Brcc3 (BRCA1/BRCA2-containing complex subunit 3) - Rat Genome Database

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Gene: Brcc3 (BRCA1/BRCA2-containing complex subunit 3) Rattus norvegicus
Analyze
Symbol: Brcc3
Name: BRCA1/BRCA2-containing complex subunit 3 (Ensembl:BRCA1/BRCA2-containing complex, subunit 3)
RGD ID: 1588543
Description: Predicted to enable deubiquitinase activity; enzyme regulator activity; and polyubiquitin modification-dependent protein binding activity. Predicted to be involved in several processes, including DNA repair-dependent chromatin remodeling; mitotic G2 DNA damage checkpoint signaling; and positive regulation of NLRP3 inflammasome complex assembly. Predicted to act upstream of or within response to X-ray. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be part of BRCA1-A complex; BRISC complex; and nuclear ubiquitin ligase complex. Orthologous to human BRCC3 (BRCA1/BRCA2-containing complex subunit 3); PARTICIPATES IN ataxia telangiectasia-mutated (ATM) signaling pathway; histone modification pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3H-1,2-dithiole-3-thione; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex, subunit 3; BRCA1/BRCA2-containing complex, subunit 3 like 1; Brcc3l1; BRISC complex subunit BRCC36; LOC316794; lys-63-specific deubiquitinase BRCC36; similar to BRCA1/BRCA2-containing complex subunit 36 isoform 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Brcc3-ps7  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr892,073,927 - 2,076,469 (+)NCBIGRCr8
mRatBN7.291,986,942 - 1,989,484 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,986,575 - 1,991,080 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx92,421,214 - 2,423,760 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.097,770,588 - 7,773,134 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.096,726,439 - 6,728,985 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.099,863,380 - 9,865,920 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl99,863,404 - 9,865,920 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.098,864,902 - 8,867,442 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera96,530,917 - 6,533,459 (-)NCBICelera
Cytogenetic Map9q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. H2A-DUBbing the mammalian epigenome: expanding frontiers for histone H2A deubiquitinating enzymes in cell biology and physiology. Belle JI and Nijnik A, Int J Biochem Cell Biol. 2014 May;50:161-74. doi: 10.1016/j.biocel.2014.03.004. Epub 2014 Mar 16.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. miR-3940-5p associated with genetic damage in workers exposed to hexavalent chromium. Li Y, etal., Toxicol Lett. 2014 Aug 17;229(1):319-26. doi: 10.1016/j.toxlet.2014.06.033. Epub 2014 Jun 25.
4. Push back to respond better: regulatory inhibition of the DNA double-strand break response. Panier S and Durocher D, Nat Rev Mol Cell Biol. 2013 Oct;14(10):661-72. doi: 10.1038/nrm3659. Epub 2013 Sep 4.
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Identification of genes differentially expressed in mouse fetuses from streptozotocin-induced diabetic pregnancy by cDNA subtraction. Sato N, etal., Endocr J. 2008 May;55(2):317-23. Epub 2008 Mar 7.
Additional References at PubMed
PMID:12477932   PMID:14636569   PMID:17525341   PMID:17728463   PMID:19202061   PMID:19214193   PMID:19261746   PMID:19261748   PMID:19261749   PMID:24075985   PMID:25931508   PMID:31184779  
PMID:33979701  


Genomics

Comparative Map Data
Brcc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr892,073,927 - 2,076,469 (+)NCBIGRCr8
mRatBN7.291,986,942 - 1,989,484 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,986,575 - 1,991,080 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx92,421,214 - 2,423,760 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.097,770,588 - 7,773,134 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.096,726,439 - 6,728,985 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.099,863,380 - 9,865,920 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl99,863,404 - 9,865,920 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.098,864,902 - 8,867,442 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera96,530,917 - 6,533,459 (-)NCBICelera
Cytogenetic Map9q11NCBI
BRCC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X155,071,508 - 155,123,077 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX155,071,420 - 155,123,077 (+)EnsemblGRCh38hg38GRCh38
GRCh37X154,299,783 - 154,351,352 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X153,952,904 - 154,004,543 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X153,863,504 - 153,915,052NCBI
CeleraX154,458,427 - 154,510,104 (+)NCBICelera
Cytogenetic MapXq28NCBI
HuRefX142,845,949 - 142,896,583 (+)NCBIHuRef
CHM1_1X154,211,322 - 154,263,032 (+)NCBICHM1_1
T2T-CHM13v2.0X153,307,916 - 153,359,479 (+)NCBIT2T-CHM13v2.0
Brcc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X74,460,234 - 74,499,307 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX74,460,234 - 74,497,607 (+)EnsemblGRCm39 Ensembl
GRCm38X75,416,628 - 75,455,702 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX75,416,628 - 75,454,001 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X72,661,967 - 72,701,040 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X71,669,420 - 71,706,717 (+)NCBIMGSCv36mm8
CeleraX66,818,616 - 66,858,058 (+)NCBICelera
Cytogenetic MapXA7.3NCBI
cM MapX38.22NCBI
Brcc3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955594554,081 - 613,661 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955594551,407 - 613,772 (-)NCBIChiLan1.0ChiLan1.0
BRCC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X155,049,262 - 155,097,994 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X155,052,870 - 155,104,458 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X144,550,320 - 144,592,795 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X154,389,179 - 154,431,616 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX154,389,283 - 154,428,669 (+)Ensemblpanpan1.1panPan2
BRCC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X123,081,262 - 123,143,509 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX123,081,050 - 123,140,133 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX108,074,648 - 108,136,853 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X126,208,828 - 126,271,057 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX126,173,490 - 126,271,057 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X121,956,711 - 122,018,913 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X124,479,132 - 124,541,327 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X124,199,851 - 124,262,068 (+)NCBIUU_Cfam_GSD_1.0
Brcc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X119,982,639 - 120,022,107 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936927341,253 - 376,700 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936927341,114 - 380,817 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BRCC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX125,383,414 - 125,439,082 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X125,383,392 - 125,439,082 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X142,991,891 - 143,046,729 (-)NCBISscrofa10.2Sscrofa10.2susScr3
BRCC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X129,358,759 - 129,406,293 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX129,358,862 - 129,403,352 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606567,336,845 - 67,385,677 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Brcc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624963145,580 - 212,064 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624963142,987 - 212,190 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Brcc3
28 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:34
Count of miRNA genes:34
Interacting mature miRNAs:34
Transcripts:ENSRNOT00000071068
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat

Markers in Region
RH130212  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2398,815,978 - 98,816,168 (+)MAPPERmRatBN7.2
mRatBN7.291,988,828 - 1,989,019 (-)MAPPERmRatBN7.2
Rnor_6.099,863,845 - 9,864,033NCBIRnor6.0
Rnor_6.03103,410,730 - 103,410,919NCBIRnor6.0
Rnor_5.098,865,367 - 8,865,555UniSTSRnor5.0
Rnor_5.03110,004,103 - 110,004,292UniSTSRnor5.0
RGSC_v3.4397,842,396 - 97,842,585UniSTSRGSC3.4
Celera96,531,382 - 6,531,572UniSTS
Celera397,813,856 - 97,814,045UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 40 57 41 19 41 8 10 74 35 34 11 8
Low 3 1 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071068   ⟹   ENSRNOP00000066438
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,986,575 - 1,991,080 (+)Ensembl
Rnor_6.0 Ensembl99,863,404 - 9,865,920 (-)Ensembl
RefSeq Acc Id: NM_001127300   ⟹   NP_001120772
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr892,073,927 - 2,076,469 (+)NCBI
mRatBN7.291,986,942 - 1,989,484 (+)NCBI
Rnor_6.099,863,380 - 9,865,920 (-)NCBI
Rnor_5.098,864,902 - 8,867,442 (-)NCBI
Celera96,530,917 - 6,533,459 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001120772 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI66833 (Get FASTA)   NCBI Sequence Viewer  
  B2RYM5 (Get FASTA)   NCBI Sequence Viewer  
  EDL83574 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000066438
  ENSRNOP00000066438.1
  ENSRNOP00055022699
  ENSRNOP00060037676
  ENSRNOP00065018454
Reference Protein Sequences
RefSeq Acc Id: NP_001120772   ⟸   NM_001127300
- UniProtKB: B2RYM5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000066438   ⟸   ENSRNOT00000071068
Protein Domains
MPN

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B2RYM5-F1-model_v2 AlphaFold B2RYM5 1-291 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696436
Promoter ID:EPDNEW_R6960
Type:initiation region
Name:Brcc3_1
Description:BRCA1/BRCA2-containing complex, subunit 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.099,865,925 - 9,865,985EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588543 AgrOrtholog
BioCyc Gene G2FUF-28486 BioCyc
Ensembl Genes ENSRNOG00000048061 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055016606 UniProtKB/Swiss-Prot
  ENSRNOG00060026217 UniProtKB/Swiss-Prot
  ENSRNOG00065014364 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000071068 ENTREZGENE
  ENSRNOT00000071068.3 UniProtKB/Swiss-Prot
  ENSRNOT00055028197 UniProtKB/Swiss-Prot
  ENSRNOT00060045378 UniProtKB/Swiss-Prot
  ENSRNOT00065023702 UniProtKB/Swiss-Prot
Gene3D-CATH Cytidine Deaminase, domain 2 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:9021884 IMAGE-MGC_LOAD
InterPro BRCC36_C UniProtKB/Swiss-Prot
  JAMM/MPN+_dom UniProtKB/Swiss-Prot
  MPN UniProtKB/Swiss-Prot
  MPN_BRCC36 UniProtKB/Swiss-Prot
KEGG Report rno:316794 UniProtKB/Swiss-Prot
MGC_CLONE MGC:188722 IMAGE-MGC_LOAD
NCBI Gene 316794 ENTREZGENE
PANTHER EUKARYOTIC TRANSLATION INITIATION FACTOR 3 -RELATED UniProtKB/Swiss-Prot
  LYS-63-SPECIFIC DEUBIQUITINASE BRCC36 UniProtKB/Swiss-Prot
Pfam BRCC36_C UniProtKB/Swiss-Prot
  JAB UniProtKB/Swiss-Prot
PhenoGen Brcc3 PhenoGen
PROSITE MPN UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000048061 RatGTEx
  ENSRNOG00055016606 RatGTEx
  ENSRNOG00060026217 RatGTEx
  ENSRNOG00065014364 RatGTEx
SMART JAB_MPN UniProtKB/Swiss-Prot
Superfamily-SCOP JAB1/MPN domain UniProtKB/Swiss-Prot
UniProt B2RYM5 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-05-05 Brcc3  BRCA1/BRCA2-containing complex subunit 3  Brcc3l1  BRCA1/BRCA2-containing complex, subunit 3 like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2023-04-13 Brcc3l1  BRCA1/BRCA2-containing complex, subunit 3 like 1  Brcc3  BRCA1/BRCA2-containing complex, subunit 3  Name and Symbol changed 629549 APPROVED
2008-03-05 Brcc3  BRCA1/BRCA2-containing complex, subunit 3  LOC316794  similar to BRCA1/BRCA2-containing complex subunit 36 isoform 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC316794  similar to BRCA1/BRCA2-containing complex subunit 36 isoform 2      Symbol and Name status set to provisional 70820 PROVISIONAL