B9d2 (B9 protein domain 2) - Rat Genome Database

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Gene: B9d2 (B9 protein domain 2) Mus musculus
Analyze
Symbol: B9d2
Name: B9 protein domain 2
RGD ID: 1622060
MGI Page MGI
Description: Enables gamma-tubulin binding activity. Involved in cilium assembly. Located in membrane. Part of MKS complex. Human ortholog(s) of this gene implicated in Joubert syndrome. Orthologous to human B9D2 (B9 domain containing 2).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: B9 domain-containing protein 2; MGC41256; stum; stumpy
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39725,380,205 - 25,385,987 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl725,380,205 - 25,385,983 (+)EnsemblGRCm39 Ensembl
GRCm38725,680,780 - 25,686,562 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl725,680,780 - 25,686,558 (+)EnsemblGRCm38mm10GRCm38
MGSCv37726,466,177 - 26,471,577 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36725,389,918 - 25,395,318 (+)NCBIMGSCv36mm8
Celera720,290,071 - 20,295,470 (+)NCBICelera
Cytogenetic Map7A3NCBI
cM Map713.97NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abdominal situs ambiguus  (IEA)
abnormal adenohypophysis morphology  (IEA)
abnormal adrenal gland morphology  (IEA)
abnormal atrioventricular cushion morphology  (IEA)
abnormal brain internal capsule morphology  (IEA)
abnormal brain morphology  (IEA)
abnormal brain vasculature morphology  (IEA)
abnormal choroid plexus morphology  (IEA)
abnormal diaphragm morphology  (IEA)
abnormal ductus venosus topology  (IEA)
abnormal ductus venosus valve topology  (IEA)
abnormal enterocyte proliferation  (IAGP)
abnormal eye muscle morphology  (IEA)
abnormal forebrain morphology  (IEA)
abnormal heart position or orientation  (IEA)
abnormal hepatic vein morphology  (IEA)
abnormal hindbrain morphology  (IEA)
abnormal hypoglossal nerve topology  (IEA)
abnormal incisor morphology  (IEA)
abnormal inflammatory response  (IAGP)
abnormal infrahyoid muscle connection  (IEA)
abnormal interatrial septum morphology  (IEA)
abnormal intestine placement  (IEA)
abnormal intrathoracic topology of vagus nerve  (IEA)
abnormal liver morphology  (IEA)
abnormal maxilla morphology  (IEA)
abnormal mitral valve cusp morphology  (IEA)
abnormal Mullerian duct morphology  (IEA)
abnormal nasal septum morphology  (IEA)
abnormal neurohypophysis morphology  (IEA)
abnormal olfactory bulb morphology  (IEA)
abnormal optic chiasm morphology  (IEA)
abnormal optic cup morphology  (IEA)
abnormal optic stalk morphology  (IEA)
abnormal ovary morphology  (IEA)
abnormal pancreas morphology  (IEA)
abnormal pectinate muscle morphology  (IEA)
abnormal regulatory T cell physiology  (IAGP)
abnormal rib morphology  (IEA)
abnormal spinal cord morphology  (IEA)
abnormal subclavian artery origin  (IEA)
abnormal T cell differentiation  (IAGP)
abnormal T-helper 17 cell differentiation  (IAGP)
abnormal thymus topology  (IEA)
abnormal tongue epithelium morphology  (IEA)
abnormal umbilical vein topology  (IEA)
abnormal vertebral arch morphology  (IEA)
abnormal vertebral artery morphology  (IEA)
abnormal vertebral artery topology  (IEA)
abnormal vertebral body morphology  (IEA)
abnormal vitelline vein topology  (IEA)
abnormal Wolffian duct connection  (IEA)
absent adenohypophysis  (IEA)
absent ductus venosus valve  (IEA)
absent intrahepatic inferior vena cava segment  (IEA)
absent oculomotor nerve  (IEA)
absent segment of anterior cerebral artery  (IEA)
absent segment of posterior cerebral artery  (IEA)
absent upper incisors  (IEA)
accessory spleen  (IEA)
additional anastomosis between intracranial vertebral arteries  (IEA)
anastomosis between internal carotid artery and basilar artery  (IEA)
anomalous pulmonary venous connection  (IEA)
aortic arch coarctation  (IEA)
aphakia  (IEA)
bicuspid pulmonary valve  (IEA)
bifid ureter  (IEA)
blood in lymph vessels  (IEA)
cachexia  (IAGP)
colitis  (IAGP)
common atrium  (IEA)
decreased Langerhans cell number  (IAGP)
decreased susceptibility to experimental autoimmune encephalomyelitis  (IAGP)
decreased T-helper 17 cell number  (IAGP)
double inlet heart left ventricle  (IEA)
double outlet left ventricle  (IEA)
double outlet right ventricle  (IEA)
double ureter  (IEA)
dual inferior vena cava  (IEA)
ductus venosus stenosis  (IEA)
ectopic ovary  (IEA)
embryo cyst  (IEA)
embryo tumor  (IEA)
enlarged brain ventricles  (IEA)
enlarged lymphatic vessel  (IEA)
fusion of vertebral arches  (IEA)
heterotaxia  (IEA)
increased hemangioma incidence  (IEA)
increased regulatory T cell number  (IAGP)
increased T-helper 1 cell number  (IAGP)
intestinal/bowel diverticulum  (IEA)
inverse situs of great intrathoracic arteries  (IEA)
left pulmonary isomerism  (IEA)
left sided inferior vena cava  (IEA)
liver inflammation  (IAGP)
lung inflammation  (IAGP)
muscular ventricular septal defect  (IEA)
perimembraneous ventricular septal defect  (IEA)
persistent right 6th pharyngeal arch artery  (IEA)
persistent right dorsal aorta  (IEA)
polydactyly  (IEA)
preweaning lethality, complete penetrance  (IEA)
reduced sympathetic cervical ganglion size  (IEA)
short tongue  (IEA)
small pancreas  (IEA)
small spleen  (IEA)
small superior cervical ganglion  (IEA)
small superior vagus ganglion  (IEA)
subcutaneous edema  (IEA)
symmetric azygos veins  (IEA)
thin motoric part of trigeminal nerve  (IEA)
thin oculomotor nerve  (IEA)
thoracoschisis  (IEA)
transposition of great arteries  (IEA)
References

References - curated
# Reference Title Reference Citation
1. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
2. Mouse MP Annotation Import Pipeline RGD automated import 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:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14610273   PMID:16141072   PMID:16141073   PMID:17481928   PMID:17938236  
PMID:18287022   PMID:18728187   PMID:21267068   PMID:21435587   PMID:21677750   PMID:21757379   PMID:21763481   PMID:21873635   PMID:22020803   PMID:22094252   PMID:22094253   PMID:22179047  
PMID:23645881   PMID:23761668   PMID:25127859   PMID:26417101   PMID:27062243   PMID:30973865   PMID:37643008   PMID:38355793   PMID:38822427  


Genomics

Comparative Map Data
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 Ensembl
GRCm38725,680,780 - 25,686,562 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl725,680,780 - 25,686,558 (+)EnsemblGRCm38mm10GRCm38
MGSCv37726,466,177 - 26,471,577 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36725,389,918 - 25,395,318 (+)NCBIMGSCv36mm8
Celera720,290,071 - 20,295,470 (+)NCBICelera
Cytogenetic Map7A3NCBI
cM Map713.97NCBI
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 (-)EnsemblGRCh38hg38GRCh38
GRCh371941,860,322 - 41,870,054 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361946,552,166 - 46,561,877 (-)NCBINCBI36Build 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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8190,315,472 - 90,323,143 (+)NCBIGRCr8
mRatBN7.2181,189,395 - 81,195,383 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl181,189,405 - 81,195,356 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx186,581,955 - 86,587,548 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0195,133,441 - 95,139,028 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0188,337,751 - 88,343,344 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0182,473,254 - 82,479,704 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl182,473,737 - 82,479,900 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0183,735,237 - 83,741,209 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4180,888,733 - 80,894,049 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera175,629,345 - 75,634,847 (+)NCBICelera
Cytogenetic Map1q21NCBI
B9d2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955555288,919 - 295,860 (-)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624907177,031 - 183,776 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in B9d2
122 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:183
Count of miRNA genes:160
Interacting mature miRNAs:173
Transcripts:ENSMUST00000108403
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300722Sle3_msystemic lupus erythmatosus susceptibility 3 (mouse)Not determined7351172887142720Mouse
25314307Mlh1fc2_mMLH1 foci count 2 (mouse)76502999133501729Mouse
4141566Femwf8_mfemur work to failure 8 (mouse)Not determined1303248547032621Mouse
1301041Prnr2_mprion resistance 2 (mouse)Not determined71872879439674033Mouse
12904742Litsq2_mlitter size QTL 2 (mouse)72267388756674033Mouse
1301622Eae12_msusceptibility to experimental allergic encephalomyelitis 12 (mouse)Not determined71928001553280104Mouse
11354952Pdcc1_mplasmacytoid dentritic cell compartment 1 (mouse)72306653157066531Mouse
38501068Tip1_mtuberculosis immunophenotype 1, spleen CFU (mouse)7360299972549748Mouse
25314314Sccor1_msynaptonemal complex length to mean MLH1 count ratio 1 (mouse)71333392547349748Mouse
10449139Eosn1_meosinophil differential 1 (mouse)71248087746480877Mouse
1301052Bhr6_mbronchial hyperresponsiveness 6 (mouse)Not determined71984225053842367Mouse
11522751Cocia17_mcocaine-induced activity, QTL 17 (mouse)71313520447135204Mouse
12792978Fbmd3_mfemoral bone mineral density 3, females only (mouse)77050288142367832Mouse
1301158Eae4_msusceptibility to experimental allergic encephalomyelitis 4 (mouse)Not determined719147398141919804Mouse
1301572Sluc30_msusceptibility to lung cancer 30 (mouse)Not determined7243169636431844Mouse
1357699Nhdlq6_mnon-HDL QTL 6 (mouse)Not determined7998886743988984Mouse
10449158Eosn3_meosinophil differential 3 (mouse)71248087746480877Mouse
10412199Sst2_msusceptibility to tuberculosis 2 (mouse)Not determined718728794119485380Mouse
1558893Spir1_mStreptococcus pneumoniae infection resistance 1 (mouse)Not determined71030579844305936Mouse
1301709Bdt4_mbone density traits 4 (mouse)Not determined72288857256888716Mouse
1559016Drsi_mDCC-related Spp1 induction (mouse)Not determined71663729349159331Mouse


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000108403   ⟹   ENSMUSP00000104040
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl725,380,583 - 25,385,983 (+)Ensembl
GRCm38.p6 Ensembl725,681,158 - 25,686,558 (+)Ensembl
Ensembl Acc Id: ENSMUST00000205325   ⟹   ENSMUSP00000145729
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl725,380,263 - 25,383,075 (+)Ensembl
GRCm38.p6 Ensembl725,680,838 - 25,683,650 (+)Ensembl
Ensembl Acc Id: ENSMUST00000205658   ⟹   ENSMUSP00000146289
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl725,380,205 - 25,385,983 (+)Ensembl
GRCm38.p6 Ensembl725,680,780 - 25,686,558 (+)Ensembl
Ensembl Acc Id: ENSMUST00000206913   ⟹   ENSMUSP00000145950
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl725,380,281 - 25,382,846 (+)Ensembl
GRCm38.p6 Ensembl725,680,856 - 25,683,421 (+)Ensembl
RefSeq Acc Id: NM_001362154   ⟹   NP_001349083
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39725,380,205 - 25,385,987 (+)NCBI
GRCm38725,680,780 - 25,686,562 (+)NCBI
Sequence:
RefSeq Acc Id: NM_172148   ⟹   NP_742160
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39725,380,583 - 25,385,987 (+)NCBI
GRCm38725,681,158 - 25,686,562 (+)NCBI
MGSCv37726,466,177 - 26,471,577 (+)RGD
Celera720,290,071 - 20,295,470 (+)RGD
cM Map7 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_742160   ⟸   NM_172148
- UniProtKB: Q8R045 (UniProtKB/Swiss-Prot),   Q3UK10 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001349083   ⟸   NM_001362154
- UniProtKB: Q3UK10 (UniProtKB/Swiss-Prot),   Q8R045 (UniProtKB/Swiss-Prot)
Ensembl Acc Id: ENSMUSP00000104040   ⟸   ENSMUST00000108403
Ensembl Acc Id: ENSMUSP00000145950   ⟸   ENSMUST00000206913
Ensembl Acc Id: ENSMUSP00000145729   ⟸   ENSMUST00000205325
Ensembl Acc Id: ENSMUSP00000146289   ⟸   ENSMUST00000205658
Protein Domains
C2 B9-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q3UK10-F1-model_v2 AlphaFold Q3UK10 1-175 view protein structure

Promoters
RGD ID:6892298
Promoter ID:EPDNEW_M9600
Type:initiation region
Name:B9d2_1
Description:Mus musculus B9 protein domain 2 , transcript variant 2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38725,680,807 - 25,680,867EPDNEW
RGD ID:6840689
Promoter ID:MM_KWN:49467
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_172148,   UC009FTO.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36726,465,584 - 26,466,084 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2387643 AgrOrtholog
Ensembl Genes ENSMUSG00000063439 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000108403 ENTREZGENE
  ENSMUST00000108403.4 UniProtKB/Swiss-Prot
  ENSMUST00000205325.2 UniProtKB/TrEMBL
  ENSMUST00000205658 ENTREZGENE
  ENSMUST00000205658.2 UniProtKB/Swiss-Prot
  ENSMUST00000206913.2 UniProtKB/TrEMBL
InterPro B9_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:232987 UniProtKB/Swiss-Prot
MGD MGI:2387643 ENTREZGENE
NCBI Gene 232987 ENTREZGENE
PANTHER B9 DOMAIN-CONTAINING PROTEIN 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12968 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam B9-C2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen B9d2 PhenoGen
PROSITE PS51381 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0U1RNW5_MOUSE UniProtKB/TrEMBL
  A0A0U1RPE5_MOUSE UniProtKB/TrEMBL
  B9D2_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q8R045 ENTREZGENE
UniProt Secondary Q8R045 UniProtKB/Swiss-Prot