Tdrd6 (tudor domain containing 6) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Tdrd6 (tudor domain containing 6) Rattus norvegicus
Analyze
Symbol: Tdrd6
Name: tudor domain containing 6
RGD ID: 1305956
Description: Predicted to be involved in P granule organization; RNA processing; and spermatogenesis. Predicted to act upstream of or within germ cell development. Predicted to be located in chromatoid body and endoplasmic reticulum. Predicted to be part of ribonucleoprotein complex. Predicted to be active in P granule and synapse. Orthologous to human TDRD6 (tudor domain containing 6); INTERACTS WITH bisphenol A; 2,2',4,4',5,5'-hexachlorobiphenyl (ortholog); 2,2',5,5'-tetrachlorobiphenyl (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC316254; tudor domain-containing protein 6
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
GRCr8924,841,259 - 24,856,621 (+)NCBIGRCr8
mRatBN7.2917,344,033 - 17,359,348 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl917,344,026 - 17,359,344 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx925,934,052 - 25,949,219 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0931,008,600 - 31,023,767 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0929,297,828 - 29,312,995 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0919,917,613 - 19,932,888 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl919,917,603 - 19,932,920 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0918,795,343 - 18,810,350 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4913,039,971 - 13,055,118 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1913,036,819 - 13,051,943 (+)NCBI
Celera915,067,715 - 15,082,864 (+)NCBICelera
Cytogenetic Map9q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16093322   PMID:17141210   PMID:17662146   PMID:19345099   PMID:28263986  


Genomics

Comparative Map Data
Tdrd6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8924,841,259 - 24,856,621 (+)NCBIGRCr8
mRatBN7.2917,344,033 - 17,359,348 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl917,344,026 - 17,359,344 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx925,934,052 - 25,949,219 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0931,008,600 - 31,023,767 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0929,297,828 - 29,312,995 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0919,917,613 - 19,932,888 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl919,917,603 - 19,932,920 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0918,795,343 - 18,810,350 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4913,039,971 - 13,055,118 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1913,036,819 - 13,051,943 (+)NCBI
Celera915,067,715 - 15,082,864 (+)NCBICelera
Cytogenetic Map9q13NCBI
TDRD6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38646,680,268 - 46,704,319 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl646,687,875 - 46,704,319 (+)EnsemblGRCh38hg38GRCh38
GRCh37646,648,005 - 46,672,056 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36646,763,825 - 46,778,109 (+)NCBINCBI36Build 36hg18NCBI36
Celera648,208,136 - 48,224,578 (+)NCBICelera
Cytogenetic Map6p12.3NCBI
HuRef646,378,891 - 46,395,328 (+)NCBIHuRef
CHM1_1646,659,038 - 46,675,469 (+)NCBICHM1_1
T2T-CHM13v2.0646,517,917 - 46,541,966 (+)NCBIT2T-CHM13v2.0
Tdrd6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391743,926,225 - 43,942,737 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1743,926,226 - 43,941,190 (-)EnsemblGRCm39 Ensembl
GRCm381743,615,334 - 43,631,846 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1743,615,335 - 43,630,299 (-)EnsemblGRCm38mm10GRCm38
MGSCv371743,752,284 - 43,767,248 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361743,078,390 - 43,093,354 (-)NCBIMGSCv36mm8
Celera1747,040,264 - 47,053,379 (-)NCBICelera
Cytogenetic Map17B3NCBI
cM Map1719.75NCBI
Tdrd6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543711,517,930 - 11,531,869 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543711,517,094 - 11,531,816 (+)NCBIChiLan1.0ChiLan1.0
TDRD6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2561,177,642 - 61,199,579 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1657,046,462 - 57,065,779 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0646,265,074 - 46,287,015 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1647,542,367 - 47,556,964 (+)NCBIpanpan1.1PanPan1.1panPan2
TDRD6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11214,850,019 - 14,863,588 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1214,849,278 - 14,863,290 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1214,881,393 - 14,894,875 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01215,349,953 - 15,363,448 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1215,349,693 - 15,361,342 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11214,865,521 - 14,879,021 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01214,954,444 - 14,967,956 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01215,100,898 - 15,114,395 (+)NCBIUU_Cfam_GSD_1.0
UU_Cfam_GSD_1.01215,051,114 - 15,064,583 (+)NCBIUU_Cfam_GSD_1.0
Tdrd6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494650,298,830 - 50,312,372 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647613,644,627 - 13,660,839 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647613,646,678 - 13,660,891 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TDRD6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl741,468,780 - 41,483,469 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1741,468,589 - 41,485,146 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2748,129,241 - 48,145,813 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TDRD6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11725,573,189 - 25,588,368 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1725,573,730 - 25,587,052 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604446,697,570 - 46,721,249 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tdrd6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475413,944,184 - 13,957,168 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475413,943,651 - 13,958,322 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tdrd6
48 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:405
Count of miRNA genes:221
Interacting mature miRNAs:254
Transcripts:ENSRNOT00000038239
Prediction methods:Microtar, Miranda, 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
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9795472022071169Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
724543Cm20Cardiac mass QTL 203.9heart mass (VT:0007028)calculated heart weight (CMO:0000073)91696139840594091Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91353377042791750Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat

Markers in Region
BE110293  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2917,359,175 - 17,359,329 (+)MAPPERmRatBN7.2
Rnor_6.0919,932,716 - 19,932,869NCBIRnor6.0
Rnor_5.0918,810,178 - 18,810,331UniSTSRnor5.0
RGSC_v3.4913,054,950 - 13,055,103UniSTSRGSC3.4
Celera915,082,696 - 15,082,849UniSTS
RH 3.4 Map9136.8UniSTS
Cytogenetic Map9q12UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 7
Low 2 2 5 3 2
Below cutoff 1 7 15 11 8 11 5 7 55 13 29 5 5

Sequence


Ensembl Acc Id: ENSRNOT00000038239   ⟹   ENSRNOP00000032495
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl917,344,026 - 17,359,344 (+)Ensembl
Rnor_6.0 Ensembl919,917,603 - 19,932,920 (+)Ensembl
RefSeq Acc Id: NM_001191583   ⟹   NP_001178512
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8924,841,454 - 24,856,621 (+)NCBI
mRatBN7.2917,344,175 - 17,359,344 (+)NCBI
Rnor_6.0919,917,741 - 19,932,884 (+)NCBI
Rnor_5.0918,795,343 - 18,810,350 (+)NCBI
Celera915,067,715 - 15,082,864 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244608   ⟹   XP_006244670
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8924,841,259 - 24,856,621 (+)NCBI
mRatBN7.2917,344,033 - 17,359,348 (+)NCBI
Rnor_6.0919,917,613 - 19,932,888 (+)NCBI
Rnor_5.0918,795,343 - 18,810,350 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244609   ⟹   XP_006244671
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8924,841,259 - 24,856,621 (+)NCBI
mRatBN7.2917,344,033 - 17,359,348 (+)NCBI
Rnor_6.0919,917,613 - 19,932,888 (+)NCBI
Rnor_5.0918,795,343 - 18,810,350 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178512 (Get FASTA)   NCBI Sequence Viewer  
  XP_006244670 (Get FASTA)   NCBI Sequence Viewer  
  XP_006244671 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000032495.7
RefSeq Acc Id: NP_001178512   ⟸   NM_001191583
- UniProtKB: D3ZXQ5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244670   ⟸   XM_006244608
- Peptide Label: isoform X1
- UniProtKB: D3ZXQ5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244671   ⟸   XM_006244609
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSRNOP00000032495   ⟸   ENSRNOT00000038239
Protein Domains
Tudor

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZXQ5-F1-model_v2 AlphaFold D3ZXQ5 1-2129 view protein structure

Transcriptome

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

Promoters
RGD ID:13696555
Promoter ID:EPDNEW_R7079
Type:initiation region
Name:Tdrd6_1
Description:tudor domain containing 6
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_6.0919,917,597 - 19,917,657EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305956 AgrOrtholog
BioCyc Gene G2FUF-28112 BioCyc
Ensembl Genes ENSRNOG00000025693 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038239.7 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.140 UniProtKB/TrEMBL
  2.40.50.90 UniProtKB/TrEMBL
InterPro Staphylococcal_nuclease/TUDOR UniProtKB/TrEMBL
  Tudor UniProtKB/TrEMBL
  Tudor_TDRD6_rpt1 UniProtKB/TrEMBL
  Tudor_TDRD6_rpt2 UniProtKB/TrEMBL
KEGG Report rno:316254 UniProtKB/TrEMBL
NCBI Gene 316254 ENTREZGENE
PANTHER PROTEIN VRETENO UniProtKB/TrEMBL
  TUDOR DOMAIN CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam TUDOR UniProtKB/TrEMBL
PhenoGen Tdrd6 PhenoGen
PROSITE TUDOR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000025693 RatGTEx
SMART TUDOR UniProtKB/TrEMBL
Superfamily-SCOP Tudor/PWWP/MBT UniProtKB/TrEMBL
UniProt D3ZXQ5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Tdrd6  tudor domain containing 6   Tdrd6_predicted  tudor domain containing 6 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Tdrd6_predicted  tudor domain containing 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED