Tdrd6 (tudor domain containing 6) - Rat Genome Database

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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; dimethylarsinic acid; 1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC316254; tudor domain-containing protein 6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8924,841,259 - 24,856,621 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl924,841,255 - 24,856,621 (+)EnsemblGRCr8
mRatBN7.2917,344,033 - 17,359,348 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl917,344,026 - 17,359,344 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx925,934,052 - 25,949,219 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0931,008,600 - 31,023,767 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0929,297,828 - 29,312,995 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0919,917,613 - 19,932,888 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl919,917,603 - 19,932,920 (+)Ensemblrn6Rnor6.0
Rnor_5.0918,795,343 - 18,810,350 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4913,039,971 - 13,055,118 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera915,067,715 - 15,082,864 (+)NCBICelera
RGSC_v3.1913,036,819 - 13,051,943 (+)NCBI
Cytogenetic Map9q13NCBI
JBrowse:




Disease 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 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl924,841,255 - 24,856,621 (+)EnsemblGRCr8
mRatBN7.2917,344,033 - 17,359,348 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl917,344,026 - 17,359,344 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx925,934,052 - 25,949,219 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0931,008,600 - 31,023,767 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0929,297,828 - 29,312,995 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0919,917,613 - 19,932,888 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl919,917,603 - 19,932,920 (+)Ensemblrn6Rnor6.0
Rnor_5.0918,795,343 - 18,810,350 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4913,039,971 - 13,055,118 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera915,067,715 - 15,082,864 (+)NCBICelera
RGSC_v3.1913,036,819 - 13,051,943 (+)NCBI
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 (+)Ensemblhg38GRCh38
GRCh37646,648,005 - 46,672,056 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36646,763,825 - 46,778,109 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm381743,615,334 - 43,631,846 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1743,615,335 - 43,630,299 (-)Ensemblmm10GRCm38
MGSCv371743,752,284 - 43,767,248 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (+)Ensembl
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1214,881,393 - 14,894,875 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01215,349,953 - 15,363,448 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_Cfam_GSD_1.0
UU_Cfam_GSD_1.01215,051,114 - 15,064,583 (+)NCBIUU_Cfam_GSD_1.0UU_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 (-)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475413,943,651 - 13,958,322 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tdrd6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1486,212,325 - 86,227,102 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tdrd6
75 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)9671488884474983Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9534647950346479Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9875049253750492Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)9131250552Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)949664545496645Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9621499551214995Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9875049253750492Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9141763315Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9534647950416711Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9671488829567695Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)949664545496645Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)92103143049025574Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)949664545496645Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9621499551214995Rat

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

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
sensory system
visual system
8 9 12 91 23 30 18 15 18 6 92 30 87 29 60 12 7 7

Sequence


Ensembl Acc Id: ENSRNOT00000038239   ⟹   ENSRNOP00000032495
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl924,841,255 - 24,856,621 (+)Ensembl
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
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  
  NP_001419573 (Get FASTA)   NCBI Sequence Viewer  
  NP_001419574 (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
- 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, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038239.8 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_domain_containing UniProtKB/TrEMBL
  Tudor_TDRD6_rpt1 UniProtKB/TrEMBL
  Tudor_TDRD6_rpt2 UniProtKB/TrEMBL
KEGG Report rno:316254 UniProtKB/TrEMBL
NCBI Gene 316254 ENTREZGENE
PANTHER FI02030P-RELATED 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