Bap1 BRCA1 associated deubiquitinase 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Bap1provided by RGD
Official Full Name: BRCA1 associated deubiquitinase 1provided by RGD
Primary source: RGD:1311938
See related: EnsemblRapid:ENSRNOG00000019097 AllianceGenome:RGD:1311938
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable chromatin DNA binding activity; cysteine-type deubiquitinase activity; and histone H2A deubiquitinase activity. Predicted to be involved in several processes, including common myeloid progenitor cell proliferation; myeloid cell differentiation; and protein deubiquitination. Predicted to act upstream of or within macrophage homeostasis; regulation of cytokine production involved in inflammatory response; and regulation of inflammatory response. Predicted to be located in cytosol and nucleoplasm. Predicted to be part of PR-DUB complex. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in basal cell carcinoma; extrahepatic bile duct adenocarcinoma; and uveal melanoma. Orthologous to human BAP1 (BRCA1 associated deubiquitinase 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 243.5), Muscle (RPKM 215.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 16p16

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	16	NC_086034.1 (6453126..6461952)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	16	NC_051351.1 (6446709..6455535)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	16	NC_005115.4 (7336685..7345511)

Chromosome 16 - NC_086034.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

MiR-31-5p alleviates septic cardiomyopathy by targeting BAP1 to inhibit SLC7A11 deubiquitination and ferroptosis.
Title: MiR-31-5p alleviates septic cardiomyopathy by targeting BAP1 to inhibit SLC7A11 deubiquitination and ferroptosis.
PLK-3-mediated phosphorylation of BAP1 prevents diabetic retinopathy.
Title: PLK-3-mediated phosphorylation of BAP1 prevents diabetic retinopathy.

Submit: New GeneRIF Correction

General gene information

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Markers

RH131028 (e-PCR)
- UniSTS:214311

RH143362 (e-PCR)
- UniSTS:232609

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables chromatin DNA binding	IEA Inferred from Electronic Annotation more info
enables chromatin DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables cysteine-type deubiquitinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables cysteine-type deubiquitinase activity	IEA Inferred from Electronic Annotation more info
enables cysteine-type deubiquitinase activity	ISO Inferred from Sequence Orthology more info
enables cysteine-type deubiquitinase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H2A deubiquitinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2A deubiquitinase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in common myeloid progenitor cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in common myeloid progenitor cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in erythrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in erythrocyte maturation	IEA Inferred from Electronic Annotation more info
involved_in erythrocyte maturation	ISO Inferred from Sequence Orthology more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in gene expression	ISO Inferred from Sequence Orthology more info
involved_in granulocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in hematopoietic stem cell homeostasis	IEA Inferred from Electronic Annotation more info
involved_in hematopoietic stem cell homeostasis	ISO Inferred from Sequence Orthology more info
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in in utero embryonic development	ISO Inferred from Sequence Orthology more info
involved_in leukocyte proliferation	IEA Inferred from Electronic Annotation more info
involved_in leukocyte proliferation	ISO Inferred from Sequence Orthology more info
involved_in macrophage homeostasis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within macrophage homeostasis	ISO Inferred from Sequence Orthology more info
involved_in mitotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in mitotic cell cycle	ISO Inferred from Sequence Orthology more info
involved_in monoubiquitinated protein deubiquitination	IEA Inferred from Electronic Annotation more info
involved_in monoubiquitinated protein deubiquitination	ISO Inferred from Sequence Orthology more info
involved_in monoubiquitinated protein deubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in myeloid cell apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in myeloid cell apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron cellular homeostasis	IEA Inferred from Electronic Annotation more info
involved_in neuron cellular homeostasis	ISO Inferred from Sequence Orthology more info
involved_in neutrophil differentiation	IEA Inferred from Electronic Annotation more info
involved_in neutrophil differentiation	ISO Inferred from Sequence Orthology more info
involved_in nucleate erythrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in nucleate erythrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in platelet morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in platelet morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein targeting to mitochondrion	ISO Inferred from Sequence Orthology more info	PubMed
involved_in protein K48-linked deubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein K48-linked deubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein K48-linked deubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein deubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein deubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell cycle	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell cycle	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell cycle	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell growth	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell growth	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell growth	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cytokine production involved in inflammatory response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of cytokine production involved in inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in regulation of inflammatory response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in thrombocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in thrombocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in tissue homeostasis	IEA Inferred from Electronic Annotation more info
involved_in tissue homeostasis	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-dependent protein catabolic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of PR-DUB complex	IEA Inferred from Electronic Annotation more info
part_of PR-DUB complex	ISO Inferred from Sequence Orthology more info
part_of PR-DUB complex	ISS Inferred from Sequence or Structural Similarity more info
located_in chromosome	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: ubiquitin carboxyl-terminal hydrolase BAP1

Names: BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase); BRCA1-associated protein 1; Brca1 associated protein 1

NP_001100762.1

EC 3.4.19.12

XP_006252668.1

EC 3.4.19.12

XP_006252669.1

EC 3.4.19.12

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001107292.1 → NP_001100762.1 ubiquitin carboxyl-terminal hydrolase BAP1

See identical proteins and their annotated locations for NP_001100762.1

Status: PROVISIONAL

Source sequence(s)

CH474046

UniProtKB/TrEMBL

A0A0A0MXZ5, A0A8I5ZQV2

Conserved Domains (1) summary

cd09617
Location:5 → 246

Peptidase_C12_UCH37_BAP1; Cysteine peptidase C12 containing ubiquitin carboxyl-terminal hydrolase (UCH) families UCH37 (UCH-L5) and BAP1

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086034.1 Reference GRCr8

Range

6453126..6461952

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006252606.5 → XP_006252668.1 ubiquitin carboxyl-terminal hydrolase BAP1 isoform X1

See identical proteins and their annotated locations for XP_006252668.1

UniProtKB/Swiss-Prot

D3ZHS6

UniProtKB/TrEMBL

A0A8I5ZQV2

Related

ENSRNOP00000025853.5, ENSRNOT00000025853.7

Conserved Domains (2) summary

cd09617
Location:5 → 233

Peptidase_C12_UCH37_BAP1; Cysteine peptidase C12 containing ubiquitin carboxyl-terminal hydrolase (UCH) families UCH37 (UCH-L5) and BAP1

pfam18031
Location:641 → 686

UCH_C; Ubiquitin carboxyl-terminal hydrolases
XM_006252607.4 → XP_006252669.1 ubiquitin carboxyl-terminal hydrolase BAP1 isoform X2

UniProtKB/TrEMBL

A0A8I5ZQV2

Related

ENSRNOP00000080792.2, ENSRNOT00000108732.2

Conserved Domains (1) summary

cd09617
Location:5 → 233

Peptidase_C12_UCH37_BAP1; Cysteine peptidase C12 containing ubiquitin carboxyl-terminal hydrolase (UCH) families UCH37 (UCH-L5) and BAP1