Gene Human Homo sapiens

BAP1

BRCA1 associated deubiquitinase 1

gene with protein product

Human BAP1MouseRat

Reading the ortholog votes for mouse and rat.

Location: Cytogenetic band 3p21.1NCBI: 3:52,401,008-52,410,008 on the minus strand, GRCh38.p14 (GCF_000001405.40), sequence NC_000003.12, annotation GCF_000001405.40-RS_2025_08 of 2025-08-01Ensembl: 3:52,398,585-52,410,038 on the minus strand, GRCh38.p14 (GCA_000001405.29), release 116Coordinates are one-based with both ends included, as each source reports them.
Also known as: hucep-6, KIAA0272, UCHL2

Gene identity, from HGNC · HGNC 2026-09-25 · read 2026-09-26 ET · HGNC:950

Silence this gene

The order page opens with BAP1 and human filled in. The sequences are designed against the transcripts below; the price is on that page.

Order for BAP1

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

A line below that says it is reading needs JavaScript to be replaced: with scripts off, it stays at that line however long you wait. Opening a card also needs JavaScript.

Ready in a moment

01 Summary and function

What BAP1 does

This gene belongs to the ubiquitin C-terminal hydrolase subfamily of…

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.

Ready in a moment

03 Expression by tissue

Where BAP1 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 BAP1 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 BAP1

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 BAP1 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 BAP1

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 BAP1

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 BAP1 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 BAP1

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 BAP1 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 BAP1

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 BAP1 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 BAP1 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

BAP1

Reading the record for BAP1 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 BAP1 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 BAP1 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 BAP1 is expressed

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

04 Protein

The protein BAP1 encodes

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

05 Interactions

Proteins STRING associates with BAP1

Waiting for the record before reading STRING.

06 Pathways

Where BAP1 acts, as Reactome curates it

Waiting for the record before reading UniProt and Reactome.

07 Disease associations

Diseases linked to BAP1

Waiting for the record before reading Open Targets and ClinGen.

08 Variants

Classified variants of BAP1

Waiting for the record before reading ClinVar.

09 Constraint

How much variation BAP1 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 BAP1

Waiting for the record before reading Ensembl and miRBase.

12 Long non-coding RNAs

Long non-coding RNAs at the BAP1 locus

Waiting for the record before reading Ensembl.

13 Literature

Papers that mention BAP1

Waiting for the record before reading Europe PMC.

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_004656.4matches ENST00000460680.6	transcript variant 1	protein coding	MANE Select	17	3,600 nt	729 aaNP_004647.1	Ready in a moment
XM_011534149.4	transcript variant X1	protein coding model	none	17	3,669 nt	752 aaXP_011532451.1	Ready in a moment
XM_011534150.4	transcript variant X2	protein coding model	none	17	3,624 nt	737 aaXP_011532452.1	Ready in a moment
XM_011534151.4	transcript variant X3	protein coding model	none	Ready in a moment

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_004656.4matches ENST00000460680.6	transcript variant 1	protein coding	MANE Select	17	3,600 nt	729 aaNP_004647.1	Ready in a moment
XM_011534149.4	transcript variant X1	protein coding model	none	17	3,669 nt	752 aaXP_011532451.1	Ready in a moment
XM_011534150.4	transcript variant X2	protein coding model	none	17	3,624 nt	737 aaXP_011532452.1	Ready in a moment
XM_011534151.4	transcript variant X3	protein coding model	none	Ready in a moment

Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
ENST00000460680.6matches NM_004656.4	BAP1-202	protein coding	MANE SelectEnsembl canonical	17	3,600 nt	729 aaENSP00000417132.1	Ready in a moment
ENST00001144370.1	BAP1-213	protein coding	none	17	6,053 nt	729 aaENSP00000813282.1	Ready in a moment
ENST00000296288.10	BAP1-201	protein coding	none	17	5,999 nt	711 aaENSP00000296288.5	Ready in a moment
ENST00000469613.5	BAP1-204	protein coding	none	5	1,654 nt	129 aaENSP00000418320.1	Ready in a moment
ENST00000478368.1	BAP1-207	protein coding	none	5	1,234 nt	253 aaENSP00000420647.1	Ready in a moment
ENST00001130110.1	BAP1-212	protein coding	none	5	696 nt	172 aaENSP00000799915.1	Ready in a moment
ENST00000490917.1	BAP1-210	nonsense mediated decay	none	6	521 nt	41 aaENSP00000419709.1	Ready in a moment
ENST00000615113.1	BAP1-211	protein coding	none	1	489 nt	162 aaENSP00000482839.1	Ready in a moment
ENST00000466093.1	BAP1-203	retained intron	none	4	1,127 nt	none	Ready in a moment
ENST00000471532.5	BAP1-206	retained intron	none	5	1,052 nt	none	Ready in a moment
ENST00000490804.1	BAP1-209	retained intron	none	3	870 nt	none	Ready in a moment
ENST00000483984.5	BAP1-208	retained intron	none	7	699 nt	none	Ready in a moment
ENST00000470173.2	BAP1-205	retained intron	none	6	578 nt	none	Ready in a moment

BAP1

What BAP1 does

The RNA a design targets

Where BAP1 is expressed

The protein BAP1 encodes

Proteins STRING associates with BAP1

Where BAP1 acts, as Reactome curates it

Diseases linked to BAP1

Classified variants of BAP1

How much variation BAP1 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within BAP1

Long non-coding RNAs at the BAP1 locus

Papers that mention BAP1

From BAP1 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

BAP1

What BAP1 does

The RNA a design targets

Where BAP1 is expressed

The protein BAP1 encodes

Proteins STRING associates with BAP1

Where BAP1 acts, as Reactome curates it

Diseases linked to BAP1

Classified variants of BAP1

How much variation BAP1 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within BAP1

Long non-coding RNAs at the BAP1 locus

Papers that mention BAP1

BAP1

What BAP1 does

Gene summary

Protein function

The RNA a design targets

RefSeq 7 transcripts

A window on one transcript

Ensembl 13 transcripts

A window on one transcript

Where BAP1 is expressed

The protein BAP1 encodes

Proteins STRING associates with BAP1

Where BAP1 acts, as Reactome curates it

Diseases linked to BAP1

Classified variants of BAP1

How much variation BAP1 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within BAP1

Long non-coding RNAs at the BAP1 locus

Papers that mention BAP1

From BAP1 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 7 transcripts

A window on one transcript

Ensembl 13 transcripts

A window on one transcript