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A chicken embryo gene expression database

	Anatomical Location
	Stage
	Gene Name
	GEISHA ID
	Multiple Parameters

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SEMA3D
semaphorin 3D

Gene

Official Symbol	SEMA3D
Official Full Name	semaphorin 3D
CGNC ID	4949
also known as	semaphorin-3D, semaphorin-3D\|COLL-2\|collapsin-2\|sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D, SEMA3D, Collapsin-2
gene type	protein-coding

Genomic Map

	Ensembl
	NCBI
	UCSC

Sequence Information

Genomic
RNA	NM_205373
Polypeptide	NP_990704

Gene Expression

In Situ Hybridization

GEISHA

Orthology

	Entrez Gene	Ensembl Gene	Genetic Phenotypes	MOD
Fruit Fly
Human	223117	ENSG00000153993		MIM:609907
Mouse	108151	ENSMUSG00000040254	All phenotypic alleles (1):Targeted, other(1)	MGI:1860118
Xenopus	100492784, 447413			490693
Zebrafish	30250	ENSDARG00000017369	ZDB-GENE-990715-2	ZFIN:ZDB-GENE-990715-2

Gene Ontology

Molecular Function	receptor activity
Biological Process	cell differentiation, nervous system development
Cellular Component	extracellular region, membrane

Links to other databases

Entrez Gene	396332
Ensembl Gene	ENSGALG00000006563
KEGG	gga:396332

Entry 1

GEISHA Id	SEMA3D.Jin.2006	Data Source	Publication
Complete cDNA Template Probe	show TGGACTACTTTTCTGAAAGCAGGCTTGTGTGTTCAATACCTGGTCCTGAAGGAGCTGACACACATTTTGATGAGCTGCA AGATATATTCTTACTTTCTACAAGAGATGAGAGAAACCCTCTTGTATATGGAGTCTTCACTACAACAAGCTCCGTCTTC AAGGGCTCTGCAGTTTGTGTGTACAGCATGGCAGATATCAGAGCTGTTTTCAATGGCCCTTATGCTCACAAAGAGAGTG CGGATCATCGATGGGTTCAATACGAAGGTCGTATCCCCTATCCCAGACCTGGTACATGCCCAAGCAAAACCTATGATCC ACTCATAAAATCTACCAGAGATTTTCCCGATGAAGTCATTAGCTTTATAAAGCGCCATCCCCTGATGTACAAATCCGTT TACCCACTGACGGGAGGACCAGTGTTCACGCGAATCAATGTGGACTATCGGCTGACTCAGATTGTGGTGGATCATGTCA TGGCAGAGGACGGGCAATATGATGTTATTTTCCTAGGAACAGACATAGGCACAGTACTGAAAGCTGTGAGTATCACCAA GGAGAAGTGGACTAAGGAGGAGGTAGTCCTGGAAGAGCTACAGATATTCAAGCACCCTTCATTTATTTCAACCATGGAG ATTTCTCAGAAGCAGCAACAATTGTACATTGGTTCCAGGGATGGATTGGTTCAGCTCTCTCTGCACAGATGTCACACGT ATGGGAAGGCTTGTGCAGACTGCTGCCTTGCCAGAGACCCATACTGTGCC
Citation	Jin Z, Chau MD, Bao ZZ. Sema3D, Sema3F, and Sema5A are expressed in overlapping and distinct patterns in chick embryonic heart. Dev Dyn. 2006 Jan;235(1):163-9.
Copyright	Copyright © 2006 Wiley-Liss, Inc.

Stage

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Location (click to highlight)

Comments (click to highlight)

25-30

stage 28

Endocardium
Heart
Myocardium
Valves

Atrioventricular Junction; Interventricular Septum
Cardiac Cushion Mesenchyme
Mesenchyme of Cardiac Cushion

31-38

stage 35

stage 38

Ventricles

Interventricular Septum

Entry 2

GEISHA Id	Sema3D.Bao.2006	Data Source	Publication
Complete cDNA Template Probe	show GAATTCCGGCCTCCCGATCCCGATCCCGATCCCGGCACCGGCCCCGGCCCCGCACAGCGCTCAGCCCGCACCGCGCCGC CTCTCCGCTCCCCGCAGATTAAACTTGGATTGTTTGAAGAGTGGGGAAATATTTCTCCATAGTGCAAAAAGTGCATAAG AAGAGAGCAGAATGAGAGCTTCCCAAGTACCGAATGCCTGCAGCCTGTTATCTTTAGCAATGCTGTTCTTTCCCGTCAC TGGAACGTCAAAACAAAATATCCCAAGACTCAAACTTTCCTATAAAGACTTGCTGCTTTCAAACAGCTGCATCCCATTC CTGGGCTCTACAGAGGGGCTAGATTTTCGAACCCTGCTGCTAGATGAGGAGAGGGGCCGGCTGCTAGTCGGGGCAAAAG ACCACATCTTCCTGCTCAACTTGGTTGATTTAAACAAAAATGTAAAAAAGATTTACTGGCCTGCAGCAAAAGAAAAAAT GGAATTATGCAAACTAGCTGGGAAAGATGCCCATACAGACTGTGCCAATTTTATTAGGGTCCTTCAGCCCTACAATCGA ACGCATGTTTATGTCTGTGGCACAGGAGCATTTCACCCTCTCTGTGGATACATTGAACTTGGCACTCACAAAGAGGAAA CAATATTCAGGCTGGATACTCAGAACTTGGAGTCGGGCAGGTTGAAATGCCCTTTCGATCCTCAGCAGCCATTTGCATC GGTGATGGCAGATGAGTATCTTTATGCTGGAACAGCTTCTGATTTCCTTGGCAAAGACACTGCTCTAACACGTTCCCTG GGCCCTTCTCACGACCACCATTACATCAGAACTGACATTTCTGAACATTACTGGCTTACTGGAGCAAAATTCATTGCAA CTTTTCCCATCCCGGACACCTATAATCCGGATGATGACAAAATCTACTTCTTCTTCCGAGAAATATCACAAGATAGTAG CACCTCTGACAAGACAATTCTTTCTCGAGTTGGGAGAGTTTGTAAGAATGATATGGGAGGTCAACGGAGCCTAATAAAC AAATGGACTACTTTTCTGAAAGCCAGGCTTGTGTGTTCAATACCTGGTCCTGAAGGAGCTGACACACATTTTGATGAGC TGCAAGATATATTCTTACTTTCTACAAGAGATGAGAGAAACCCTCTTGTATATGGAGTCTTCACTACAACAAGCTCCGT CTTCAAGGGCTCTGCAGTTTGTGTGTACAGCATGGCAGATATCAGAGCTGTTTTCAATGGCCCTTATGCTCACAAAGAG AGTGCGGATCATCGATGGGTTCAATACGAAGGTCGTATCCCCTATCCCAGACCTGGTACATGCCCAAGCAAAACCTATG ATCCACTCATAAAATCTACCAGAGATTTTCCCGATGAAGTCATTAGCTTTATAAAGCGCCATCCCCTGATGTACAAATC CGTTTACCCACTGACGGGAGGACCAGTGTTCACGCGAATCAATGTGGACTATCGGCTGACTCAGATTGTGGTGGATCAT GTCATGGCAGAGGACGGGCAATATGATGTTATTTTCCTAGGAACAGACATAGGCACAGTACTGAAAGCTGTGAGTATCA CCAAGGAGAAGTGGACTAAGGAGGAGGTAGTCCTGGAAGAGCTACAGATATTCAAGCACCCTTCATTTATTTCAACCAT GGAGATTTCTCAGAAGCAGCAACAATTGTACATTGGTTCCAGGGATGGATTGGTTCAGCTCTCTCTGCACAGATGTCAC ACGTATGGGAAGGCTTGTGCAGACTGCTGCCTTGCCAGAGACCCATACTGTGCCTGGGATGGAAACTCCTGTTCCAGAT ACGCCCCCACTTCTAAAAGGAGAGCCAGAAGGCAAGATGTCAAATATGGAGACCCTGTCGCACAATGCTGGGATGTAGA AGACAGCATTAGTCATGAAACTGCTGATGAAAAGGTGATTTTTGGCATTGAATTTAATTCAACTTTTCTGGAATGTATT CCTAAGTCCCAGCAAGCCTCTATTAGGTGGTATATTCAACGCTCTGGAGAAGAGCATCGAGAAGAGCTGAAGGCAGACG AAAGGATCATCAAAACAGAACATGGGCTGCTGATCCGCAGCTTGCAAAGGAGGGATGCAGGAGCCTATTTCTGCAAAGC CCAGGAACACACCTTCATCCACACCATTGTGAAGCTGAATTTAAATGTCATTGAGAATGGGCAAATGGAAAGCACACAG AAAACTGAGGATGAGGAGGGTCGGGTGAGGGATTTGCTGACAGAGTCCCGTCTGAGGTACAAGGACTATATCCAGCTCG TGAGCAGCCCCAGCTTTAGCCTGGATGAGTACTGTGAACAAATGTGGCACCGGGAGAAACGACGACAGCGAAACAAAGG TGGTGCCAAATGGAAGCATGTGCAGGAGATGAAAAAAAAGCGAAACCGAAGGCATCATGAGCCAGCCAGGCCACCATCC ACATAGTTTGCAAACACTATTTAAAGAAAGGACACTTTCCAGGAAAAAAAAAATACTGTGTTTCGGTTTTGTGCATATT GCCTATGAATTAGTACTGCTTCTCCTTGACATCAGATAACTCATCATCACTATTAATCTGTACATGACTGAACAATGGG GTTTGATACCTTATTGGAGTGCCACCCACCAGGCAATAATTCCAAATTCATTCATTAAAAAGAAAAGATGTACACTTGT AGCTAATTTCTGGACAGCCTGAGGCTACG
Citation	Bao ZZ, Jin Z. Sema3D and Sema7A have distinct expression patterns in chick embryonic development. Dev Dyn. 2006 Aug;235(8):2282-9.
Copyright	Copyright © 2006 Wiley-Liss, Inc.
Comments	This reference associated with full length mRNA in NCBI (NM_205373).

Stage

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7-12

stage 7

stage 10

stage 12

Diencephalon
Ear/Otic Placode
Eye
Forebrain
Hindbrain
Midbrain
Neural Crest
Neural Plate/Tube
Notochord

13-18

stage 17

Leg
Leg AER
Lens
Nasal Placode/Nerve
Neural Crest
Neural Plate/Tube
Outflow Tract
Surface Ectoderm
Wing
Wing AER

19-20

stage 20

Diencephalon
Leg AER
Outflow Tract
Surface Ectoderm
Wing AER

Entry 3

GEISHA Id	Sema3D.Riley.2010	Data Source	Publication
Complete cDNA Template Probe	show GAATTCCGGCCTCCCGATCCCGATCCCGATCCCGGCACCGGCCCCGGCCCCGCACAGCGCTCAGCCCGCACCGCGCCGC CTCTCCGCTCCCCGCAGATTAAACTTGGATTGTTTGAAGAGTGGGGAAATATTTCTCCATAGTGCAAAAAGTGCATAAG AAGAGAGCAGAATGAGAGCTTCCCAAGTACCGAATGCCTGCAGCCTGTTATCTTTAGCAATGCTGTTCTTTCCCGTCAC TGGAACGTCAAAACAAAATATCCCAAGACTCAAACTTTCCTATAAAGACTTGCTGCTTTCAAACAGCTGCATCCCATTC CTGGGCTCTACAGAGGGGCTAGATTTTCGAACCCTGCTGCTAGATGAGGAGAGGGGCCGGCTGCTAGTCGGGGCAAAAG ACCACATCTTCCTGCTCAACTTGGTTGATTTAAACAAAAATGTAAAAAAGATTTACTGGCCTGCAGCAAAAGAAAAAAT GGAATTATGCAAACTAGCTGGGAAAGATGCCCATACAGACTGTGCCAATTTTATTAGGGTCCTTCAGCCCTACAATCGA ACGCATGTTTATGTCTGTGGCACAGGAGCATTTCACCCTCTCTGTGGATACATTGAACTTGGCACTCACAAAGAGGAAA CAATATTCAGGCTGGATACTCAGAACTTGGAGTCGGGCAGGTTGAAATGCCCTTTCGATCCTCAGCAGCCATTTGCATC GGTGATGGCAGATGAGTATCTTTATGCTGGAACAGCTTCTGATTTCCTTGGCAAAGACACTGCTCTAACACGTTCCCTG GGCCCTTCTCACGACCACCATTACATCAGAACTGACATTTCTGAACATTACTGGCTTACTGGAGCAAAATTCATTGCAA CTTTTCCCATCCCGGACACCTATAATCCGGATGATGACAAAATCTACTTCTTCTTCCGAGAAATATCACAAGATAGTAG CACCTCTGACAAGACAATTCTTTCTCGAGTTGGGAGAGTTTGTAAGAATGATATGGGAGGTCAACGGAGCCTAATAAAC AAATGGACTACTTTTCTGAAAGCCAGGCTTGTGTGTTCAATACCTGGTCCTGAAGGAGCTGACACACATTTTGATGAGC TGCAAGATATATTCTTACTTTCTACAAGAGATGAGAGAAACCCTCTTGTATATGGAGTCTTCACTACAACAAGCTCCGT CTTCAAGGGCTCTGCAGTTTGTGTGTACAGCATGGCAGATATCAGAGCTGTTTTCAATGGCCCTTATGCTCACAAAGAG AGTGCGGATCATCGATGGGTTCAATACGAAGGTCGTATCCCCTATCCCAGACCTGGTACATGCCCAAGCAAAACCTATG ATCCACTCATAAAATCTACCAGAGATTTTCCCGATGAAGTCATTAGCTTTATAAAGCGCCATCCCCTGATGTACAAATC CGTTTACCCACTGACGGGAGGACCAGTGTTCACGCGAATCAATGTGGACTATCGGCTGACTCAGATTGTGGTGGATCAT GTCATGGCAGAGGACGGGCAATATGATGTTATTTTCCTAGGAACAGACATAGGCACAGTACTGAAAGCTGTGAGTATCA CCAAGGAGAAGTGGACTAAGGAGGAGGTAGTCCTGGAAGAGCTACAGATATTCAAGCACCCTTCATTTATTTCAACCAT GGAGATTTCTCAGAAGCAGCAACAATTGTACATTGGTTCCAGGGATGGATTGGTTCAGCTCTCTCTGCACAGATGTCAC ACGTATGGGAAGGCTTGTGCAGACTGCTGCCTTGCCAGAGACCCATACTGTGCCTGGGATGGAAACTCCTGTTCCAGAT ACGCCCCCACTTCTAAAAGGAGAGCCAGAAGGCAAGATGTCAAATATGGAGACCCTGTCGCACAATGCTGGGATGTAGA AGACAGCATTAGTCATGAAACTGCTGATGAAAAGGTGATTTTTGGCATTGAATTTAATTCAACTTTTCTGGAATGTATT CCTAAGTCCCAGCAAGCCTCTATTAGGTGGTATATTCAACGCTCTGGAGAAGAGCATCGAGAAGAGCTGAAGGCAGACG AAAGGATCATCAAAACAGAACATGGGCTGCTGATCCGCAGCTTGCAAAGGAGGGATGCAGGAGCCTATTTCTGCAAAGC CCAGGAACACACCTTCATCCACACCATTGTGAAGCTGAATTTAAATGTCATTGAGAATGGGCAAATGGAAAGCACACAG AAAACTGAGGATGAGGAGGGTCGGGTGAGGGATTTGCTGACAGAGTCCCGTCTGAGGTACAAGGACTATATCCAGCTCG TGAGCAGCCCCAGCTTTAGCCTGGATGAGTACTGTGAACAAATGTGGCACCGGGAGAAACGACGACAGCGAAACAAAGG TGGTGCCAAATGGAAGCATGTGCAGGAGATGAAAAAAAAGCGAAACCGAAGGCATCATGAGCCAGCCAGGCCACCATCC ACATAGTTTGCAAACACTATTTAAAGAAAGGACACTTTCCAGGAAAAAAAAAATACTGTGTTTCGGTTTTGTGCATATT GCCTATGAATTAGTACTGCTTCTCCTTGACATCAGATAACTCATCATCACTATTAATCTGTACATGACTGAACAATGGG GTTTGATACCTTATTGGAGTGCCACCCACCAGGCAATAATTCCAAATTCATTCATTAAAAAGAAAAGATGTACACTTGT AGCTAATTTCTGGACAGCCTGAGGCTACG
Citation	Riley KL, Gledhill S, Schubert FR. Early expression of axon guidance molecules in the embryonic chick mesencephalon and pretectum. Int J Dev Biol. 2010;54(4):743-53.
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_205373.1).