Reading the record for CLN8 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 CLN8 opens with the record, which decides which product it carries. The order page itself is open now.
Cytogenetic band 8p23.3NCBI: 8:1,753,059-1,786,570 on the plus strand, GRCh38.p14 (GCF_000001405.40), sequence NC_000008.11, annotation GCF_000001405.40-RS_2025_08 of 2025-08-01Ensembl: 8:1,755,778-1,801,711 on the plus 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
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.
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.
14 / Silencing this gene
From CLN8 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.
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.
Ready in a moment
04 / Protein
The protein CLN8 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 CLN8
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.
Ready in a moment
06 / Pathways
Where CLN8 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 CLN8
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.
Ready in a moment
08 / Variants
Classified variants of CLN8
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.
Ready in a moment
09 / Constraint
How much variation CLN8 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.
Ready in a moment
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 CLN8
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 CLN8 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 CLN8
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.
This gene encodes a transmembrane protein belonging to a family of proteins…
NCBI Gene summary
Gene summary
This gene encodes a transmembrane protein belonging to a family of proteins containing TLC domains, which are postulated to function in lipid synthesis, transport, or sensing. The protein localizes to the endoplasmic reticulum (ER), and may recycle between the ER and ER-Golgi intermediate compartment. Mutations in this gene are associated with a disorder characterized by progressive epilepsy with cognitive disabilities (EPMR), which is a subtype of neuronal ceroid lipofuscinoses (NCL). Patients with mutations in this gene have altered levels of sphingolipid and phospholipids in the brain.
Provided by RefSeq, Jul 2017, through NCBI Gene. NCBI disclaimer
Could play a role in cell proliferation during neuronal differentiation and in protection against cell death
NCBI Gene summary · NCBI Gene annotation RS_2025_08 · read · NCBI Gene 2055Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
UniProtKB function · 2026_03 · read · UniProt Q9UBY8UniProt data are available under the Creative Commons Attribution 4.0 licence.
pLI below 0.0001 and LOEUF 1.39 in gnomAD v4 (GRCh38), on ENST00000331222.6.
gnomAD
54 GTEx tissues; the highest median in Brain - Spinal cord (cervical c-1), 21.6 TPM.
GTEx
1,302 Open Targets disease associations; neuronal ceroid lipofuscinosis 8 first, at 0.83.
Open Targets
Reactome v97 maps no pathway to Q9UBY8 in human.
Reactome
17 RefSeq and 40 Ensembl transcripts on GRCh38.p14; MANE Select NM_018941.4.
NCBI Datasets · Ensembl
The 25 highest-scoring STRING partners at or above a combined score of 0.4, of up to 25 asked for; CLN6, CLN5, PPT1 lead.
STRING v12.0
Placed on GRCh38.p14 (GCF_000001405.40). MANE Select marks the one transcript RefSeq and Ensembl agree is the reference for this gene.
RefSeq 17 transcripts
coding sequence, tall
untranslated region, thin
non-coding exon
intron, fixed width
Genomic strand: plus. Drawn 5' to 3', so exon 1 sits at the left here and at the lowest coordinate on the chromosome.
NM_018941.4NM_018941.4MANE Select
XM_054330441.1XM_054
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 18.37.0; GCF_000001405.40-RS_2025_08 · read · NCBI Gene 2055Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
Ensembl 40 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.
330441.1
XM_005266022.2XM_005266022.2
XM_054330443.1XM_054330443.1
XM_011534746.3XM_011534746.3
XM_054330440.1XM_054330440.1
XM_054330442.1XM_054330442.1
XM_011534745.2XM_011534745.2
XM_047421512.1XM_047421512.1
XM_054330445.1XM_054330445.1
XM_005266021.5XM_005266021.5
XM_005266023.2XM_005266023.2
XM_054330444.1XM_054330444.1
XM_047421513.1XM_047421513.1
XM_011534747.3XM_011534747.3
XM_054330447.1XM_054330447.1
XM_054330446.1XM_054330446.1
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.
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 4 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.
Mouse Cln8 by 3 of 3 votes; rat Cln8 by 3 of 3 votes. RGD is not answering, so the ortholog list could not be shown. Try again later. Reference f586a365-8e5.
Alliance · NCBI · Ensembl Compara
ClinVar: 772 records for CLN8, 217 pathogenic or likely pathogenic.
ClinVar
Europe PMC did not answer in time, so the literature search could not be shown. Try again in a minute. Reference 33f16e2b-d97.
