Gene Human Homo sapiens

NKX6-3

NK6 homeobox 3

gene with protein product

Human NKX6-3MouseRat

Reading the ortholog votes for mouse and rat.

Location: Cytogenetic band 8p11.21NCBI: 8:41,645,177-41,650,817 on the minus strand, GRCh38.p14 (GCF_000001405.40), sequence NC_000008.11, annotation GCF_000001405.40-RS_2025_08 of 2025-08-01Ensembl: 8:41,645,177-41,650,817 on the minus strand, GRCh38.p14 (GCA_000001405.29), release 116Coordinates are one-based with both ends included, as each source reports them.
Also known as: FLJ25169

Gene identity, from HGNC · HGNC 2026-10-02 · read 2026-10-03 ET · HGNC:26328

Silence this gene

The order page opens with NKX6-3 and human filled in. The sequences are designed against the transcripts below; the price is on that page.

Order for NKX6-3

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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Ready in a moment

01 Summary and function

What NKX6-3 does

The NKX family of homeodomain proteins controls numerous developmental…

NCBI Gene summary

Ready in a moment

02 Transcripts and isoforms

The RNA a design targets

2 RefSeq and 2 Ensembl transcripts on GRCh38.p14; MANE Select NM_001364841.2.

NCBI Datasets · Ensembl

Ready in a moment

03 Expression by tissue

Where NKX6-3 is expressed

Reading GTEx and the Human Protein Atlas.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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04 Protein

The protein NKX6-3 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 NKX6-3

The 17 highest-scoring STRING partners at or above a combined score of 0.4, of up to 25 asked for; NKX2-3, NKX1-1, HLX lead.

STRING v12.0

Ready in a moment

06 Pathways

Where NKX6-3 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 NKX6-3

Reading Open Targets and ClinGen.Still reading. A first read of a gene can take a while; this page waits up to 105 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

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08 Variants

Classified variants of NKX6-3

Reading ClinVar.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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09 Constraint

How much variation NKX6-3 tolerates

Reading gnomAD and Open Targets.Still reading. A first read of a gene can take a while; this page waits up to 45 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

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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 NKX6-3

No annotated microRNA lies within NKX6-3 in Ensembl release 116, on GRCh38.p14.

Ensembl · miRBase

Ready in a moment

12 Long non-coding RNAs

Long non-coding RNAs at the NKX6-3 locus

No annotated long non-coding RNA overlaps NKX6-3 in Ensembl release 116, on GRCh38.p14.

Ensembl

Ready in a moment

13 Literature

Papers that mention NKX6-3

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.

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14 Silencing this gene

From NKX6-3 to a sequence that silences it

The AUMsilence platform designs the sequences against the human 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 NKX6-3 Bring your own sequence The usage guide Selection guide

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

Gene Human Homo sapiens

NKX6-3

Reading the record for NKX6-3 from HGNC, 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 NKX6-3 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 NKX6-3 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 NKX6-3 is expressed

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

04 Protein

The protein NKX6-3 encodes

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

05 Interactions

Proteins STRING associates with NKX6-3

Waiting for the record before reading STRING.

06 Pathways

Where NKX6-3 acts, as Reactome curates it

Waiting for the record before reading UniProt and Reactome.

07 Disease associations

Diseases linked to NKX6-3

Waiting for the record before reading Open Targets and ClinGen.

08 Variants

Classified variants of NKX6-3

Waiting for the record before reading ClinVar.

09 Constraint

How much variation NKX6-3 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 NKX6-3

Waiting for the record before reading Ensembl and miRBase.

12 Long non-coding RNAs

Long non-coding RNAs at the NKX6-3 locus

Waiting for the record before reading Ensembl.

13 Literature

Papers that mention NKX6-3

Waiting for the record before reading Europe PMC.

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_001364841.2matches ENST00000518699.4	transcript variant 1	protein coding	MANE Select	3	2,395 nt	265 aaNP_001351770.1	Ready in a moment
NM_152568.3matches ENST00000524115.3	transcript variant 2	protein coding	none	2	1,683 nt	135 aaNP_689781.1	Ready in a moment

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
ENST00000518699.4matches NM_001364841.2	NKX6-3-201	protein coding	MANE SelectEnsembl canonical	3	2,395 nt	265 aaENSP00000428361.2	Ready in a moment
ENST00000524115.3	NKX6-3-202	protein coding	none	2	1,684 nt	135 aaENSP00000429553.2	Ready in a moment

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_001364841.2matches ENST00000518699.4	transcript variant 1	protein coding	MANE Select	3	2,395 nt	265 aaNP_001351770.1	Ready in a moment
NM_152568.3matches ENST00000524115.3	transcript variant 2	protein coding	none	2	1,683 nt	135 aaNP_689781.1	Ready in a moment

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
ENST00000518699.4matches NM_001364841.2	NKX6-3-201	protein coding	MANE SelectEnsembl canonical	3	2,395 nt	265 aaENSP00000428361.2	Ready in a moment
ENST00000524115.3	NKX6-3-202	protein coding	none	2	1,684 nt	135 aaENSP00000429553.2	Ready in a moment

NKX6-3

What NKX6-3 does

The RNA a design targets

Where NKX6-3 is expressed

The protein NKX6-3 encodes

Proteins STRING associates with NKX6-3

Where NKX6-3 acts, as Reactome curates it

Diseases linked to NKX6-3

Classified variants of NKX6-3

How much variation NKX6-3 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within NKX6-3

Long non-coding RNAs at the NKX6-3 locus

Papers that mention NKX6-3

From NKX6-3 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

NKX6-3

What NKX6-3 does

The RNA a design targets

Where NKX6-3 is expressed

The protein NKX6-3 encodes

Proteins STRING associates with NKX6-3

Where NKX6-3 acts, as Reactome curates it

Diseases linked to NKX6-3

Classified variants of NKX6-3

How much variation NKX6-3 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within NKX6-3

Long non-coding RNAs at the NKX6-3 locus

Papers that mention NKX6-3

NKX6-3

What NKX6-3 does

Gene summary

Protein function

The RNA a design targets

RefSeq 2 transcripts

A window on one transcript

Ensembl 2 transcripts

A window on one transcript

Where NKX6-3 is expressed

The protein NKX6-3 encodes

Proteins STRING associates with NKX6-3

Where NKX6-3 acts, as Reactome curates it

Diseases linked to NKX6-3

Classified variants of NKX6-3

How much variation NKX6-3 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within NKX6-3

Long non-coding RNAs at the NKX6-3 locus

Papers that mention NKX6-3

From NKX6-3 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 2 transcripts

A window on one transcript