Gene Rat Rattus norvegicus

Hif3a

hypoxia inducible factor 3 subunit alpha

protein coding

HumanMouseRat Hif3a

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 1q21NCBI: 1:86,850,554-86,877,838 on the minus strand, GRCr8 (GCF_036323735.1), sequence NC_086019.1, annotation GCF_036323735.1-RS_2026_08 of 2026-08-17Ensembl: 1:86,850,554-86,877,838 on the minus strand, GRCr8 (GCA_036323735.1), release 116Coordinates are one-based with both ends included, as each source reports them.
Also known as: Ipas, Mop7

Gene identity, from NCBI Datasets · NCBI Datasets 18.38.0 · read 2026-10-02 ET · RGD:70332Data from NCBI, provided as is; NCBI's policies and disclaimers apply.

Silence this gene

The order page opens with Hif3a and rat filled in. The sequences are designed against the transcripts below; the price is on that page.

Order for Hif3a

sdASO, toASO or siRNA

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

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01 Summary and function

What Hif3a does

Enables DNA-binding transcription factor activity.

NCBI Gene summary

Ready in a moment

02 Transcripts and isoforms

The RNA a design targets

Reading NCBI Datasets and Ensembl.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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03 Expression by tissue

Where Hif3a 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 Hif3a 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 Hif3a

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 Hif3a 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.

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07 Disease associations

Diseases linked to Hif3a

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

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08 Variants

Classified variants of Hif3a

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

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09 Constraint

How much variation Hif3a 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.

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11 MicroRNAs

MicroRNAs hosted within Hif3a

Reading Ensembl and miRBase.Still reading. A first read of a gene can take a while; this page waits up to 110 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

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12 Long non-coding RNAs

Long non-coding RNAs at the Hif3a locus

Reading Ensembl.Still reading. A first read of a gene can take a while; this page waits up to 110 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

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13 Literature

Papers that mention Hif3a

1,628 PubMed-indexed papers mention Hif3a at Europe PMC, newest first. Europe PMC ignores letter case, so the count also covers the human symbol where it differs from this one only in case.

Europe PMC

Ready in a moment

14 Silencing this gene

From Hif3a 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 Hif3a 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

Hif3a

Reading the record for Hif3a 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 Hif3a 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 Hif3a 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 Hif3a is expressed

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

04 Protein

The protein Hif3a encodes

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

05 Interactions

Proteins STRING associates with Hif3a

Waiting for the record before reading STRING.

06 Pathways

Where Hif3a acts, as Reactome curates it

Waiting for the record before reading UniProt and Reactome.

07 Disease associations

Diseases linked to Hif3a

Waiting for the record before reading Open Targets and ClinGen.

08 Variants

Classified variants of Hif3a

Waiting for the record before reading ClinVar.

09 Constraint

How much variation Hif3a 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 Hif3a

Waiting for the record before reading Ensembl and miRBase.

12 Long non-coding RNAs

Long non-coding RNAs at the Hif3a locus

Waiting for the record before reading Ensembl.

13 Literature

Papers that mention Hif3a

Waiting for the record before reading Europe PMC.

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_001388512.1matches ENSRNOT00000099745.2	transcript variant 2	protein coding	RefSeq Select	15	2,107 nt	664 aaNP_001375441.1	Ready in a moment
NM_022528.3matches ENSRNOT00000023490.5	transcript variant 1	protein coding	none	15	2,065 nt	662 aaNP_071973.2	Ready in a moment

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_001388512.1matches ENSRNOT00000099745.2	transcript variant 2	protein coding	RefSeq Select	15	2,107 nt	664 aaNP_001375441.1	Ready in a moment
NM_022528.3matches ENSRNOT00000023490.5	transcript variant 1	protein coding	none	15	2,065 nt	662 aaNP_071973.2	Ready in a moment

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
ENSRNOT00000099745.2	Hif3a-202	protein coding	Ensembl canonical	15	2,107 nt	664 aaENSRNOP00000097060.1	Ready in a moment
ENSRNOT00000101762.2	Hif3a-203	protein coding	none	14	2,144 nt	662 aaENSRNOP00000087469.2	Ready in a moment
ENSRNOT00000023490.5	Hif3a-201	protein coding	none	15	2,065 nt	662 aaENSRNOP00000023490.2	Ready in a moment

Hif3a

What Hif3a does

The RNA a design targets

Where Hif3a is expressed

The protein Hif3a encodes

Proteins STRING associates with Hif3a

Where Hif3a acts, as Reactome curates it

Diseases linked to Hif3a

Classified variants of Hif3a

How much variation Hif3a tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within Hif3a

Long non-coding RNAs at the Hif3a locus

Papers that mention Hif3a

From Hif3a 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

Hif3a

What Hif3a does

The RNA a design targets

Where Hif3a is expressed

The protein Hif3a encodes

Proteins STRING associates with Hif3a

Where Hif3a acts, as Reactome curates it

Diseases linked to Hif3a

Classified variants of Hif3a

How much variation Hif3a tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within Hif3a

Long non-coding RNAs at the Hif3a locus

Papers that mention Hif3a

Hif3a

What Hif3a does

Gene summary

Protein function

The RNA a design targets

RefSeq 2 transcripts

A window on one transcript

Ensembl 3 transcripts

A window on one transcript

Where Hif3a is expressed

The protein Hif3a encodes

Proteins STRING associates with Hif3a

Where Hif3a acts, as Reactome curates it

Diseases linked to Hif3a

Classified variants of Hif3a

How much variation Hif3a tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within Hif3a

Long non-coding RNAs at the Hif3a locus

Papers that mention Hif3a

From Hif3a 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 2 transcripts

A window on one transcript

Ensembl 3 transcripts

A window on one transcript