Tuba3b (tubulin, alpha 3B) - Rat Genome Database

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Gene: Tuba3b (tubulin, alpha 3B) Rattus norvegicus
Analyze
Symbol: Tuba3b (Ensembl: Tuba3a)
Name: tubulin, alpha 3B (Ensembl:tubulin, alpha 3A)
RGD ID: 1565155
Description: Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in microtubule cytoskeleton organization and mitotic cell cycle. Predicted to act upstream of or within male germ-line stem cell population maintenance. Predicted to be located in microtubule cytoskeleton. Predicted to be active in cytoplasm and microtubule. Human ortholog(s) of this gene implicated in keratoconus. Orthologous to several human genes including TUBA3D (tubulin alpha 3d); PARTICIPATES IN phagocytosis pathway; INTERACTS WITH acetamide; ammonium chloride; DDT.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: alpha-tubulin 3; LOC500363; RGD1565155; similar to Tubulin alpha-3 chain (Alpha-tubulin 3); Tuba3a; tubulin alpha-3 chain
RGD Orthologs
Human
Mouse
Dog
Pig
Alliance Orthologs
More Info more info ...
Related Pseudogenes: tuba1c-ps1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84180,319,600 - 180,325,149 (+)NCBIGRCr8
mRatBN7.24178,588,779 - 178,594,328 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4178,588,779 - 178,594,326 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4184,874,407 - 184,879,962 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04180,658,915 - 180,664,470 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04179,279,330 - 179,284,885 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04179,905,154 - 179,910,703 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4179,905,116 - 179,910,704 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04244,079,934 - 244,085,483 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44183,289,130 - 183,294,679 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4167,094,233 - 167,099,782 (+)NCBICelera
Cytogenetic Map4q44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. A revised nomenclature for the human and rodent alpha-tubulin gene family. Khodiyar VK, etal., Genomics. 2007 May 31;.
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:15632090   PMID:21630459  


Genomics

Comparative Map Data
Tuba3b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84180,319,600 - 180,325,149 (+)NCBIGRCr8
mRatBN7.24178,588,779 - 178,594,328 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4178,588,779 - 178,594,326 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4184,874,407 - 184,879,962 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04180,658,915 - 180,664,470 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04179,279,330 - 179,284,885 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04179,905,154 - 179,910,703 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4179,905,116 - 179,910,704 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04244,079,934 - 244,085,483 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44183,289,130 - 183,294,679 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4167,094,233 - 167,099,782 (+)NCBICelera
Cytogenetic Map4q44NCBI
TUBA3D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382131,476,119 - 131,482,934 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2131,476,119 - 131,482,934 (+)EnsemblGRCh38hg38GRCh38
GRCh372132,233,692 - 132,240,507 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362131,950,136 - 131,956,977 (+)NCBINCBI36Build 36hg18NCBI36
Cytogenetic Map2q21.1NCBI
HuRef2124,227,036 - 124,233,962 (+)NCBIHuRef
CHM1_12132,237,201 - 132,244,128 (+)NCBICHM1_1
T2T-CHM13v2.02131,910,887 - 131,917,702 (+)NCBIT2T-CHM13v2.0
Tuba3b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396145,561,689 - 145,567,203 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6145,561,483 - 145,567,205 (+)EnsemblGRCm39 Ensembl
GRCm386145,615,963 - 145,621,477 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6145,615,757 - 145,621,479 (+)EnsemblGRCm38mm10GRCm38
MGSCv376145,564,483 - 145,569,997 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366145,573,198 - 145,578,628 (+)NCBIMGSCv36mm8
Celera6148,691,160 - 148,696,674 (+)NCBICelera
Cytogenetic Map6G3NCBI
cM Map677.62NCBI
LOC608051
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12630,428,955 - 30,437,431 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2630,428,954 - 30,437,353 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2630,387,644 - 30,399,096 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02631,837,791 - 31,849,503 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12629,883,647 - 29,895,338 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02629,507,858 - 29,519,551 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02630,597,289 - 30,608,735 (-)NCBIUU_Cfam_GSD_1.0
LOC100510930
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11450,594,115 - 50,600,789 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21454,042,851 - 54,049,328 (-)NCBISscrofa10.2Sscrofa10.2susScr3

Variants

.
Variants in Tuba3b
17 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:29
Interacting mature miRNAs:33
Transcripts:ENSRNOT00000052352
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
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat


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
nervous system
renal system
reproductive system
respiratory system
15 12 32 100 105 106 64 39 64 11 223 96 75 39 113 42

Sequence


Ensembl Acc Id: ENSRNOT00000052352   ⟹   ENSRNOP00000039152
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4178,588,779 - 178,594,326 (+)Ensembl
Rnor_6.0 Ensembl4179,905,116 - 179,910,704 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000117473   ⟹   ENSRNOP00000087234
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4178,590,977 - 178,594,326 (+)Ensembl
RefSeq Acc Id: NM_001024336   ⟹   NP_001019507
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84180,319,600 - 180,325,149 (+)NCBI
mRatBN7.24178,588,779 - 178,594,328 (+)NCBI
Rnor_6.04179,905,154 - 179,910,703 (+)NCBI
Rnor_5.04244,079,934 - 244,085,483 (+)NCBI
RGSC_v3.44183,289,130 - 183,294,679 (+)RGD
Celera4167,094,233 - 167,099,782 (+)RGD
Sequence:
RefSeq Acc Id: NP_001019507   ⟸   NM_001024336
- UniProtKB: Q68FR8 (UniProtKB/Swiss-Prot),   A6ILT9 (UniProtKB/TrEMBL),   A0A8I6ALV8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000039152   ⟸   ENSRNOT00000052352
Ensembl Acc Id: ENSRNOP00000087234   ⟸   ENSRNOT00000117473
Protein Domains
Tubulin/FtsZ 2-layer sandwich   Tubulin/FtsZ GTPase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q68FR8-F1-model_v2 AlphaFold Q68FR8 1-450 view protein structure

Transcriptome

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

Promoters
RGD ID:13693501
Promoter ID:EPDNEW_R4024
Type:initiation region
Name:Tuba3a_1
Description:tubulin, alpha 3A
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_6.04179,905,130 - 179,905,190EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565155 AgrOrtholog
BioCyc Gene G2FUF-42450 BioCyc
Ensembl Genes ENSRNOG00000031707 UniProtKB/Swiss-Prot
  ENSRNOG00000032967 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00000053468 UniProtKB/TrEMBL
  ENSRNOG00055009520 UniProtKB/Swiss-Prot
  ENSRNOG00055009536 UniProtKB/Swiss-Prot
  ENSRNOG00060000904 UniProtKB/Swiss-Prot
  ENSRNOG00060032688 UniProtKB/Swiss-Prot
  ENSRNOG00065000811 UniProtKB/Swiss-Prot
  ENSRNOG00065005909 UniProtKB/Swiss-Prot
  ENSRNOG00065033030 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000044425.3 UniProtKB/Swiss-Prot
  ENSRNOT00000052352.4 UniProtKB/Swiss-Prot
  ENSRNOT00000107560.1 UniProtKB/TrEMBL
  ENSRNOT00055016093 UniProtKB/Swiss-Prot
  ENSRNOT00055016204 UniProtKB/Swiss-Prot
  ENSRNOT00060001166 UniProtKB/Swiss-Prot
  ENSRNOT00060056676 UniProtKB/Swiss-Prot
  ENSRNOT00065001114 UniProtKB/Swiss-Prot
  ENSRNOT00065008886 UniProtKB/Swiss-Prot
  ENSRNOT00065056843 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.287.600 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.1330.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.1440 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7132665 IMAGE-MGC_LOAD
InterPro Alpha_tubulin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tub_FtsZ_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tubulin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tubulin/FtsZ-like_C UniProtKB/TrEMBL
  Tubulin/FtsZ_2-layer-sand-dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tubulin/FtsZ_C_sf UniProtKB/Swiss-Prot
  Tubulin/FtsZ_GTPase_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tubulin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tubulin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tubulin_FtsZ_GTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:500319 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  rno:500363 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:94324 IMAGE-MGC_LOAD
NCBI Gene 500363 ENTREZGENE
PANTHER PTHR11588 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TUBULIN ALPHA-1A CHAIN UniProtKB/TrEMBL
  TUBULIN ALPHA-3C CHAIN-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Tubulin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tubulin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tuba3b PhenoGen
PRINTS ALPHATUBULIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TUBULIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TUBULIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000031707 RatGTEx
  ENSRNOG00000032967 RatGTEx
  ENSRNOG00000053468 RatGTEx
  ENSRNOG00055009520 RatGTEx
  ENSRNOG00055009536 RatGTEx
  ENSRNOG00060000904 RatGTEx
  ENSRNOG00060032688 RatGTEx
  ENSRNOG00065000811 RatGTEx
  ENSRNOG00065005909 RatGTEx
  ENSRNOG00065033030 RatGTEx
SMART Tubulin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tubulin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52490 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF55307 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6ALV8 ENTREZGENE, UniProtKB/TrEMBL
  A6ILT9 ENTREZGENE, UniProtKB/TrEMBL
  Q68FR8 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-05-17 Tuba3b  tubulin, alpha 3B  RGD1565155_predicted  similar to Tubulin alpha-3 chain (Alpha-tubulin 3) (predicted)  Symbol and Name updated 1624988 APPROVED
2006-03-07 RGD1565155_predicted  similar to Tubulin alpha-3 chain (Alpha-tubulin 3) (predicted)  LOC500363  similar to Tubulin alpha-3 chain (Alpha-tubulin 3)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC500363  similar to Tubulin alpha-3 chain (Alpha-tubulin 3)      Symbol and Name status set to provisional 70820 PROVISIONAL