAGTGGGGGATACCCGGATTTCCCTGCCAGCCCGGCCTCCTGGCTGGATGAAGTCGATCACGCTCAGTTT TGATAGAGG
Citation	Davey MG, Paton IR, Yin Y, Schmidt M, Bangs FK, Morrice DR, Smith TG, Buxton P, Stamataki D, Tanaka M, Münsterberg AE, Briscoe J, Tickle C, Burt DW. The chicken talpid3 gene encodesa novel protein essentialfor Hedgehog signaling. Genes Dev. 2006 May 15; 20(10): 13651377.
Copyright	Copyright © 2006, Cold Spring Harbor Laboratory Press

Stage

Image (click image to view full size)

Location (click to highlight)

Comments (click to highlight)

19-20

stage 20

Spinal Cord

Entry 6

GEISHA Id	LIM3.Fischer.2009	Data Source	Publication
Complete cDNA Template Probe	show `CTGGTGTGCAAGGCTGACTACGAGACGGCCAAGCAGAGAGAGGCCGAGTCCACGGCCAAGAGGCCCCGCACCACCATCA CAGCCAAGCAGCTGGAGACCCTCAAAAACGCCTACAACAACTCGCCCAAGCCGGCGCGGCACGTCCGGGAGCAGCTCTC GTCGGAGACGGGGTTGGATATGCGGGTGGTGCAGGTCTGGTTCCAGAACCGCAGGGCCAAGGAGAAGCGGCTGAAGAAG GA`
Citation	Fischer AJ, Foster S, Scott MA, Sherwood P.. The transient expression of LIM-domain transcription factors is coincident with the delayed maturation of photoreceptors in the chicken retina. J Comp Neurol. 2008 February 1; 506(4): 584603.
Copyright	Copyright © 2007 Wiley-Liss, Inc.
Comments	The probe was amplified by PCR using the following primers: 5′-CTG GTG TGC AAG GCT GAC TA-3′ and 5′-AGG TCG TGG TAC TGG TCC TG-3′ and was extracted from NCBI Acc# AF461699.1.