About   Help   FAQ
Gene Expression Data
Assay Details
Assay
Reference: J:15715 Monaghan AP, et al., Postimplantation expression patterns indicate a role for the mouse forkhead/HNF-3 alpha, beta and gamma genes in determination of the definitive endoderm, chordamesoderm and neuroectoderm. Development. 1993 Nov;119(3):567-78
Assay type: RNA in situ
MGI Accession ID: MGI:3778013
Gene symbol: Foxa1
Gene name: forkhead box A1
Probe: HNF3a cDNA
Probe preparation: Antisense labelled with S35 RNA
Visualized with: Autoradiography
Results
Specimen 2A: embryonic day 7.5 (more )
Note: This is a sagittal section.
Structure Level Pattern Image Note
TS11: embryo Absent 2A
TS11: neural ectoderm Absent 2A

Specimen 2D: embryonic day 8.0 (more )
Structure Level Pattern Image Note
TS12: foregut diverticulum endoderm Strong 2D A gradient of expression extends from the more caudal parts of the invagination to the node.
TS12: embryo endoderm Present Regionally restricted 2D Expression extends from the dorsal endoderm to the node.
TS12: primitive streak Present Regionally restricted 2D Expression extends from the dorsal endoderm to the node.
TS12: notochord Weak 2D

Specimen 2G: embryonic day 8.75-9.0 (more )
Structure Level Pattern Image Note
TS14: gut epithelium Present Regionally restricted 2G Expression is present in the endoderm of the foregut and hindgut pocket.
TS14: future spinal cord neural fold Present Regionally restricted 2G Expression is present in the base of the neural folds.

Specimen 3A: embryonic day 9.0 (more )
Note: This is a sagittal section.
Structure Level Pattern Image Note
TS14: embryo endoderm Present Regionally restricted 3A Expression is restricted to cells of the digestive track located posterior to the oral plate.
TS14: future diencephalon Present 3A
TS14: notochord Present 3A
TS14: floor plate Weak 3A
TS14: stomatodeum Absent 3A

Specimen Not shown: embryonic day 9.5 (more )
Structure Level Pattern Image Note
TS15: septum transversum Strong Regionally restricted Expression is present in the ventral floor of the foregut at the site of the primary hepatic diverticulum.

Specimen 3D: embryonic day 10.0 (more )
Note: This is a sagittal section.
Structure Level Pattern Image Note
TS16: embryo endoderm Present 3D
TS16: central nervous system Present 3D Expression is present in the neuroepithelium.
TS16: floor plate Present 3D
TS16: liver Present 3D
TS16: lung epithelium Present 3D
TS16: foregut Present Regionally restricted 3D Expression is present in the stomach.
TS16: Rathke's pouch Absent 3D

Specimen 4A: embryonic day 11.5 (more )
Note: This is a sagittal section.
Structure Level Pattern Image Note
TS19: embryo mesenchyme Present 4A
TS19: esophagus Present 4A
TS19: floor plate Present 4A
TS19: intestine Present 4A
TS19: lung epithelium Present 4A
TS19: tongue Strong Regionally restricted 4A Expression is present in the epithelium.
TS19: foregut gland Present Regionally restricted 4A Expression is present in the thymus.
TS19: liver Present 4A Expression in the liver is decreasing.
TS19: heart Absent 4A

Specimen Not shown: postnatal adult (more )
Structure Level Pattern Image Note
TS28: lung epithelium Present

Specimen Not shown: embryonic day 14.0 (more )
Structure Level Pattern Image Note
TS22: esophagus Present
TS22: trachea Present
TS22: tongue Absent

Specimen Not shown: embryonic day 11.5-12.5 (more )
Structure Level Pattern Image Note
TS20: gallbladder Present
TS20: dorsal mesogastrium Present Regionally restricted Expression is present in the developing spleen.

Specimen Not shown: embryonic day 16.0 (more )
Structure Level Pattern Image Note
TS24: skeleton Absent There is no expression in developing bone tissue.

Specimen 5A: embryonic day 12.5 (more )
Note: This is a transverse section.
Structure Level Pattern Image Note
TS20: floor plate Present 5A Expression is localized to the developing floor plate cells as soon as the floor plate becomes morphologically distinct.
TS20: esophagus Present 5A
TS20: notochord Present 5A
TS20: trachea Present 5A
TS20: embryo mesenchyme Present Regionally restricted 5A Expression is present in the mesenchyme surrounding the notochord; a thin band extends from the notochord toward the oesophagus and a broader triangle of expressing cells extends towards the floorplate.

Specimen 5C: embryonic day 12.5 (more )
Note: This is a transverse section.
Structure Level Pattern Image Note
TS20: floor plate Present 5C
TS20: intestine Present 5C
TS20: lung epithelium Present 5C
TS20: notochord Present 5C
TS20: liver Present 5C Expression is continuing to decrease.
TS20: stomach Strong 5C

Specimen 6A: embryonic day 7.75 (more )
Note: This is a transverse section.
Structure Level Pattern Image Note
TS11: embryo Absent 6A
TS11: neural ectoderm Absent 6A

Specimen 6C: embryonic day 12.5 (more )
Note: This is a transverse section through the brain.
Structure Level Pattern Image Note
TS20: diencephalon lateral wall ventricular layer Present 6C
TS20: midbrain ventricular layer Present Regionally restricted 6C Expression is excluded from two small areas.
TS20: spinal cord floor plate Present 6C
TS20: hypothalamus Present 6C
TS20: thalamus Present Regionally restricted 6C Expression is present in the ventral thalamus, with an anterior border located in the ventral/dorsal thalamic boundary region.

Specimen Not shown: embryonic day 15.5 (more )
Structure Level Pattern Image Note
TS23: hindbrain Present Regionally restricted Expression is present in cells in the ventricular zone of the fourth ventricle.
TS23: pons Present Regionally restricted Expression is present in the ventral tegmental nucleus.
TS23: midbrain tegmentum Present Regionally restricted Expression is present in the red nucleus.
TS23: thalamus Present Regionally restricted Expression is present in the dorsal thalamic regions.

Specimen Table 1: embryonic day 6.5 (more )
Structure Level Pattern Image Note
TS9: embryo Absent

Specimen Table 1: embryonic day 7.5 (more )
Structure Level Pattern Image Note
TS11: embryo Absent

Specimen Table 1: embryonic day 8.5 (more )
Structure Level Pattern Image Note
TS13: primitive streak Present Regionally restricted Expression is present in the node.
TS13: embryo ectoderm Present
TS13: embryo endoderm Present
TS13: embryo mesenchyme Present
TS13: foregut diverticulum Present
TS13: future prosencephalon Present
TS13: hindgut diverticulum Present
TS13: neural fold Present
TS13: neural plate Present
TS13: notochord Present

Specimen Table 1: embryonic day 9.5 (more )
Structure Level Pattern Image Note
TS15: embryo endoderm Present
TS15: floor plate Present
TS15: future forebrain Present
TS15: hindgut Present
TS15: lung Present
TS15: midgut Present
TS15: notochord Present
TS15: pharynx Present
TS15: foregut Present Expression is present in the foregut, including the stomach.
TS15: hepatic primordium Present
TS15: pancreas primordium Present

Specimen Table 1: embryonic day 10.5 (more )
Structure Level Pattern Image Note
TS17: esophagus Present
TS17: floor plate Present
TS17: forebrain Present
TS17: foregut Present
TS17: hindgut Present
TS17: liver Present
TS17: lung Present
TS17: midgut Present
TS17: notochord Present
TS17: pharynx Present
TS17: stomach Present
TS17: thyroid primordium Present
TS17: pancreas primordium Present
TS17: gland Present Regionally restricted Expression is present in the adrenal.

Specimen Table 1: embryonic day 11.5 (more )
Structure Level Pattern Image Note
TS19: esophagus Present
TS19: floor plate Present
TS19: forebrain Present
TS19: foregut Present
TS19: hindgut Present
TS19: liver Present
TS19: lung Present
TS19: midgut Present
TS19: notochord Present
TS19: pancreas primordium Present
TS19: pharynx Present
TS19: stomach Present
TS19: thyroid gland Present
TS19: tongue Present
TS19: oral region gland Present Regionally restricted Expression is present in the submandibular gland.
TS19: gland Present Regionally restricted Expression is present in the adrenal.

Specimen Table 1: embryonic day 12.5 (more )
Structure Level Pattern Image Note
TS20: esophagus Present
TS20: floor plate Present
TS20: forebrain Present
TS20: foregut Present
TS20: hindgut Present
TS20: liver Present
TS20: lung Present
TS20: midgut Present
TS20: notochord Present
TS20: pancreas Present
TS20: pharynx Present
TS20: stomach Present
TS20: thyroid gland Present
TS20: tongue Present
TS20: oral region gland Present Regionally restricted Expression is present in the submandibular gland.
TS20: gland Present Regionally restricted Expression is present in the adrenal.

Specimen Table 1: embryonic day 13.5 (more )
Structure Level Pattern Image Note
TS21: esophagus Present
TS21: floor plate Present
TS21: forebrain Present
TS21: foregut Present
TS21: hindgut Present
TS21: lung Present
TS21: midgut Present
TS21: pancreas Present
TS21: pharynx Present
TS21: stomach Present
TS21: submandibular gland primordium Present
TS21: tongue Present
TS21: embryo Present Regionally restricted Expression is present in the notochord.
TS21: gland Present Regionally restricted Expression is present in the adrenal.

Specimen Table 1: embryonic day 14.5 (more )
Structure Level Pattern Image Note
TS22: adrenal gland Present
TS22: esophagus Present
TS22: floor plate Present
TS22: forebrain Present
TS22: foregut Present
TS22: hindgut Present
TS22: lung Present
TS22: midgut Present
TS22: pharynx Present
TS22: stomach Present
TS22: tongue Present
TS22: embryo Present Regionally restricted Expression is present in notochord.

Specimen Table 1: embryonic day 15.5 (more )
Structure Level Pattern Image Note
TS23: foregut Present
TS23: hindgut Present
TS23: liver Present
TS23: lung Present
TS23: midgut Present
TS23: stomach Present

Specimen Table 1: postnatal adult (more )
Structure Level Pattern Image Note
TS28: liver Present
TS28: lung Present
TS28: stomach Present
TS28: gut Present Expression is present in the foregut, midgut, and hindgut.


Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources
Funding Information
Warranty Disclaimer, Privacy Notice, Licensing, & Copyright
Send questions and comments to User Support.
last database update
03/25/2025
MGI 6.24
The Jackson Laboratory