Gene Human Homo sapiens

SCX

scleraxis bHLH transcription factor

gene with protein product

Location: Cytogenetic band 8q24.3NCBI: 8:144,266,453-144,268,481 on the plus strand, GRCh38.p14 (GCF_000001405.40), sequence NC_000008.11, annotation GCF_000001405.40-RS_2025_08 of 2025-08-01Ensembl: 8:144,266,446-144,268,481 on the plus strand, GRCh38.p14 (GCA_000001405.29), release 116Coordinates are one-based with both ends included, as each source reports them.
Also known as: bHLHa48, bHLHa41
Previous symbols: SCXA, SCXB

Gene identity, from HGNC · HGNC 2026-09-29 · read 2026-10-03 ET · HGNC:32322

Silence this gene

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

Order for SCX

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 SCX does

Enables DNA-binding transcription activator activity, RNA polymerase…

NCBI Gene summary

Ready in a moment

02 Transcripts and isoforms

The RNA a design targets

1 RefSeq and 4 Ensembl transcripts on GRCh38.p14; MANE Select NM_001080514.3.

NCBI Datasets · Ensembl

Ready in a moment

03 Expression by tissue

Where SCX is expressed

54 GTEx tissues; the highest median in Thyroid, 69.3 TPM.

GTEx

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04 Protein

The protein SCX 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.

Ready in a moment

05 Interactions

Proteins STRING associates with SCX

The 25 highest-scoring STRING partners at or above a combined score of 0.4, of up to 25 asked for; TNMD, MKX, PAX1 lead.

STRING v12.0

Ready in a moment

06 Pathways

Where SCX 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 SCX

278 Open Targets disease associations; Dupuytren Contracture first, at 0.27.

Open Targets

Ready in a moment

08 Variants

Classified variants of SCX

ClinVar: 72 records for SCX, 57 pathogenic or likely pathogenic.

ClinVar

Ready in a moment

09 Constraint

How much variation SCX tolerates

pLI 0.03793 and LOEUF 1.08 in gnomAD v4 (GRCh38), on ENST00000567180.3.

gnomAD

Ready in a moment

10 Orthologs

The same gene in mouse, rat and human

Mouse Scx by 3 of 3 votes; rat Scx by 3 of 3 votes. RGD is not answering, so the ortholog list could not be shown. Try again later. Reference d650aa14-121.

Alliance · NCBI · Ensembl Compara

Ready in a moment

11 MicroRNAs

MicroRNAs hosted within SCX

No annotated microRNA lies within SCX in Ensembl release 116, on GRCh38.p14.

Ensembl · miRBase

Ready in a moment

12 Long non-coding RNAs

Long non-coding RNAs at the SCX locus

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

Ensembl

Ready in a moment

13 Literature

Papers that mention SCX

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 SCX 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 SCX 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

SCX

Reading the record for SCX 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 SCX 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 SCX 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 SCX is expressed

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

04 Protein

The protein SCX encodes

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

05 Interactions

Proteins STRING associates with SCX

Waiting for the record before reading STRING.

06 Pathways

Where SCX acts, as Reactome curates it

Waiting for the record before reading UniProt and Reactome.

07 Disease associations

Diseases linked to SCX

Waiting for the record before reading Open Targets and ClinGen.

08 Variants

Classified variants of SCX

Waiting for the record before reading ClinVar.

09 Constraint

How much variation SCX 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 SCX

Waiting for the record before reading Ensembl and miRBase.

12 Long non-coding RNAs

Long non-coding RNAs at the SCX locus

Waiting for the record before reading Ensembl.

13 Literature

Papers that mention SCX

Waiting for the record before reading Europe PMC.

SCX

scleraxis bHLH transcription factor

gene with protein product

Location

Cytogenetic band 8q24.3NCBI: 8:144,266,453-144,268,481 on the plus strand, GRCh38.p14 (GCF_000001405.40), sequence NC_000008.11, annotation GCF_000001405.40-RS_2025_08 of 2025-08-01Ensembl: 8:144,266,446-144,268,481 on the plus strand, GRCh38.p14 (GCA_000001405.29), release 116Coordinates are one-based with both ends included, as each source reports them.

Also known as

bHLHa48, bHLHa41

Previous symbols

SCXA, SCXB

Gene identity, from HGNC · HGNC 2026-09-29 · read 2026-10-03 ET · HGNC:32322

RefSeq transcripts of this gene
Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_001080514.3matches ENST00000567180.3	none given	protein coding	MANE Select	2	1,106 nt	201 aaNP_001073983.1	Ready in a moment

Accession

Name

Biotype

Labels

Exons

Spliced length

Protein

Sequence

NM_001080514.3matches ENST00000567180.3

none given

protein coding

MANE Select

1,106 nt

201 aaNP_001073983.1

Ready in a moment

Ensembl transcripts of this gene
Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
ENST00000567180.3matches NM_001080514.3	SCX-201	protein coding	MANE SelectEnsembl canonical	2	1,106 nt	201 aaENSP00000476384.1	Ready in a moment
ENST00001128157.1	SCX-203	protein coding	none	2	1,343 nt	203 aaENSP00000797962.1	Ready in a moment
ENST00001135167.1	SCX-204	protein coding	none	2	1,113 nt	201 aaENSP00000814541.1	Ready in a moment
ENST00000942843.2	SCX-202	protein coding	none	2	593 nt	30 aaENSP00000612902.1	Ready in a moment

Accession

Name

Biotype

Labels

Exons

Spliced length

Protein

Sequence

ENST00000567180.3matches NM_001080514.3

SCX-201

protein coding

MANE SelectEnsembl canonical

1,106 nt

201 aaENSP00000476384.1

Ready in a moment

ENST00001128157.1

SCX-203

protein coding

none

1,343 nt

203 aaENSP00000797962.1

Ready in a moment

ENST00001135167.1

SCX-204

protein coding

none

1,113 nt

201 aaENSP00000814541.1

Ready in a moment

ENST00000942843.2

SCX-202

protein coding

none

593 nt

30 aaENSP00000612902.1

Ready in a moment

From SCX to a sequence that silences it

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.

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.

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.

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.

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.

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.

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

RefSeq transcripts of this gene
Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_001080514.3matches ENST00000567180.3	none given	protein coding	MANE Select	2	1,106 nt	201 aaNP_001073983.1	Ready in a moment

Accession

Name

Biotype

Labels

Exons

Spliced length

Protein

Sequence

NM_001080514.3matches ENST00000567180.3

none given

protein coding

MANE Select

1,106 nt

201 aaNP_001073983.1

Ready in a moment

Ensembl transcripts of this gene
Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
ENST00000567180.3matches NM_001080514.3	SCX-201	protein coding	MANE SelectEnsembl canonical	2	1,106 nt	201 aaENSP00000476384.1	Ready in a moment
ENST00001128157.1	SCX-203	protein coding	none	2	1,343 nt	203 aaENSP00000797962.1	Ready in a moment
ENST00001135167.1	SCX-204	protein coding	none	2	1,113 nt	201 aaENSP00000814541.1	Ready in a moment
ENST00000942843.2	SCX-202	protein coding	none	2	593 nt	30 aaENSP00000612902.1	Ready in a moment

Accession

Name

Biotype

Labels

Exons

Spliced length

Protein

Sequence

ENST00000567180.3matches NM_001080514.3

SCX-201

protein coding

MANE SelectEnsembl canonical

1,106 nt

201 aaENSP00000476384.1

Ready in a moment

ENST00001128157.1

SCX-203

protein coding

none

1,343 nt

203 aaENSP00000797962.1

Ready in a moment

ENST00001135167.1

SCX-204

protein coding

none

1,113 nt

201 aaENSP00000814541.1

Ready in a moment

ENST00000942843.2

SCX-202

protein coding

none

593 nt

30 aaENSP00000612902.1

Ready in a moment

SCX

What SCX does

The RNA a design targets

Where SCX is expressed

The protein SCX encodes

Proteins STRING associates with SCX

Where SCX acts, as Reactome curates it

Diseases linked to SCX

Classified variants of SCX

How much variation SCX tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within SCX

Long non-coding RNAs at the SCX locus

Papers that mention SCX

From SCX 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

SCX

What SCX does

The RNA a design targets

Where SCX is expressed

The protein SCX encodes

Proteins STRING associates with SCX

Where SCX acts, as Reactome curates it

Diseases linked to SCX

Classified variants of SCX

How much variation SCX tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within SCX

Long non-coding RNAs at the SCX locus

Papers that mention SCX

SCX

What SCX does

Gene summary

Protein function

The RNA a design targets

RefSeq 1 transcript

A window on one transcript

Ensembl 4 transcripts

A window on one transcript

Where SCX is expressed

The protein SCX encodes

Proteins STRING associates with SCX

Where SCX acts, as Reactome curates it

Diseases linked to SCX

Classified variants of SCX

How much variation SCX tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within SCX

Long non-coding RNAs at the SCX locus

Papers that mention SCX

From SCX 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 1 transcript

A window on one transcript

Ensembl 4 transcripts

A window on one transcript