Reading the record for CNTNAP3 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 CNTNAP3 opens with the record, which decides which product it carries. The order page itself is open now.
Cytogenetic band 9p12NCBI: 9:39,064,710-39,288,167 on the minus strand, GRCh38.p14 (GCF_000001405.40), sequence NC_000009.12, annotation GCF_000001405.40-RS_2025_08 of 2025-08-01Ensembl: 9:39,064,710-39,288,611 on the minus strand, GRCh38.p14 (GCA_000001405.29), release 116Coordinates are one-based with both ends included, as each source reports them.
Reading NCBI Gene and UniProt.Still reading. A first read of a gene can take a while; this page waits up to 30 seconds for it, and its scripts then bring in the panel, or a line saying what did not arrive.
02 / Transcripts and isoforms
The RNA a design targets
Ready in a moment
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 the panel, or a line saying what did not arrive.
03 / Expression by tissue
Where CNTNAP3 is expressed
Ready in a moment
14 / Silencing this gene
From CNTNAP3 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.
The median is the middle sample of a tissue, so a gene expressed in a few cells of a mixed tissue reads low here and may still be the one your cell type needs. Nothing on this panel is adjusted or averaged across tissues; each figure is the source's own, and a tissue GTEx did not sample is absent from the chart.
04 / Protein
The protein CNTNAP3 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 CNTNAP3
Ready in a moment
06 / Pathways
Where CNTNAP3 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 CNTNAP3
Ready in a moment
08 / Variants
Classified variants of CNTNAP3
Ready in a moment
09 / Constraint
How much variation CNTNAP3 tolerates
Ready in a moment
10 / Orthologs
The same gene in mouse, rat and human
Ready in a moment
11 /MicroRNAs
MicroRNAs hosted within CNTNAP3
Ready in a moment
12 / Long non-coding RNAs
Long non-coding RNAs at the CNTNAP3 locus
Ready in a moment
13 / Literature
Papers that mention CNTNAP3
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
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.
For research use only. Not for use in diagnostic or therapeutic procedures.
The protein encoded by this gene belongs to the NCP family of…
NCBI Gene summary
2 RefSeq and 36 Ensembl transcripts on GRCh38.p14; MANE Select NM_033655.5.
NCBI Datasets · Ensembl
54 GTEx tissues; the highest median in Esophagus - Muscularis, 9.19 TPM.
GTEx
The 9 highest-scoring STRING partners at or above a combined score of 0.4, of up to 25 asked for; APBA1, EPB41, CNTNAP3B lead.
STRING v12.0
51 Open Targets disease associations; basal cell carcinoma first, at 0.05.
Open Targets
ClinVar: 281 records for CNTNAP3, 51 pathogenic or likely pathogenic.
ClinVar
pLI 0.7589 and LOEUF 0.516 in gnomAD v4 (GRCh38), on ENST00000297668.11.
gnomAD
Mouse Cntnap3 by 3 of 3 votes; rat Cntnap3 by 3 of 3 votes. RGD is not answering, so the ortholog list could not be shown. Try again later. Reference 04d22874-b28.
Alliance · NCBI · Ensembl Compara
No annotated microRNA lies within CNTNAP3 in Ensembl release 116, on GRCh38.p14.
Ensembl · miRBase
No annotated long non-coding RNA overlaps CNTNAP3 in Ensembl release 116, on GRCh38.p14.
Ensembl
Gene summary
The protein encoded by this gene belongs to the NCP family of cell-recognition molecules. This family represents a distinct subgroup of the neurexins. NCP proteins mediate neuron-glial interactions in vertebrates and glial-glial contact in invertebrates. The protein encoded by this gene may play a role in cell recognition within the nervous system. Alternatively spliced transcript variants encoding different isoforms have been described but their biological nature has not been determined.
Provided by RefSeq, Jul 2008, through NCBI Gene. NCBI disclaimer
NCBI Gene summary · NCBI Gene annotation RS_2025_08 · read · NCBI Gene 79937Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
UniProtKB function · 2026_03 · read · UniProt Q9BZ76UniProt data are available under the Creative Commons Attribution 4.0 licence.
Placed on GRCh38.p14 (GCF_000001405.40). MANE Select marks the one transcript RefSeq and Ensembl agree is the reference for this gene.
RefSeq 2 transcripts
coding sequence, tall
untranslated region, thin
non-coding exon
intron, fixed width
Genomic strand: minus. Drawn 5' to 3', so exon 1 sits at the left here and at the highest coordinate on the chromosome.
NM_033655.5NM_033655.5MANE Select
NM_001393379.1NM_001393379.1
scale
Drawn 5' to 3' from each transcript's exons as placed on the reference assembly; exon 1 is the 5' exon on the transcript's own strand. Exon blocks are to scale with each other, except 2 blocks too short to see, widened to a fixed few pixels; introns are drawn at one fixed width whatever their length, so the map is not to scale along the chromosome. Numbers are exon ranks along the strand; a rank is omitted where the exon is too narrow to carry it.
A window on one transcript
One pixel of the map above stands for several bases, and a block too short to see is drawn wider than its own scale, so the map chooses a region and the sequence here chooses the window. Click an exon on a row of the map, or drag across a row; then set the exact start and end below.
These controls are ready in a moment.
No transcript is chosen.
Once a window is chosen this panel shows its length, its G and C count as a percentage of that length, the letters it is made of, the exons it falls in, whether it crosses a junction, and its antisense strand.
NCBI Datasets, RefSeq transcripts · NCBI Datasets 18.38.0; GCF_000001405.40-RS_2025_08 · read · NCBI Gene 79937Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
Ensembl 36 transcripts
A window on one transcript
One pixel of the map above stands for several bases, and a block too short to see is drawn wider than its own scale, so the map chooses a region and the sequence here chooses the window. Click an exon on a row of the map, or drag across a row; then set the exact start and end below.
These controls are ready in a moment.
No transcript is chosen.
Once a window is chosen this panel shows its length, its G and C count as a percentage of that length, the letters it is made of, the exons it falls in, whether it crosses a junction, and its antisense strand.
Lengths are spliced lengths, as each source states them. Exon ranks follow the strand: on a minus-strand gene exon 1 has the highest genomic coordinate. Reference assembly for human: GRCh38.
coding sequence, tall
untranslated region, thin
non-coding exon
intron, fixed width
Genomic strand: minus. Drawn 5' to 3', so exon 1 sits at the left here and at the highest coordinate on the chromosome.
Drawn 5' to 3' from each transcript's exons as placed on the reference assembly; exon 1 is the 5' exon on the transcript's own strand. Exon blocks are to scale with each other, except 9 blocks too short to see, widened to a fixed few pixels; introns are drawn at one fixed width whatever their length, so the map is not to scale along the chromosome. Numbers are exon ranks along the strand; a rank is omitted where the exon is too narrow to carry it.
224 PubMed-indexed papers mention CNTNAP3 at Europe PMC, newest first. Europe PMC ignores letter case, so the count also covers another species' symbol spelled with the same letters.
Europe PMC
1,288 residues, reviewed Q9BZ76; 23 entries from the member databases this page shows along the chain; mean pLDDT 82.88; no experimental structure at PDBe.
