Gene Rat Rattus norvegicus

Foxa1

forkhead box A1

protein coding

HumanMouseRat Foxa1

Reading the ortholog votes for human and mouse.

HGNC and MANE Select: not available for rat. HGNC names human genes; RGD is the authority here, and MANE Select is defined for human transcripts only.

Location: Cytogenetic band 6q23NCBI: 6:80,835,681-80,871,436 on the minus strand, GRCr8 (GCF_036323735.1), sequence NC_086024.1, annotation GCF_036323735.1-RS_2026_08 of 2026-08-17Ensembl: no location was read.Coordinates are one-based with both ends included, as each source reports them.
Also known as: Hnf3a

Gene identity, from NCBI Datasets · NCBI Datasets 18.38.0 · read 2026-10-01 ET · RGD:2807Data from NCBI, provided as is; NCBI's policies and disclaimers apply.

Notes from the sources

Ensembl did not answer (upstream error).
Ensembl did not answer (upstream error); the Ensembl location and release are missing

Silence this gene

The order page opens with Foxa1 and rat filled in. The sequences are designed against the transcripts below; the price is on that page.

Order for Foxa1

sdASO, toASO or siRNA, chosen on the next page

Bring your own sequence Transcripts

For research use only. Not for use in diagnostic or therapeutic procedures.

Summary
Transcripts
Expression
Protein
Interactions
Pathways
Disease
Variants
Constraint
Orthologs
MicroRNAs
Long non-coding RNAs
Literature
Silencing this gene

A line below that says it is reading needs JavaScript to be replaced: with scripts off, it stays at that line however long you wait. Opening a card also needs JavaScript.

Ready in a moment

01 Summary and function

What Foxa1 does

Enables several functions, including DNA binding activity; DNA-binding…

NCBI Gene summary

Ready in a moment

02 Transcripts and isoforms

The RNA a design targets

5 RefSeq transcripts on GRCr8; RefSeq Select NM_012742.2. Ensembl is not answering, so the Ensembl transcripts could not be shown. Try again later. Reference 85e97314-025.

NCBI Datasets

Ready in a moment

03 Expression by tissue

Where Foxa1 is expressed

Expression by tissue: not available for rat. GTEx holds human tissues only, and the Human Protein Atlas is keyed on human genes.

Ready in a moment

04 Protein

The protein Foxa1 encodes

Reading UniProt, InterPro, AlphaFold DB and PDBe.Still reading. A first read of a gene can take a while; this page waits up to 80 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

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05 Interactions

Proteins STRING associates with Foxa1

Reading STRING.Still reading. A first read of a gene can take a while; this page waits up to 50 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

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06 Pathways

Where Foxa1 acts, as Reactome curates it

Reading UniProt and Reactome.Still reading. A first read of a gene can take a while; this page waits up to 60 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

Ready in a moment

07 Disease associations

Diseases linked to Foxa1

Disease associations: not available for rat. Open Targets and ClinGen curate human genes only. The human ortholog's page carries the associations.

Ready in a moment

08 Variants

Classified variants of Foxa1

Clinical variants: not available for rat. ClinVar holds human variants only.

Ready in a moment

09 Constraint

How much variation Foxa1 tolerates

Constraint: not available for rat. gnomAD and Open Targets carry constraint for human genes only.

Ready in a moment

10 Orthologs

The same gene in mouse, rat and human

Reading the Alliance, NCBI, Ensembl Compara and RGD.Still reading. A first read of a gene can take a while; this page waits up to 145 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

Ready in a moment

11 MicroRNAs

MicroRNAs hosted within Foxa1

Ensembl is not answering, so the non-coding annotation could not be shown. Try again later. Reference 2bae6372-bcd.

Ready in a moment

12 Long non-coding RNAs

Long non-coding RNAs at the Foxa1 locus

Ensembl is not answering, so the non-coding annotation could not be shown. Try again later. Reference 2bae6372-bcd.

Ready in a moment

13 Literature

Papers that mention Foxa1

Reading Europe PMC.Still reading. A first read of a gene can take a while; this page waits up to 55 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

Ready in a moment

14 Silencing this gene

From Foxa1 to a sequence that silences it

The AUMsilence platform designs the sequences against the rat transcripts on this page. Six decisions are yours before it does. What is written under each is AUM's guidance; the timings and the concentrations are in the usage guide below.

01
Choose the region
A knockdown oligonucleotide can sit in the 5' untranslated region, the coding sequence or the 3' untranslated region, and all three are used. The coding sequence and the 3' untranslated region are the usual first choices for an RNase H design; the 5' end near the start codon suits a steric block. The map above shows where each region sits on the isoforms it draws.
02
Cover the isoforms you mean
An exon every isoform carries silences the whole gene; an exon only some isoforms carry silences those and spares the rest. Decide which you want before a sequence is chosen, and check the reference transcript (MANE Select in human; RefSeq Select and Ensembl canonical in mouse and rat) is the one your cells express.
03
Think across species early
The orthologs panel says whether mouse and rat carry the same gene. Whether one oligonucleotide can serve two species is a sequence question, settled at design by matching the candidate against each transcript, not by the protein identity shown there.
04
Check expression in your model
A transcript that is not expressed in your cells cannot show knockdown. Confirm the gene is expressed in the cell type and condition you will use, from your own data or a reference atlas, before the order. The expression panel above gives GTEx's median per tissue for a human gene; for mouse and rat it says that no atlas is on this page yet.
05
Run the controls
A scramble control of the same chemistry, a positive control against a gene known to knock down in your cells, untreated cells, and a mock condition where a transfection reagent is used. Read knockdown at the RNA level first, then at the protein; the usage guide gives the timing and the concentrations to start from.
06
Pick the product
AUMsilence sdASO needs no transfection reagent and works in the cells that resist one. AUMsilence toASO is the transfection-optimised version of the same design, and AUMsiRNA is the siRNA route. The selection guide compares them.

Order for Foxa1 Bring your own sequence The usage guide Selection guide

For research use only. Not for use in diagnostic or therapeutic procedures.

Gene Rat Rattus norvegicus

Foxa1

Reading the record for Foxa1 from NCBI Gene and Ensembl.Still reading. A first read of a gene can take a while; this page waits up to 115 seconds for it, and its scripts then bring in the page, or a line saying what did not arrive.

The full name, the identifiers, the location and the notes from the sources arrive with the record. Nothing is filled in ahead of it.

Order door

The door to order for Foxa1 opens with the record, which decides which product it carries. The order page itself is open now.

Bring your own sequence

For research use only. Not for use in diagnostic or therapeutic procedures.

This page is still reading the record. Its scripts replace this shell with the record when it arrives; with scripts off, it stays at this shell however long you wait.

01 Summary and function

What Foxa1 does

Waiting for the record before reading NCBI Gene and UniProt.

02 Transcripts and isoforms

The RNA a design targets

Waiting for the record before reading NCBI Datasets and Ensembl.

03 Expression by tissue

Where Foxa1 is expressed

Waiting for the record before reading GTEx and the Human Protein Atlas.

04 Protein

The protein Foxa1 encodes

Waiting for the record before reading UniProt, InterPro, AlphaFold DB and PDBe.

05 Interactions

Proteins STRING associates with Foxa1

Waiting for the record before reading STRING.

06 Pathways

Where Foxa1 acts, as Reactome curates it

Waiting for the record before reading UniProt and Reactome.

07 Disease associations

Diseases linked to Foxa1

Waiting for the record before reading Open Targets and ClinGen.

08 Variants

Classified variants of Foxa1

Waiting for the record before reading ClinVar.

09 Constraint

How much variation Foxa1 tolerates

Waiting for the record before reading gnomAD and Open Targets.

10 Orthologs

The same gene in mouse, rat and human

Waiting for the record before reading the Alliance, NCBI, Ensembl Compara and RGD.

11 MicroRNAs

MicroRNAs hosted within Foxa1

Waiting for the record before reading Ensembl and miRBase.

12 Long non-coding RNAs

Long non-coding RNAs at the Foxa1 locus

Waiting for the record before reading Ensembl.

13 Literature

Papers that mention Foxa1

Waiting for the record before reading Europe PMC.

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_012742.2matches ENSRNOT00000119772.2	none given	protein coding	RefSeq Select	2	2,881 nt	468 aaNP_036874.2	Ready in a moment
XM_039111792.3matches ENSRNOT00000009940.8	transcript variant X1	protein coding model	none	3	5,081 nt	475 aaXP_038967720.1	Ready in a moment
XM_039111793.3	transcript variant X3	protein coding model	none	3	4,134 nt	461 aaXP_038967721.1	Ready in a moment
XM_087619877.1	transcript variant X2	protein coding model	none	3	3,254 nt	462 aaXP_087476003.1	Ready in a moment
XR_015661386.1	transcript variant X4	non coding model	none	4	3,238 nt	none	Ready in a moment

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_012742.2matches ENSRNOT00000119772.2	none given	protein coding	RefSeq Select	2	2,881 nt	468 aaNP_036874.2	Ready in a moment
XM_039111792.3matches ENSRNOT00000009940.8	transcript variant X1	protein coding model	none	3	5,081 nt	475 aaXP_038967720.1	Ready in a moment
XM_039111793.3	transcript variant X3	protein coding model	none	3	4,134 nt	461 aaXP_038967721.1	Ready in a moment
XM_087619877.1	transcript variant X2	protein coding model	none	3	3,254 nt	462 aaXP_087476003.1	Ready in a moment
XR_015661386.1	transcript variant X4	non coding model	none	4	3,238 nt	none	Ready in a moment

Foxa1

What Foxa1 does

The RNA a design targets

Where Foxa1 is expressed

The protein Foxa1 encodes

Proteins STRING associates with Foxa1

Where Foxa1 acts, as Reactome curates it

Diseases linked to Foxa1

Classified variants of Foxa1

How much variation Foxa1 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within Foxa1

Long non-coding RNAs at the Foxa1 locus

Papers that mention Foxa1

From Foxa1 to a sequence that silences it

Choose the region

Cover the isoforms you mean

Think across species early

Check expression in your model

Run the controls

Pick the product

Foxa1

What Foxa1 does

The RNA a design targets

Where Foxa1 is expressed

The protein Foxa1 encodes

Proteins STRING associates with Foxa1

Where Foxa1 acts, as Reactome curates it

Diseases linked to Foxa1

Classified variants of Foxa1

How much variation Foxa1 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within Foxa1

Long non-coding RNAs at the Foxa1 locus

Papers that mention Foxa1

Foxa1

What Foxa1 does

Gene summary

Protein function

The RNA a design targets

RefSeq 5 transcripts

A window on one transcript

Ensembl 0 transcripts

Where Foxa1 is expressed

The protein Foxa1 encodes

Proteins STRING associates with Foxa1

Where Foxa1 acts, as Reactome curates it

Diseases linked to Foxa1

Classified variants of Foxa1

How much variation Foxa1 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within Foxa1

Long non-coding RNAs at the Foxa1 locus

Papers that mention Foxa1

From Foxa1 to a sequence that silences it

Choose the region

Cover the isoforms you mean

Think across species early

Check expression in your model

Run the controls

Pick the product

Gene summary

Protein function

RefSeq 5 transcripts

A window on one transcript

Ensembl 0 transcripts