Tgds (TDP-glucose 4,6-dehydratase) - Rat Genome Database

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Gene: Tgds (TDP-glucose 4,6-dehydratase) Rattus norvegicus
Analyze
Symbol: Tgds
Name: TDP-glucose 4,6-dehydratase
RGD ID: 1306544
Description: Predicted to enable dTDP-glucose 4,6-dehydratase activity. Predicted to be involved in nucleotide-sugar metabolic process. Human ortholog(s) of this gene implicated in Catel Manzke syndrome. Orthologous to human TGDS (TDP-glucose 4,6-dehydratase); INTERACTS WITH 6-propyl-2-thiouracil; amitrole; azoxystrobin.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: dTDP-D-glucose 4,6-dehydratase; LOC306164
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
GRCr815101,581,765 - 101,602,779 (-)NCBIGRCr8
mRatBN7.21595,175,064 - 95,195,555 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1595,174,608 - 95,195,554 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1599,079,895 - 99,100,420 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.015100,211,853 - 100,232,378 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01597,140,542 - 97,161,068 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.015103,319,268 - 103,340,239 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15103,319,268 - 103,340,240 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015106,757,794 - 106,778,765 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415102,906,505 - 102,927,476 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.115102,886,389 - 102,947,401 (-)NCBI
Celera1594,026,655 - 94,047,623 (-)NCBICelera
Cytogenetic Map15q24NCBI
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

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
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Tgds
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr815101,581,765 - 101,602,779 (-)NCBIGRCr8
mRatBN7.21595,175,064 - 95,195,555 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1595,174,608 - 95,195,554 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1599,079,895 - 99,100,420 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.015100,211,853 - 100,232,378 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01597,140,542 - 97,161,068 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.015103,319,268 - 103,340,239 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15103,319,268 - 103,340,240 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015106,757,794 - 106,778,765 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415102,906,505 - 102,927,476 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.115102,886,389 - 102,947,401 (-)NCBI
Celera1594,026,655 - 94,047,623 (-)NCBICelera
Cytogenetic Map15q24NCBI
TGDS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381394,574,054 - 94,596,273 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1394,574,054 - 94,596,242 (-)EnsemblGRCh38hg38GRCh38
GRCh371395,226,308 - 95,248,406 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361394,024,309 - 94,046,512 (-)NCBINCBI36Build 36hg18NCBI36
Build 341394,024,276 - 94,046,484NCBI
Celera1376,074,266 - 76,096,482 (-)NCBICelera
Cytogenetic Map13q32.1NCBI
HuRef1375,823,580 - 75,845,722 (-)NCBIHuRef
CHM1_11395,195,749 - 95,217,972 (-)NCBICHM1_1
T2T-CHM13v2.01393,777,561 - 93,799,780 (-)NCBIT2T-CHM13v2.0
Tgds
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914118,349,323 - 118,370,177 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl14118,349,323 - 118,370,167 (-)EnsemblGRCm39 Ensembl
GRCm3814118,111,911 - 118,132,765 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14118,111,911 - 118,132,755 (-)EnsemblGRCm38mm10GRCm38
MGSCv3714118,511,133 - 118,531,987 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3614116,994,822 - 117,015,076 (-)NCBIMGSCv36mm8
Celera14116,666,336 - 116,687,188 (-)NCBICelera
Cytogenetic Map14E4NCBI
cM Map1461.74NCBI
Tgds
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540415,279,866 - 15,298,295 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540415,279,956 - 15,298,295 (+)NCBIChiLan1.0ChiLan1.0
TGDS
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21496,103,255 - 96,125,454 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11394,771,940 - 94,794,266 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01375,747,686 - 75,770,010 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11394,903,511 - 94,925,637 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1394,903,511 - 94,925,637 (-)Ensemblpanpan1.1panPan2
TGDS
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12245,384,119 - 45,400,128 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2245,384,412 - 45,400,314 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2245,170,937 - 45,186,953 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02245,814,910 - 45,831,319 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2245,814,910 - 45,831,337 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12245,468,436 - 45,484,465 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02245,509,305 - 45,525,339 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02245,518,896 - 45,534,916 (-)NCBIUU_Cfam_GSD_1.0
Tgds
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945180,932,345 - 180,958,550 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647214,993,710 - 15,014,408 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647214,993,579 - 15,016,270 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TGDS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1163,695,638 - 63,716,568 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11163,695,612 - 63,716,614 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21169,863,218 - 69,884,205 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TGDS
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1373,403,520 - 73,424,985 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl373,400,485 - 73,424,892 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604629,788,007 - 29,814,614 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tgds
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248791,366,151 - 1,384,601 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248791,365,464 - 1,384,726 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tgds
86 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:124
Count of miRNA genes:97
Interacting mature miRNAs:107
Transcripts:ENSRNOT00000067309
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
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1567588667101769107Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat
1576315Schws6Schwannoma susceptibility QTL 60.0069nervous system integrity trait (VT:0010566)post-insult time of death (CMO:0002005)155380615298806152Rat
1549844Bss7Bone structure and strength QTL 76.4femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1575788062101769107Rat
2300326Plaw1Placental weight QTL 1150.005placenta mass (VT:0004257)placenta wet weight (CMO:0002088)1568327165100062518Rat
1300118Bp190Blood pressure QTL 1902.94arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)158226252098288169Rat
70155Gcs1Gastric cancer susceptibility QTL13.8stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)1576306099101769107Rat
1300120Kidm7Kidney mass QTL 73.55kidney mass (VT:0002707)left kidney wet weight to body weight ratio (CMO:0001954)158226252098288169Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1558156477101769107Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1581519Cm59Cardiac mass QTL 592.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)158885347095840528Rat
1641889Colcr6Colorectal carcinoma resistance QTL 62.90.0126intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)157369051899794247Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
2317055Aia10Adjuvant induced arthritis QTL 103.41joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1575788062101769107Rat


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: ENSRNOT00000067309   ⟹   ENSRNOP00000062674
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl15103,319,268 - 103,340,239 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000088909   ⟹   ENSRNOP00000071162
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1595,174,608 - 95,195,554 (-)Ensembl
Rnor_6.0 Ensembl15103,319,279 - 103,340,240 (-)Ensembl
RefSeq Acc Id: NM_001394729   ⟹   NP_001381658
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr815101,582,227 - 101,602,718 (-)NCBI
mRatBN7.21595,175,064 - 95,195,555 (-)NCBI
RefSeq Acc Id: XM_063274347   ⟹   XP_063130417
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr815101,583,635 - 101,602,779 (-)NCBI
RefSeq Acc Id: XM_063274348   ⟹   XP_063130418
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr815101,581,765 - 101,591,859 (-)NCBI
RefSeq Acc Id: XR_010057831
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr815101,583,606 - 101,602,777 (-)NCBI
RefSeq Acc Id: XR_010057832
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr815101,583,606 - 101,602,778 (-)NCBI
Ensembl Acc Id: ENSRNOP00000062674   ⟸   ENSRNOT00000067309
Ensembl Acc Id: ENSRNOP00000071162   ⟸   ENSRNOT00000088909
RefSeq Acc Id: NP_001381658   ⟸   NM_001394729
- UniProtKB: A0A0G2JZS4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063130418   ⟸   XM_063274348
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063130417   ⟸   XM_063274347
- Peptide Label: isoform X1
Protein Domains
NAD(P)-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JZS4-F1-model_v2 AlphaFold A0A0G2JZS4 1-355 view protein structure

Transcriptome

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

Promoters
RGD ID:13699871
Promoter ID:EPDNEW_R10394
Type:multiple initiation site
Name:Tgds_1
Description:TDP-glucose 4,6-dehydratase
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_6.015103,340,216 - 103,340,276EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306544 AgrOrtholog
BioCyc Gene G2FUF-12452 BioCyc
Ensembl Genes ENSRNOG00000009661 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000088909.2 UniProtKB/TrEMBL
Gene3D-CATH NAD(P)-binding Rossmann-like Domain UniProtKB/TrEMBL
  UDP-galactose 4-epimerase, domain 1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7309713 IMAGE-MGC_LOAD
InterPro dTDP_Gluc_deHydtase UniProtKB/TrEMBL
  NAD(P)-bd_dom UniProtKB/TrEMBL
  NAD(P)-bd_dom_sf UniProtKB/TrEMBL
MGC_CLONE MGC:189124 IMAGE-MGC_LOAD
NCBI Gene 306164 ENTREZGENE
PANTHER DTDP-D-GLUCOSE 4,6-DEHYDRATASE UniProtKB/TrEMBL
  DTDP-D-GLUCOSE 4,6-DEHYDRATASE-RELATED UniProtKB/TrEMBL
Pfam GDP_Man_Dehyd UniProtKB/TrEMBL
PhenoGen Tgds PhenoGen
RatGTEx ENSRNOG00000009661 RatGTEx
Superfamily-SCOP SSF51735 UniProtKB/TrEMBL
UniProt A0A0G2JZS4 ENTREZGENE, UniProtKB/TrEMBL
  B2RZ18_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Tgds  TDP-glucose 4,6-dehydratase   Tgds_predicted  TDP-glucose 4,6-dehydratase (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Tgds_predicted  TDP-glucose 4,6-dehydratase (predicted)      Symbol and Name status set to approved 70820 APPROVED