Gene Rat Rattus norvegicus

Shh

sonic hedgehog signaling molecule

protein coding

HumanMouseRat Shh

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 4q11NCBI: 4:7,687,872-7,697,025 on the plus strand, GRCr8 (GCF_036323735.1), sequence NC_086022.1, annotation GCF_036323735.1-RS_2026_08 of 2026-08-17Ensembl: 4:7,687,846-7,697,901 on the plus strand, GRCr8 (GCA_036323735.1), release 116Coordinates are one-based with both ends included, as each source reports them.
Also known as: ShhNC

Gene identity, from NCBI Datasets · NCBI Datasets 18.38.0 · read 2026-10-02 ET · RGD:3673Data from NCBI, provided as is; NCBI's policies and disclaimers apply.

Silence this gene

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

Order for Shh

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

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01 Summary and function

What Shh does

Predicted to enable several functions, including cholesterol-protein…

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 Shh is expressed

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

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04 Protein

The protein Shh 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 Shh

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 Shh 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 Shh

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 Shh

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

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09 Constraint

How much variation Shh tolerates

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

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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.

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11 MicroRNAs

MicroRNAs hosted within Shh

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.

Ready in a moment

12 Long non-coding RNAs

Long non-coding RNAs at the Shh 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.

Ready in a moment

13 Literature

Papers that mention Shh

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 Shh 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 Shh 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

Shh

Reading the record for Shh 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 Shh 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 Shh 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 Shh is expressed

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

04 Protein

The protein Shh encodes

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

05 Interactions

Proteins STRING associates with Shh

Waiting for the record before reading STRING.

06 Pathways

Where Shh acts, as Reactome curates it

Waiting for the record before reading UniProt and Reactome.

07 Disease associations

Diseases linked to Shh

Waiting for the record before reading Open Targets and ClinGen.

08 Variants

Classified variants of Shh

Waiting for the record before reading ClinVar.

09 Constraint

How much variation Shh 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 Shh

Waiting for the record before reading Ensembl and miRBase.

12 Long non-coding RNAs

Long non-coding RNAs at the Shh locus

Waiting for the record before reading Ensembl.

13 Literature

Papers that mention Shh

Waiting for the record before reading Europe PMC.

Shh

What Shh does

The RNA a design targets

Where Shh is expressed

The protein Shh encodes

Proteins STRING associates with Shh

Where Shh acts, as Reactome curates it

Diseases linked to Shh

Classified variants of Shh

How much variation Shh tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within Shh

Long non-coding RNAs at the Shh locus

Papers that mention Shh

From Shh 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

Shh

What Shh does

The RNA a design targets

Where Shh is expressed

The protein Shh encodes

Proteins STRING associates with Shh

Where Shh acts, as Reactome curates it

Diseases linked to Shh

Classified variants of Shh

How much variation Shh tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within Shh

Long non-coding RNAs at the Shh locus

Papers that mention Shh

Shh

What Shh does

Gene summary

Protein function

The RNA a design targets

RefSeq 1 transcript

A window on one transcript

Ensembl 1 transcript

A window on one transcript

Where Shh is expressed

The protein Shh encodes

Proteins STRING associates with Shh

Where Shh acts, as Reactome curates it

Diseases linked to Shh

Classified variants of Shh

How much variation Shh tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within Shh

Long non-coding RNAs at the Shh locus

Papers that mention Shh

From Shh 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 1 transcript

A window on one transcript