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EMAGE:5031

Sema3f sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F ( MGI:1096347)
TS16 (11 dpc)
in situ hybridisation

Data Images
EMAGE:5031
Figure 5B. Copyright: Reprinted with permission from Cell Press from [doi:10.1016/S0896-6273(00)80869-7] Neuron 25: 29-41, Giger RJ; Cloutier JF; Sahay A; Prinjha RK; Levengood DV; Moore SE; Pickering S; Simmons D; Rastan S; Walsh FS; Kolodkin AL; Ginty DD; Geppert M, "Neuropilin-2 is required in vivo for selective axon guidance responses to secreted semaphorins." Copyright 2000. [PMID:10707970]

Expression pattern clarity: three stars
Find spatially similar wholemount expression patterns: Find spatially similar wholemount patterns
Notes:
Note: developing eye (open arrowhead); hindbrain-midbrain junction (arrow).
Expression Pattern Description
Spatial Annotation:
EMAGE:5031Annotation colour key:  
strong strong      
gene expression moderate moderate    
gene expression weak weak        
gene expression possible possible    
gene expression not detected not detected
wholemount mapping

Download individual expression domains:
5031_wholemount_moderate.wlz
5031_wholemount_weak.wlz
5031_wholemount_possible.wlz
5031_wholemount_notDetected.wlz
5031_wholemount_strong.wlz
(what is wlz format?)
Download all expression domains: EMAGE:5031_all_domains.zip
Find spatially similar wholemount expression patterns:  EMAGE spatially similar wholemount patterns
Morphological match to the template: three stars
Text Annotation:
StructureLevelPatternNotes
future midbrain
detected detected
regionalProminent Sema3F expression in the caudal midbrain and the rostral hindbrain with a striking gap, however, at the hindbrain-midbrain junction. Expressed in an increasing rostral to caudal gradient in the midbrain.
future hindbrain
detected detected
regionalProminent Sema3F expression in the caudal midbrain and the rostral hindbrain with a striking gap, however, at the hindbrain-midbrain junction.
telencephalic vesicle
detected detected
regionalExpressed dorsally.
eye
detected detected
regionalExpressed around the dorsal surface of the eye anlage.
Annotation Validation: EMAGE Editor
Detection Reagent
Type:in situ hybridisation probe
Identifier:Sema3f probeA
Entity Detected:Sema3f, sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F ( MGI:1096347)
Notes:The Sema3f (SemaIV) probe used in this study by Giger et al., 2000 [PMID:10707970] was generated from a "rat Sema3F template for riboprobe synthesis (nucleotides 697-2995) (which) spans most of the ORF as previously described (Giger et al., 1998 [PMID:9856463] ". Giger et al define the probe as follows: "A rat semaIV cDNA was isolated from a lambda-ZAP (Stratagene) phage library made from E14 spinal cord and DRG (A. K. and D. G., unpublished data), cloned into pBluescript, and sequenced on both strands. Analysis of this sequence revealed that this clone contains most of the semaIV ORF 700 bp of 3'UTR; however, the 5'-300 bp are non-semaIV sequences resulting from a cloning artifact. Antisense probes were generated with T3 RNA polymerase by linearizing the rat semaIV cDNA in the 5'-most portion of the semaIV ORF with Age I (nucleotides 697-2995)". Editors Note: Giger et al., 1998 do not refer their nucleotide co-ordinates to a published sequence. The rat Sema3f cDNA RefSeq (NM_017310.1) is 2319nt in length. It is unclear from this description of the region covered by this probe.
Chemistry:RNA
Strand:antisense
Specimen
Organism:mouse
Age:11 dpc
Theiler Stage:TS16
Mutations:none (wild-type)
Preparation:wholemount
Procedures
General Information
Authors:Giger RJ; Cloutier JF; Sahay A; Prinjha RK; Levengood DV; Moore SE; Pickering S; Simmons D; Rastan S; Walsh FS; Kolodkin AL; Ginty DD; Geppert M, 2000 [PMID:10707970] . Indexed and spatially mapped by EMAGE.
Submitted by:EMAGE EDITOR, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, UK EH4 2XU
Experiment type:non-screen
References:[ doi:10.1016/S0896-6273(00)80869-7] [ PMID:10707970] Giger RJ, Cloutier JF, Sahay A, Prinjha RK, Levengood DV, Moore SE, Pickering S, Simmons D, Rastan S, Walsh FS, Kolodkin AL, Ginty DD, Geppert M 2000 Neuropilin-2 is required in vivo for selective axon guidance responses to secreted semaphorins. Neuron (25):29-41
 [ doi:10.1016/S0896-6273(00)80625-X] [ PMID:9856463] Giger RJ, Urquhart ER, Gillespie SK, Levengood DV, Ginty DD, Kolodkin AL 1998 Neuropilin-2 is a receptor for semaphorin IV: insight into the structural basis of receptor function and specificity. Neuron (21):1079-92
Links: Ensembl same gene
  Allen Brain Atlas same gene
  BioGPS same gene
  International Mouse Knockout Project Status same gene
  GEISHA Chicken ISH Database same gene
  EMBL-EBI Gene Expression Atlas same gene
  BrainStars same gene
  ViBrism same gene
Data SourceEMAGE