Reading the record for CBX3 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 CBX3 opens with the record, which decides which product it carries. The order page itself is open now.
Cytogenetic band 7p15.2NCBI: 7:26,201,443-26,213,607 on the plus strand, GRCh38.p14 (GCF_000001405.40), sequence NC_000007.14, annotation GCF_000001405.40-RS_2025_08 of 2025-08-01Ensembl: 7:26,200,568-26,213,607 on the plus strand, GRCh38.p14 (GCA_000001405.29), release 116Coordinates are one-based with both ends included, as each source reports them.
At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent…
NCBI Gene summary
Ready in a moment
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.
03 / Expression by tissue
Where CBX3 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.
Ready in a moment
04 / Protein
The protein CBX3 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 CBX3
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 CBX3 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 CBX3
313 Open Targets disease associations; endometriosis first, at 0.25.
Open Targets
Ready in a moment
08 / Variants
Classified variants of CBX3
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 CBX3 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 CBX3
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 CBX3 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 CBX3
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 CBX3 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.
For research use only. Not for use in diagnostic or therapeutic procedures.
Gene summary
At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene.
Provided by RefSeq, Mar 2011, through NCBI Gene. NCBI disclaimer
Component of heterochromatin, which recognizes and binds histone H3 tails methylated at 'Lys-9', leading to epigenetic repression (PubMed:11242053). Also recognizes and binds histone H1.4 methylated at 'Lys-26' (H1.4K26me) (PubMed:16127177). Excluded from chromatin when histone H1.4 is Simultaneously methylated at Lys-26 (H1.4K26me) and phosphorylated at Ser-27 (H1.4S27Ph) (PubMed:16127177). Involved in the formation of functional kinetochore through interaction with MIS12 complex proteins (PubMed:15502821). Contributes to the conversion of local chromatin to a heterochromatin-like repressive state through H3 'Lys-9' trimethylation, mediates the recruitment of the methyltransferases SUV39H1 and/or SUV39H2 by the PER complex to the E-box elements of the circadian target genes such as PER2 itself or PER1 (By similarity). Mediates the recruitment of NIPBL to sites of DNA damage at double-strand breaks (DSBs) (PubMed:28167679)
NCBI Gene summary · NCBI Gene annotation RS_2025_08 · read · NCBI Gene 11335Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
UniProtKB function · 2026_03 · read · UniProt Q13185UniProt data are available under the Creative Commons Attribution 4.0 licence.
pLI 0.9889 and LOEUF 0.465 in gnomAD v4 (GRCh38), on ENST00000396386.7.
gnomAD
2,010 PubMed-indexed papers mention CBX3 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
54 GTEx tissues; the highest median in Cells - EBV-transformed lymphocytes, 188 TPM.
GTEx
4 curated, 0 inferred Reactome pathways for Q13185 in human, v97.
Reactome
Mouse Cbx3 by 2 of 3 votes; rat: 2 candidates named (Cbx3, Cbx3l2) and the votes differ. RGD is not answering, so the ortholog list could not be shown. Try again later. Reference e5d88d12-fa0.
Alliance · NCBI · Ensembl Compara
The 25 highest-scoring STRING partners at or above a combined score of 0.4, of up to 25 asked for; H3-5, H3-3B, H3-4 lead.
STRING v12.0
183 residues, reviewed Q13185; 16 entries from the member databases this page shows along the chain; mean pLDDT 75.38; 8 PDB entries.
UniProt · InterPro · AlphaFold DB · PDBe
ClinVar: 62 records for CBX3, 30 pathogenic or likely pathogenic.
ClinVar
No annotated microRNA lies within CBX3 in Ensembl release 116, on GRCh38.p14.
Ensembl · miRBase
No annotated long non-coding RNA overlaps CBX3 in Ensembl release 116, on GRCh38.p14.
Ensembl
4 RefSeq and 49 Ensembl transcripts on GRCh38.p14; MANE Select NM_016587.4.
NCBI Datasets · Ensembl
Placed on GRCh38.p14 (GCF_000001405.40). MANE Select marks the one transcript RefSeq and Ensembl agree is the reference for this gene.
RefSeq 4 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_016587.4NM_016587.4MANE Select
XM_005249611.5XM_005249611.5
NM_007276.5NM_007276.5
NM_001410866.1NM_001410866.1
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; 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.
Not listed, because the source places them on another assembly only: XM_054357182.1 (not placed on GRCh38.p14).
NCBI Datasets, RefSeq transcripts · NCBI Datasets 18.37.0; GCF_000001405.40-RS_2025_08 · read · NCBI Gene 11335Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
Ensembl 49 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.
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; 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.
