Gene Human Homo sapiens

PCDHA4

protocadherin alpha 4

complex locus constituent

Human PCDHA4MouseRat

Reading the ortholog votes for mouse and rat.

Location: Cytogenetic band 5q31.3NCBI: 5:140,807,068-141,012,347 on the plus strand, GRCh38.p14 (GCF_000001405.40), sequence NC_000005.10, annotation GCF_000001405.40-RS_2025_08 of 2025-08-01Ensembl: 5:140,807,037-141,012,347 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: CNR1, CRNR1, PCDH-ALPHA4, CNRN1

Gene identity, from HGNC · HGNC 2026-09-29 · read 2026-10-02 ET · HGNC:8670

Notes from the sources

HGNC lists more than one mouse id for this gene (MGI:1298406, MGI:5610241); MGI:1298406 is used
NCBI places this gene on more than one sequence of GRCh38.p14 (5 NC_000005.10, 5 NW_025791778.1); the coordinates shown are the 5 placement

Silence this gene

The order page opens with PCDHA4 and human filled in. The sequences are designed against the transcripts below; the price is on that page.

Order for PCDHA4

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 PCDHA4 does

This gene is a member of the protocadherin alpha gene cluster, one of three…

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 PCDHA4 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 PCDHA4 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 PCDHA4

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 PCDHA4 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 PCDHA4

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 PCDHA4

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 PCDHA4 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.

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11 MicroRNAs

MicroRNAs hosted within PCDHA4

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 PCDHA4 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 PCDHA4

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 PCDHA4 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 PCDHA4 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

PCDHA4

Reading the record for PCDHA4 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 PCDHA4 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 PCDHA4 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 PCDHA4 is expressed

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

04 Protein

The protein PCDHA4 encodes

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

05 Interactions

Proteins STRING associates with PCDHA4

Waiting for the record before reading STRING.

06 Pathways

Where PCDHA4 acts, as Reactome curates it

Waiting for the record before reading UniProt and Reactome.

07 Disease associations

Diseases linked to PCDHA4

Waiting for the record before reading Open Targets and ClinGen.

08 Variants

Classified variants of PCDHA4

Waiting for the record before reading ClinVar.

09 Constraint

How much variation PCDHA4 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 PCDHA4

Waiting for the record before reading Ensembl and miRBase.

12 Long non-coding RNAs

Long non-coding RNAs at the PCDHA4 locus

Waiting for the record before reading Ensembl.

13 Literature

Papers that mention PCDHA4

Waiting for the record before reading Europe PMC.

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_018907.4matches ENST00000530339.2 NCBI's product report carries no genomic placement for this transcript, so its exon coordinates are not available from NCBI	transcript variant 1	protein coding	MANE Select	not placed	5,374 nt	947 aaNP_061730.1	Ready in a moment
NM_031500.3matches ENST00000618834.1 NCBI's product report carries no genomic placement for this transcript, so its exon coordinates are not available from NCBI	transcript variant 2	protein coding	none	not placed	10,526 nt	798 aaNP_113688.1	Ready in a moment

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_018907.4matches ENST00000530339.2 NCBI's product report carries no genomic placement for this transcript, so its exon coordinates are not available from NCBI	transcript variant 1	protein coding	MANE Select	not placed	5,374 nt	947 aaNP_061730.1	Ready in a moment
NM_031500.3matches ENST00000618834.1 NCBI's product report carries no genomic placement for this transcript, so its exon coordinates are not available from NCBI	transcript variant 2	protein coding	none	not placed	10,526 nt	798 aaNP_113688.1	Ready in a moment

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
ENST00000530339.2matches NM_018907.4	PCDHA4-202	protein coding	MANE SelectEnsembl canonical	4	5,374 nt	947 aaENSP00000435300.1	Ready in a moment
ENST00000618834.1	PCDHA4-203	protein coding	none	1	10,557 nt	798 aaENSP00000481220.1	Ready in a moment
ENST00001135007.1	PCDHA4-205	protein coding	none	4	5,379 nt	947 aaENSP00000813820.1	Ready in a moment
ENST00000512229.7	PCDHA4-201	protein coding	none	5	4,939 nt	901 aaENSP00000423470.2	Ready in a moment
ENST00000672575.2	PCDHA4-204	protein coding	none	2	2,826 nt	806 aaENSP00000500758.1	Ready in a moment

PCDHA4

What PCDHA4 does

The RNA a design targets

Where PCDHA4 is expressed

The protein PCDHA4 encodes

Proteins STRING associates with PCDHA4

Where PCDHA4 acts, as Reactome curates it

Diseases linked to PCDHA4

Classified variants of PCDHA4

How much variation PCDHA4 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within PCDHA4

Long non-coding RNAs at the PCDHA4 locus

Papers that mention PCDHA4

From PCDHA4 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

PCDHA4

What PCDHA4 does

The RNA a design targets

Where PCDHA4 is expressed

The protein PCDHA4 encodes

Proteins STRING associates with PCDHA4

Where PCDHA4 acts, as Reactome curates it

Diseases linked to PCDHA4

Classified variants of PCDHA4

How much variation PCDHA4 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within PCDHA4

Long non-coding RNAs at the PCDHA4 locus

Papers that mention PCDHA4

PCDHA4

What PCDHA4 does

Gene summary

Protein function

The RNA a design targets

RefSeq 2 transcripts

Ensembl 5 transcripts

A window on one transcript

Where PCDHA4 is expressed

The protein PCDHA4 encodes

Proteins STRING associates with PCDHA4

Where PCDHA4 acts, as Reactome curates it

Diseases linked to PCDHA4

Classified variants of PCDHA4

How much variation PCDHA4 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within PCDHA4

Long non-coding RNAs at the PCDHA4 locus

Papers that mention PCDHA4

From PCDHA4 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

Ensembl 5 transcripts

A window on one transcript