Tpgs1 (tubulin polyglutamylase complex subunit 1) - Rat Genome Database

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Gene: Tpgs1 (tubulin polyglutamylase complex subunit 1) Rattus norvegicus
Analyze
Symbol: Tpgs1
Name: tubulin polyglutamylase complex subunit 1
RGD ID: 1588613
Description: Predicted to enable microtubule binding activity and tubulin-glutamic acid ligase activity. Predicted to be involved in sperm axoneme assembly. Predicted to act upstream of or within several processes, including adult behavior; chemical synaptic transmission; and protein polyglutamylation. Predicted to be located in centrosome. Predicted to be active in microtubule organizing center. Orthologous to human TPGS1 (tubulin polyglutamylase complex subunit 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; fenvalerate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: gene trap ROSA b-geo 22; Gtrgeo22; LOC691093; PGs1; similar to gene trap ROSA b-geo 22
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8710,680,461 - 10,686,383 (-)NCBIGRCr8
mRatBN7.2710,029,842 - 10,035,764 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl710,029,854 - 10,035,764 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx712,910,831 - 12,916,733 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0714,788,910 - 14,794,812 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0712,648,201 - 12,654,116 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0712,912,251 - 12,918,173 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,912,263 - 12,918,173 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0713,080,966 - 13,086,888 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4711,546,760 - 11,552,682 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera78,203,089 - 8,209,005 (-)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12242242   PMID:12972506   PMID:17360631   PMID:21399614  


Genomics

Comparative Map Data
Tpgs1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8710,680,461 - 10,686,383 (-)NCBIGRCr8
mRatBN7.2710,029,842 - 10,035,764 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl710,029,854 - 10,035,764 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx712,910,831 - 12,916,733 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0714,788,910 - 14,794,812 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0712,648,201 - 12,654,116 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0712,912,251 - 12,918,173 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,912,263 - 12,918,173 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0713,080,966 - 13,086,888 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4711,546,760 - 11,552,682 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera78,203,089 - 8,209,005 (-)NCBICelera
Cytogenetic Map7q11NCBI
TPGS1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3819507,497 - 519,654 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl19507,497 - 519,654 (+)EnsemblGRCh38hg38GRCh38
GRCh3719507,497 - 519,654 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3619458,497 - 470,654 (+)NCBINCBI36Build 36hg18NCBI36
Celera19297,964 - 310,121 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef19277,653 - 289,928 (+)NCBIHuRef
CHM1_119507,000 - 518,651 (+)NCBICHM1_1
T2T-CHM13v2.019460,069 - 472,226 (+)NCBIT2T-CHM13v2.0
Tpgs1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391079,505,273 - 79,511,961 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1079,505,203 - 79,511,961 (+)EnsemblGRCm39 Ensembl
GRCm381079,669,439 - 79,676,127 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1079,669,369 - 79,676,127 (+)EnsemblGRCm38mm10GRCm38
MGSCv371079,132,155 - 79,138,871 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361079,072,539 - 79,079,066 (+)NCBIMGSCv36mm8
Celera1080,683,145 - 80,689,861 (+)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Tpgs1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554957,181,907 - 7,189,726 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554957,181,907 - 7,189,726 (-)NCBIChiLan1.0ChiLan1.0
TPGS1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2204,836,574 - 4,847,852 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1194,075,184 - 4,087,405 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v019614,279 - 625,715 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
TPGS1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12057,971,465 - 57,977,525 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2057,971,704 - 57,977,486 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2057,774,240 - 57,780,320 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02058,715,047 - 58,721,138 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2058,712,782 - 58,721,073 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12057,768,615 - 57,774,692 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02058,248,466 - 58,254,560 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02058,451,731 - 58,457,810 (-)NCBIUU_Cfam_GSD_1.0
Tpgs1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118217,679,298 - 217,684,505 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936588150,486 - 156,519 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936588150,465 - 155,485 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TPGS1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl277,776,277 - 77,783,416 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1277,776,269 - 77,783,434 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TPGS1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.16236,753 - 248,531 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl6237,462 - 248,526 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660818,843,203 - 8,888,590 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tpgs1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248287,946,301 - 7,953,653 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248287,946,158 - 7,953,633 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tpgs1
13 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:105
Count of miRNA genes:86
Interacting mature miRNAs:91
Transcripts:ENSRNOT00000011010
Prediction methods:Microtar, 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
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat

Markers in Region
AV005629  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2710,029,950 - 10,030,076 (+)MAPPERmRatBN7.2
Rnor_6.0712,912,360 - 12,912,485NCBIRnor6.0
Rnor_5.0713,081,075 - 13,081,200UniSTSRnor5.0
RGSC_v3.4711,546,869 - 11,546,994UniSTSRGSC3.4
Celera78,203,198 - 8,203,323UniSTS
Cytogenetic Map7q11UniSTS


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
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000011010   ⟹   ENSRNOP00000011010
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl710,029,854 - 10,035,764 (-)Ensembl
Rnor_6.0 Ensembl712,912,263 - 12,918,173 (-)Ensembl
RefSeq Acc Id: NM_001109621   ⟹   NP_001103091
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8710,680,461 - 10,686,383 (-)NCBI
mRatBN7.2710,029,842 - 10,035,764 (-)NCBI
Rnor_6.0712,912,251 - 12,918,173 (-)NCBI
Rnor_5.0713,080,966 - 13,086,888 (-)NCBI
RGSC_v3.4711,546,760 - 11,552,682 (-)RGD
Celera78,203,089 - 8,209,005 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001103091 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL89412 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000011010.4
RefSeq Acc Id: NP_001103091   ⟸   NM_001109621
- UniProtKB: D4A463 (UniProtKB/TrEMBL),   A6K8Z2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000011010   ⟸   ENSRNOT00000011010

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A463-F1-model_v2 AlphaFold D4A463 1-303 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588613 AgrOrtholog
BioCyc Gene G2FUF-34880 BioCyc
Ensembl Genes ENSRNOG00000008296 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011010.8 UniProtKB/TrEMBL
Gene3D-CATH cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain UniProtKB/TrEMBL
InterPro DD_TPGS1 UniProtKB/TrEMBL
  TPGS1 UniProtKB/TrEMBL
KEGG Report rno:691093 UniProtKB/TrEMBL
NCBI Gene 691093 ENTREZGENE
PANTHER PTHR31932 UniProtKB/TrEMBL
  TUBULIN POLYGLUTAMYLASE COMPLEX SUBUNIT 1 UniProtKB/TrEMBL
PhenoGen Tpgs1 PhenoGen
RatGTEx ENSRNOG00000008296 RatGTEx
Superfamily-SCOP Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit UniProtKB/TrEMBL
UniProt A6K8Z2 ENTREZGENE, UniProtKB/TrEMBL
  D4A463 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-12-06 Tpgs1  tubulin polyglutamylase complex subunit 1  Gtrgeo22  gene trap ROSA b-geo 22  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC691093  similar to gene trap ROSA b-geo 22      Symbol and Name status set to provisional 70820 PROVISIONAL