Reading the record for UBE3B 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 UBE3B opens with the record, which decides which product it carries. The order page itself is open now.
Cytogenetic band 12q24.11NCBI: 12:109,477,634-109,547,829 on the plus strand, GRCh38.p14 (GCF_000001405.40), sequence NC_000012.12, annotation GCF_000001405.40-RS_2025_08 of 2025-08-01Ensembl: 12:109,477,375-109,536,705 on the plus strand, GRCh38.p14 (GCA_000001405.29), release 116Coordinates are one-based with both ends included, as each source reports them.
The modification of proteins with ubiquitin is an important cellular…
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
22 RefSeq transcripts on GRCh38.p14; MANE Select NM_130466.4. 14 RefSeq transcripts of UBE3B carry no exon placement. Ensembl is not answering, so the Ensembl transcripts could not be shown. Try again later. Reference b13369a4-54f.
NCBI Datasets
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 UBE3B 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 UBE3B 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 UBE3B
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 UBE3B 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 UBE3B
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 UBE3B
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 UBE3B 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.
Ready in a moment
11 /MicroRNAs
MicroRNAs hosted within UBE3B
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 UBE3B 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 UBE3B
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 UBE3B 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
The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: E1 ubiquitin-activating enzymes, E2 ubiquitin-conjugating enzymes, and E3 ubiquitin-protein ligases. This gene encodes a member of the E3 ubiquitin-conjugating enzyme family which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme and transfers the ubiquitin to the targeted substrates. A HECT (homology to E6-AP C-terminus) domain in the C-terminus of the longer isoform of this protein is the catalytic site of ubiquitin transfer and forms a complex with E2 conjugases. Shorter isoforms of this protein which lack the C-terminal HECT domain are therefore unlikely to bind E2 enzymes. Alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene.
Provided by RefSeq, Jul 2012, through NCBI Gene. NCBI disclaimer
E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Ubiquitinates BCKDK and targets it for degradation, thereby regulating various metabolic processes (By similarity). Involved in the positive regulation of neurite branching in hippocampal neurons and the control of neuronal spine number and morphology, through the ubiquitination of PPP3CC (By similarity)
NCBI Gene summary · NCBI Gene annotation RS_2025_08 · read · NCBI Gene 89910Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
UniProtKB function · 2026_03 · read · UniProt Q7Z3V4UniProt 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 36 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_130466.4NM_130466.4MANE Select
XM_011538961.2XM_011538961.2
XM_047429852.1XM_047429852.1
XM_047429851.1XM_047429851.1
XM_047429844.1XM_047429844.1
XM_006719681.4XM_006719681.4
XM_006719682.3XM_006719682.3
XM_047429845.1XM_047429845.1
XM_047429847.1XM_047429847.1
XM_047429846.1XM_047429846.1
XM_047429849.1XM_047429849.1
XM_047429848.1XM_047429848.1
XM_047429850.1XM_047429850.1
XM_005253987.3XM_005253987.3
NM_183415.3NM_183415.3
XM_011538959.3XM_011538959.3
XM_047429853.1XM_047429853.1
XM_047429854.1XM_047429854.1
NM_001270449.2NM_001270449.2
NM_001270451.2NM_001270451.2
NM_001270450.2NM_001270450.2
XM_017020196.2XM_017020196.2
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 7 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. Not drawn, because the source gave no placement: NM_001445879.1, NM_001445878.1, NM_001445877.1, NM_001445873.1, NM_001445874.1, NM_001445876.1, NM_001445872.1, NM_001445875.1, NM_001445871.1, NM_001445869.1, NM_001445870.1, NM_001445868.1, NR_201561.1, NR_201562.1.
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's product report carries no genomic placement for this transcript, so its exon coordinates are not available from NCBI
none given
non coding
none
not placed
5,574 nt
none
Ready in a moment
Not listed, because the source places them on another assembly only: XM_054373765.1 (not placed on GRCh38.p14); XM_054373766.1 (not placed on GRCh38.p14); XM_054373767.1 (not placed on GRCh38.p14); XM_054373768.1 (not placed on GRCh38.p14); XM_054373769.1 (not placed on GRCh38.p14); XM_054373770.1 (not placed on GRCh38.p14); XM_054373771.1 (not placed on GRCh38.p14); XM_054373772.1 (not placed on GRCh38.p14); XM_054373773.1 (not placed on GRCh38.p14); XM_054373774.1 (not placed on GRCh38.p14); XM_054373775.1 (not placed on GRCh38.p14); XM_054373776.1 (not placed on GRCh38.p14); XM_054373777.1 (not placed on GRCh38.p14); XM_054373778.1 (not placed on GRCh38.p14); XM_054373779.1 (not placed on GRCh38.p14); XM_054373780.1 (not placed on GRCh38.p14); XM_054373781.1 (not placed on GRCh38.p14).
NCBI Datasets, RefSeq transcripts · NCBI Datasets 18.38.0; GCF_000001405.40-RS_2025_08 · read · NCBI Gene 89910Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
Ensembl 0 transcripts
Ensembl is not answering, so the Ensembl transcripts could not be shown. Try again later.
Reference b13369a4-54f
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.
Mouse Ube3b by 2 of 2 votes; rat Ube3b by 2 of 2 votes. RGD is not answering, so the ortholog list could not be shown. Try again later. Reference 60beafac-1a6.
Alliance · NCBI
pLI below 0.0001 and LOEUF 0.728 in gnomAD v4 (GRCh38), on ENST00000342494.8.
gnomAD
Ensembl is not answering, so the non-coding annotation could not be shown. Try again later. Reference 10b71a4a-733.
Ensembl is not answering, so the non-coding annotation could not be shown. Try again later. Reference 10b71a4a-733.
1,068 residues, reviewed Q7Z3V4; 11 entries from the member databases this page shows along the chain; mean pLDDT 84.69; no experimental structure at PDBe.
UniProt · InterPro · AlphaFold DB · PDBe
1 curated, 0 inferred Reactome pathways for Q7Z3V4 in human, v97.
Reactome
482 PubMed-indexed papers mention UBE3B 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
1,251 Open Targets disease associations; oculocerebrofacial syndrome, Kaufman type first, at 0.80.
Open Targets
54 GTEx tissues; the highest median in Thyroid, 22.4 TPM.
GTEx
The 17 highest-scoring STRING partners at or above a combined score of 0.4, of up to 25 asked for; TRPV4, ATP2B1, ZNF18 lead.
STRING v12.0
ClinVar: 618 records for UBE3B, 85 pathogenic or likely pathogenic.
