EMAGE mouse gene expression spatial database

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EMAGE:20029

Slc9a3r1 solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1 ( MGI:1349482)
TS23 (14.5 dpc)
in situ hybridisation

Data Images


"Pseudo-wholemount" of euxassay_012152. This image has been made by aligning and collapsing the constitutent sections. Information about the method.	euxassay_012152_01	euxassay_012152_02	euxassay_012152_03	euxassay_012152_04

euxassay_012152_05	euxassay_012152_06	euxassay_012152_07	euxassay_012152_08	euxassay_012152_09

euxassay_012152_10	euxassay_012152_11	euxassay_012152_12	euxassay_012152_13	euxassay_012152_14

euxassay_012152_15	euxassay_012152_16	euxassay_012152_17	euxassay_012152_18	euxassay_012152_19

euxassay_012152_20	euxassay_012152_21	euxassay_012152_22	euxassay_012152_23	euxassay_012152_24

View assay images:
Expression pattern clarity:
Find spatially similar wholemount expression patterns:

Expression Pattern Description

Spatial Annotation:

Annotation colour key:

	strong
	moderate
	weak
	possible
	not detected

wholemount mapping

Download individual expression domains:

20029_wholemount_strong.wlz

20029_wholemount_moderate.wlz

20029_wholemount_weak.wlz

20029_wholemount_possible.wlz

20029_wholemount_not_detected.wlz

(what is wlz format?)

Download all expression domains:

EMAGE:20029_all_domains.zip

Find spatially similar wholemount expression patterns:

EMAGE spatially similar wholemount patterns

Morphological match to the template:

Text Annotation:

Structure

Level

Pattern

Notes

pleura

moderate

regional

moderate expression: see section 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23

thymus primordium

moderate

regional

moderate expression: see section 10 11 12 13 14

pituitary gland

moderate

regional

moderate expression: see section 11 12 13 14 15 16

diencephalon lateral wall ventricular layer

moderate

regional

moderate expression: see section 11 12 13 14 15 16 17 18 19

telencephalon ventricular layer

moderate

regional

moderate expression: see section 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 weak expression: see section 04

medulla oblongata alar plate marginal layer

moderate

regional

moderate expression: see section 19

medulla oblongata alar plate ventricular layer

moderate

regional

moderate expression: see section 07 08 09 10 11 12 14 15 16 17 18

medulla oblongata basal plate ventricular layer

moderate

regional

moderate expression: see section 07 08 09 10 11 12 14 15 16 17 18 19

rest of cerebellum ventricular layer

moderate

regional

moderate expression: see section 04 05 06 07 08 09 10 11 12 14 15 16 17 18 19 20 21 22 23 24

pons ventricular layer

moderate

regional

moderate expression: see section 04 05 06 07 08 09 10 11 12 14 15 16 17 18 19 20 21 22 23 24

midbrain ventricular layer

moderate

regional

moderate expression: see section 09 10 11 12 13 14 15 16 17 18 19

trigeminal v ganglion

moderate

regional

moderate expression: see section 05 06 07 08 18 19 20 21 22 23

vestibulocochlear viii ganglion

moderate

regional

moderate expression: see section 05 06 07 08 09 17 18 19 20 21 22 23

spinal cord ventricular layer

moderate

regional

moderate expression: see section 12 13 14

pharyngo-tympanic tube

moderate

regional

moderate expression: see section 01 02 03 04 05 20 21 22 23 24

cornea epithelium

moderate

regional

moderate expression: see section 02 03 04 23 24

anterior naris epithelium

strong

regional

strong expression: see section 11 12 14 15

external naris epithelium

strong

regional

strong expression: see section 10 15

nasal cavity olfactory epithelium

strong

regional

strong expression: see section 08 09 10 11 12 14 15 16 17 18

vomeronasal organ

strong

regional

strong expression: see section 14

stomach

moderate

regional

moderate expression: see section 03 04 05

rectum

moderate

regional

moderate expression: see section 12

midgut

moderate

regional

moderate expression: see section 04 05 06 07 08 09 10 11 12 13 14 15 16 17

lower jaw incisor

moderate

regional

moderate expression: see section 10 11 14 15 16

lower jaw molar

moderate

regional

moderate expression: see section 06 07 19 20

upper jaw incisor

moderate

regional

moderate expression: see section 10 14 15 16

upper jaw molar

moderate

regional

moderate expression: see section 06 19 20

liver

moderate

regional

moderate expression: see section 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24

urogenital mesentery

moderate

regional

moderate expression: see section 01 02 03 04 05 06 07 08 09 17 18 19 20 21 22

kidney calyx

moderate

regional

moderate expression: see section 07 08 16 17 18

Annotation Validation:

spatial mapping by EMAGE editor, text annotation by author

Detection Reagent

Type:	in situ hybridisation probe
Identifier:	T37046
Entity Detected:	Slc9a3r1, solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1 ( MGI:1349482)
Sequence:	sense strand is shown >T37046 CCCTTCAGCAATGGAGAGATACAGAAGGAGAGCAGCCGTGAAGCCCTGGTGGAGCCAGCTTCAGAGAGCC CCAGGCCAGCCCTGGCAAGATCTGCCTCCAGCGATACCAGTGAGGAGCTAAATTCCCAAGACAGCCCCAA GAGACAAGTTTCCACAGAGCCCTCATCTACCTCCTCCTCCTCCTCTGACCCCATCTTGGACCTCAACATC TCCTTGGCTGTGGCTAAAGAGAGGGCCCACCAGAAGCGCAGTAGCAAGAGGGCCCCGCAGATGGACTGGA GCAAGAAAAATGAACTCTTCAGCAACCTCTGAGCATCCCACCTCCGTGGGCTTGTGCTAGAGGGTGGGGC TGCCCACCCTACCTAGCTCCCCTTCCCTTCTCCCCAGGTGCCCACCAATCAACATTCAGATCAGCATCAG CACCCACCCCACTTCCTGACAAATCTGATTTTTCTAGAATCCTGTTCTTCCCTCACCTTAGGGAAGGAGA ATGTTTGTCCTGTCTCCCTACACTTCCCTGAGGGCTTCTTCCTACCAAAGTGTCCCCTCACCAGTCTGCC TAGAGCATCACTGGAACCC
Notes:	The probe template was received by the EURExpress consortium as an aliquot of PCR product from the Allen Brain Atlas (originally amplified from wild type C57BL/6J mouse whole brain cDNA), and this was re-amplified using the gene-specific Allen Brain Atlas Primer Pair 99734. Forward Primer - name:099734_F_cDNA_Slc9a3r1, sequence:CCCTTCAGCAATGGAGAGATAC; Reverse Primer - name:099734_N_SP6_cDNA_Slc9a3r1, sequence:GGGTTCCAGTGATGCTCTAGG. The reverse primer contains a 5' extension containing an Sp6 RNA polymerase binding site (this extension is not shown in the primer sequence listed here). Anti-sense probe was transcribed from the PCR amplified template using Sp6 polymerase.
Chemistry:	RNA
Strand:	antisense
Label:	digoxigenin

Specimen

Organism:	mouse
Strain:	C57BL/6
Age:	14.5 dpc
Theiler Stage:	TS23
Mutations:	none (wild-type)
Preparation:	section

Procedures

Fixation:	none
Embedding:	cryosection (OCT)
Staining procedure:	alkaline phosphatase + NBT/BCIP

General Information

Authors:	Dr. Graciana Diez-Roux, Prof. Gregor Eichele, Prof. Richard Baldock, Dr. Duncan Davidson, Prof. Stylianos Antonarakis, Dr. Marie Laure Yaspo, Prof. Salvador Martinez Perez, Dr. Pascal Dolle, Dr. David Tannahill, Prof. Pier Paolo Di Fiore, Mr. Stefan Kruse, Mr. Paolo Sarmientos, Dr. Uwe Radelof, Prof. Andrea Ballabio.
Principal investigator:	Professor Andrea Ballabio, Fondazione Telethon, TIGEM Instituto di Genetica e Medicina, Via Pietro Castellino 111 80131, Napoli, Italy 80131
Submitted by:	EMAGE EDITOR, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, UK EH4 2XU
Experiment type:	screen
References:	[ doi:10.1371/journal.pbio.1000582] [ PMID:21267068] Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, et al 2011 A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo PLoS Biol (9)
Links:	EMAGE:20028 same embryo
	EMAGE:20031 same embryo
	EMAGE:20030 same embryo
	EMAGE:20027 same embryo
	EMAGE:20032 same embryo
	EurExpress:euxassay_012152 same experiment
	MGI:4828289 same experiment
	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 Source