Atad2b (ATPase family, AAA domain containing 2B) - Rat Genome Database

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Gene: Atad2b (ATPase family, AAA domain containing 2B) Rattus norvegicus
Analyze
Symbol: Atad2b
Name: ATPase family, AAA domain containing 2B
RGD ID: 1566199
Description: Predicted to enable ATP hydrolysis activity; chromatin binding activity; and lysine-acetylated histone binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Orthologous to human ATAD2B (ATPase family AAA domain containing 2B); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; valproic acid.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: ATPase family AAA domain-containing protein 2B; hypothetical protein LOC500625; LOC500625; two AAA domain containing protein; uncharacterized protein LOC500625
RGD Orthologs
Human
Mouse
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2627,914,546 - 28,070,103 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl627,912,862 - 28,067,047 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0628,998,080 - 29,066,850 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl629,012,007 - 29,163,134 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0640,820,600 - 40,889,050 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4628,213,288 - 28,282,067 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera627,380,882 - 27,449,240 (+)NCBICelera
Cytogenetic Map6q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (IBA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:22464331   PMID:24561620  


Genomics

Comparative Map Data
Atad2b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2627,914,546 - 28,070,103 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl627,912,862 - 28,067,047 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0628,998,080 - 29,066,850 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl629,012,007 - 29,163,134 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0640,820,600 - 40,889,050 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4628,213,288 - 28,282,067 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera627,380,882 - 27,449,240 (+)NCBICelera
Cytogenetic Map6q14NCBI
ATAD2B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38223,677,969 - 23,927,123 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl223,748,664 - 23,927,123 (-)EnsemblGRCh38hg38GRCh38
GRCh37223,971,534 - 24,149,993 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36223,825,038 - 24,003,438 (-)NCBINCBI36Build 36hg18NCBI36
Celera223,812,998 - 23,990,337 (-)NCBICelera
Cytogenetic Map2p24.1-p23.3NCBI
HuRef223,711,485 - 23,889,159 (-)NCBIHuRef
CHM1_1223,901,223 - 24,079,326 (-)NCBICHM1_1
T2T-CHM13v2.0223,783,746 - 23,961,815 (-)NCBIT2T-CHM13v2.0
Atad2b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39124,964,404 - 5,097,396 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl124,967,353 - 5,097,394 (+)EnsemblGRCm39 Ensembl
GRCm38124,914,404 - 5,047,396 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl124,917,353 - 5,047,394 (+)EnsemblGRCm38mm10GRCm38
MGSCv37124,924,159 - 5,054,216 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36124,943,266 - 5,073,418 (+)NCBIMGSCv36mm8
Celera124,848,669 - 4,978,500 (+)NCBICelera
Cytogenetic Map12A1.1NCBI
ATAD2B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3114,722,321 - 114,846,644 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13114,722,225 - 114,843,705 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23121,986,100 - 122,108,728 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ATAD2B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11483,737,449 - 83,959,824 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1483,738,288 - 83,908,485 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604528,252,753 - 28,424,768 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Atad2b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247386,143,025 - 6,302,579 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247386,139,729 - 6,302,875 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Atad2b
190 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:39
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000052041
Prediction methods:Miranda, Rnahybrid, Targetscan
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
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat

Markers in Region
D6Rat176  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2627,917,050 - 27,917,198 (+)MAPPERmRatBN7.2
Rnor_6.0629,002,281 - 29,002,428NCBIRnor6.0
Rnor_5.0640,884,702 - 40,884,849UniSTSRnor5.0
RGSC_v3.4628,217,474 - 28,217,622RGDRGSC3.4
RGSC_v3.4628,217,475 - 28,217,622UniSTSRGSC3.4
RGSC_v3.1628,220,427 - 28,220,575RGD
Celera627,385,069 - 27,385,216UniSTS
FHH x ACI Map625.9599RGD
FHH x ACI Map625.9599UniSTS
Cytogenetic Map6q14UniSTS


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 2 28 40 24 19 24 3 3 65 28 37 11 3
Low 1 15 17 17 17 5 8 9 7 4 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000079077   ⟹   ENSRNOP00000070114
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl627,933,523 - 28,067,047 (+)Ensembl
Rnor_6.0 Ensembl629,012,207 - 29,163,134 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084560   ⟹   ENSRNOP00000073823
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl627,925,412 - 28,067,047 (+)Ensembl
Rnor_6.0 Ensembl629,106,141 - 29,162,330 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085612   ⟹   ENSRNOP00000075548
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl627,912,862 - 27,981,222 (+)Ensembl
Rnor_6.0 Ensembl629,012,007 - 29,061,581 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092223   ⟹   ENSRNOP00000068587
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl629,061,618 - 29,074,704 (+)Ensembl
RefSeq Acc Id: XM_039113113   ⟹   XP_038969041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,926,639 - 28,061,447 (+)NCBI
RefSeq Acc Id: XM_039113114   ⟹   XP_038969042
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,926,639 - 28,061,448 (+)NCBI
RefSeq Acc Id: XM_039113115   ⟹   XP_038969043
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,926,639 - 28,061,447 (+)NCBI
RefSeq Acc Id: XM_039113116   ⟹   XP_038969044
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,944,409 - 28,061,448 (+)NCBI
RefSeq Acc Id: XM_039113117   ⟹   XP_038969045
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,927,273 - 28,061,448 (+)NCBI
RefSeq Acc Id: XM_039113118   ⟹   XP_038969046
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,926,640 - 28,070,103 (+)NCBI
RefSeq Acc Id: XM_039113119   ⟹   XP_038969047
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,914,546 - 28,061,448 (+)NCBI
RefSeq Acc Id: XM_039113120   ⟹   XP_038969048
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,932,757 - 28,061,448 (+)NCBI
RefSeq Acc Id: XM_039113121   ⟹   XP_038969049
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,926,640 - 28,026,370 (+)NCBI
RefSeq Acc Id: XM_039113122   ⟹   XP_038969050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2628,012,650 - 28,061,453 (+)NCBI
RefSeq Acc Id: XR_005505748
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,926,640 - 28,039,827 (+)NCBI
Reference Sequences
RefSeq Acc Id: ENSRNOP00000068587   ⟸   ENSRNOT00000092223
RefSeq Acc Id: ENSRNOP00000070114   ⟸   ENSRNOT00000079077
RefSeq Acc Id: ENSRNOP00000073823   ⟸   ENSRNOT00000084560
RefSeq Acc Id: ENSRNOP00000075548   ⟸   ENSRNOT00000085612
RefSeq Acc Id: XP_038969047   ⟸   XM_039113119
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038969042   ⟸   XM_039113114
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038969041   ⟸   XM_039113113
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038969043   ⟸   XM_039113115
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038969046   ⟸   XM_039113118
- Peptide Label: isoform X6
- UniProtKB: A0A096MJU1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038969049   ⟸   XM_039113121
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038969045   ⟸   XM_039113117
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038969048   ⟸   XM_039113120
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038969044   ⟸   XM_039113116
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038969050   ⟸   XM_039113122
- Peptide Label: isoform X9
Protein Domains
AAA   Bromo

Transcriptome

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

Promoters
RGD ID:13694474
Promoter ID:EPDNEW_R4998
Type:multiple initiation site
Name:Atad2b_2
Description:ATPase family, AAA domain containing 2B
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R4999  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0629,011,992 - 29,012,052EPDNEW
RGD ID:13694477
Promoter ID:EPDNEW_R4999
Type:single initiation site
Name:Atad2b_1
Description:ATPase family, AAA domain containing 2B
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R4998  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0629,012,198 - 29,012,258EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566199 AgrOrtholog
BioCyc Gene G2FUF-38257 BioCyc
Ensembl Genes ENSRNOG00000058973 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000070114 ENTREZGENE
  ENSRNOP00000070114.2 UniProtKB/TrEMBL
  ENSRNOP00000073823 ENTREZGENE
  ENSRNOP00000073823.2 UniProtKB/TrEMBL
  ENSRNOP00000075548.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000079077 ENTREZGENE
  ENSRNOT00000079077.2 UniProtKB/TrEMBL
  ENSRNOT00000084560 ENTREZGENE
  ENSRNOT00000084560.2 UniProtKB/TrEMBL
  ENSRNOT00000085612.2 UniProtKB/TrEMBL
Gene3D-CATH 1.20.920.10 UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7115192 IMAGE-MGC_LOAD
InterPro AAA_lid_3 UniProtKB/TrEMBL
  ATAD2-like UniProtKB/TrEMBL
  ATPase_AAA+_core UniProtKB/TrEMBL
  ATPase_AAA_core UniProtKB/TrEMBL
  ATPase_AAA_CS UniProtKB/TrEMBL
  Bromodomain UniProtKB/TrEMBL
  Bromodomain-like_sf UniProtKB/TrEMBL
  Bromodomain_CS UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
MGC_CLONE MGC:93983 IMAGE-MGC_LOAD
NCBI Gene 500625 ENTREZGENE
PANTHER PTHR23069 UniProtKB/TrEMBL
Pfam AAA UniProtKB/TrEMBL
  AAA_lid_3 UniProtKB/TrEMBL
  Bromodomain UniProtKB/TrEMBL
PhenoGen Atad2b PhenoGen
PRINTS BROMODOMAIN UniProtKB/TrEMBL
PROSITE AAA UniProtKB/TrEMBL
  BROMODOMAIN_1 UniProtKB/TrEMBL
  BROMODOMAIN_2 UniProtKB/TrEMBL
SMART AAA UniProtKB/TrEMBL
  BROMO UniProtKB/TrEMBL
Superfamily-SCOP SSF47370 UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt A0A096MJU1 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2JX30_RAT UniProtKB/TrEMBL
  Q66HB4_RAT UniProtKB/TrEMBL
UniProt Secondary A0A096MKB6 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-09 Atad2b  ATPase family, AAA domain containing 2B  LOC500625  hypothetical protein LOC500625  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC500625  hypothetical protein LOC500625      Symbol and Name status set to provisional 70820 PROVISIONAL