B9d2 (B9 domain containing 2) - Rat Genome Database

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Gene: B9d2 (B9 domain containing 2) Rattus norvegicus
Analyze
Symbol: B9d2
Name: B9 domain containing 2
RGD ID: 1566122
Description: Predicted to enable gamma-tubulin binding activity. Predicted to be involved in cilium assembly. Predicted to be located in ciliary transition zone; membrane; and microtubule organizing center. Predicted to be part of MKS complex. Human ortholog(s) of this gene implicated in Joubert syndrome. Orthologous to human B9D2 (B9 domain containing 2); INTERACTS WITH 6-propyl-2-thiouracil; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: B9 domain-containing protein 2; B9 protein domain 2; LOC308443; RGD1566122; similar to CDNA sequence BC028440
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8190,315,472 - 90,323,143 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl190,317,200 - 90,323,175 (+)EnsemblGRCr8
mRatBN7.2181,189,395 - 81,195,383 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl181,189,405 - 81,195,356 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx186,581,955 - 86,587,548 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0195,133,441 - 95,139,028 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0188,337,751 - 88,343,344 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0182,473,254 - 82,479,704 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl182,473,737 - 82,479,900 (+)Ensemblrn6Rnor6.0
Rnor_5.0183,735,237 - 83,741,209 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4180,888,733 - 80,894,049 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera175,629,345 - 75,634,847 (+)NCBICelera
Cytogenetic Map1q21NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
axoneme  (IEA)
centrosome  (IEA,ISO,ISS)
ciliary basal body  (IEA,ISO,ISS)
ciliary transition zone  (ISO)
cilium  (IEA)
membrane  (IEA,ISO)
MKS complex  (IBA,IEA,ISO,ISS)
nucleus  (IEA)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15916950   PMID:18287022   PMID:19208769   PMID:21422230   PMID:21763481   PMID:22179047   PMID:39455645  


Genomics

Comparative Map Data
B9d2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8190,315,472 - 90,323,143 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl190,317,200 - 90,323,175 (+)EnsemblGRCr8
mRatBN7.2181,189,395 - 81,195,383 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl181,189,405 - 81,195,356 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx186,581,955 - 86,587,548 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0195,133,441 - 95,139,028 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0188,337,751 - 88,343,344 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0182,473,254 - 82,479,704 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl182,473,737 - 82,479,900 (+)Ensemblrn6Rnor6.0
Rnor_5.0183,735,237 - 83,741,209 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4180,888,733 - 80,894,049 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera175,629,345 - 75,634,847 (+)NCBICelera
Cytogenetic Map1q21NCBI
B9D2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381941,354,417 - 41,364,149 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1941,354,417 - 41,364,165 (-)Ensemblhg38GRCh38
GRCh371941,860,322 - 41,870,054 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361946,552,166 - 46,561,877 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1938,660,483 - 38,669,951 (-)NCBICelera
Cytogenetic Map19q13.2NCBI
HuRef1938,292,411 - 38,301,879 (-)NCBIHuRef
CHM1_11941,859,986 - 41,869,742 (-)NCBICHM1_1
T2T-CHM13v2.01944,175,285 - 44,184,729 (-)NCBIT2T-CHM13v2.0
B9d2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39725,380,205 - 25,385,987 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl725,380,205 - 25,385,983 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38725,680,780 - 25,686,562 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl725,680,780 - 25,686,558 (+)Ensemblmm10GRCm38
MGSCv37726,466,177 - 26,471,577 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36725,389,918 - 25,395,318 (+)NCBIMGSCv36mm8
Celera720,290,071 - 20,295,470 (+)NCBICelera
Cytogenetic Map7A3NCBI
cM Map713.97NCBI
B9d2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955555288,919 - 295,860 (-)Ensembl
ChiLan1.0NW_004955555288,919 - 295,861 (-)NCBIChiLan1.0ChiLan1.0
B9D2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22047,564,531 - 47,576,762 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11949,433,306 - 49,442,722 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01938,347,505 - 38,357,319 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11946,853,954 - 46,864,036 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1946,853,954 - 46,864,014 (-)EnsemblpanPan2panpan1.1
B9d2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934915,330,962 - 15,337,206 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366613,758,909 - 3,765,513 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366613,759,031 - 3,765,361 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
B9D2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl649,349,708 - 49,366,012 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1649,349,704 - 49,358,420 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2645,142,563 - 45,151,259 (-)NCBISscrofa10.2Sscrofa10.2susScr3
B9D2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1635,674,786 - 35,684,646 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl635,674,539 - 35,683,215 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366607313,909,119 - 13,920,077 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
B9d2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624907176,827 - 184,574 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624907177,031 - 183,776 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
B9d2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12169,108,492 - 169,114,534 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in B9d2
62 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:185
Count of miRNA genes:134
Interacting mature miRNAs:142
Transcripts:ENSRNOT00000028029
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)151940904101229020Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)187889942132889942Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)139728272132889942Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14630261591302615Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151941022208479811Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)14630261591302615Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)151940904168768703Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)187785026142582336Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183019780128019780Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)166404680111404680Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134184556172281316Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)14630261591302615Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)18126986099645535Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)166009857160501508Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)14630261591302615Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)166400974132889942Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)184107164115183752Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)151511344153680016Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16540563796805205Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15190920691302615Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)186622262131622262Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)158769992103769992Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)14630261591302615Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)166077886111077886Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
152025249Scl82Serum cholesterol level QTL 824.77blood cholesterol amount (VT:0000180)152891222109116986Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)186993904131993904Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)187558587132558587Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)14630261591302615Rat

Markers in Region
RH139885  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2181,194,907 - 81,195,093 (+)MAPPERmRatBN7.2
Rnor_6.0182,479,244 - 82,479,429NCBIRnor6.0
Rnor_5.0183,740,753 - 83,740,938UniSTSRnor5.0
Celera175,634,392 - 75,634,577UniSTS
RH 3.4 Map1826.0UniSTS
Cytogenetic Map1q22UniSTS
Cytogenetic Map1q21UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
23 13 80 211 91 90 59 154 59 6 480 277 22 189 113 124 31 33 33

Sequence


Ensembl Acc Id: ENSRNOT00000028029   ⟹   ENSRNOP00000028029
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl190,317,200 - 90,323,175 (+)Ensembl
mRatBN7.2 Ensembl181,189,422 - 81,195,356 (+)Ensembl
Rnor_6.0 Ensembl182,473,737 - 82,479,900 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000105804   ⟹   ENSRNOP00000077704
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl190,317,200 - 90,320,157 (+)Ensembl
mRatBN7.2 Ensembl181,189,405 - 81,192,376 (+)Ensembl
RefSeq Acc Id: NM_001107494   ⟹   NP_001100964
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8190,317,550 - 90,323,143 (+)NCBI
mRatBN7.2181,189,767 - 81,195,363 (+)NCBI
Rnor_6.0182,474,106 - 82,479,699 (+)NCBI
Rnor_5.0183,735,237 - 83,741,209 (+)NCBI
RGSC_v3.4180,888,733 - 80,894,049 (+)RGD
Celera175,629,345 - 75,634,847 (+)RGD
Sequence:
RefSeq Acc Id: XM_006228438   ⟹   XP_006228500
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8190,315,472 - 90,323,139 (+)NCBI
mRatBN7.2181,189,395 - 81,195,383 (+)NCBI
Rnor_6.0182,473,254 - 82,479,704 (+)NCBI
Rnor_5.0183,735,237 - 83,741,209 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100964 (Get FASTA)   NCBI Sequence Viewer  
  XP_006228500 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM07999 (Get FASTA)   NCBI Sequence Viewer  
  EDM08000 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000028029
  ENSRNOP00000028029.5
GenBank Protein P0C5J3 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001100964   ⟸   NM_001107494
- UniProtKB: P0C5J3 (UniProtKB/Swiss-Prot),   A6J984 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006228500   ⟸   XM_006228438
- Peptide Label: isoform X1
- UniProtKB: P0C5J3 (UniProtKB/Swiss-Prot),   A6J984 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000028029   ⟸   ENSRNOT00000028029
Ensembl Acc Id: ENSRNOP00000077704   ⟸   ENSRNOT00000105804
Protein Domains
C2 B9-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P0C5J3-F1-model_v2 AlphaFold P0C5J3 1-175 view protein structure

Transcriptome

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

Promoters
RGD ID:13689822
Promoter ID:EPDNEW_R346
Type:multiple initiation site
Name:B9d2_1
Description:B9 domain containing 2
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_6.0182,473,767 - 82,473,827EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566122 AgrOrtholog
BioCyc Gene G2FUF-60372 BioCyc
Ensembl Genes ENSRNOG00000028753 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000028029 ENTREZGENE
  ENSRNOT00000028029.7 UniProtKB/Swiss-Prot
InterPro B9_dom UniProtKB/Swiss-Prot
KEGG Report rno:308443 UniProtKB/Swiss-Prot
NCBI Gene 308443 ENTREZGENE
PANTHER B9 DOMAIN-CONTAINING PROTEIN 2 UniProtKB/Swiss-Prot
  PTHR12968 UniProtKB/Swiss-Prot
Pfam B9-C2 UniProtKB/Swiss-Prot
PhenoGen B9d2 PhenoGen
PROSITE PS51381 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000028753 RatGTEx
UniProt A0A8I5Y6N1_RAT UniProtKB/TrEMBL
  A6J984 ENTREZGENE, UniProtKB/TrEMBL
  B9D2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-08-18 B9d2  B9 domain containing 2  B9d2  B9 protein domain 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 B9d2  B9 protein domain 2  RGD1566122_predicted  similar to CDNA sequence BC028440 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1566122_predicted  similar to CDNA sequence BC028440 (predicted)  LOC308443  similar to CDNA sequence BC028440  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC308443  similar to CDNA sequence BC028440      Symbol and Name status set to provisional 70820 PROVISIONAL