Ttc39d (tetratricopeptide repeat domain 39D) - Rat Genome Database

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Gene: Ttc39d (tetratricopeptide repeat domain 39D) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Ttc39d
Name: tetratricopeptide repeat domain 39D
RGD ID: 1311615
Description: Predicted to be involved in several processes, including cholesterol homeostasis; negative regulation of cholesterol storage; and regulation of cholesterol efflux.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: LOC366531; RGD1311615; similar to hypothetical protein FLJ33868
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2614,802,753 - 14,811,516 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl614,786,089 - 14,811,978 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx615,100,773 - 15,109,702 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0615,423,367 - 15,432,127 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0614,919,642 - 14,928,402 (-)NCBIRnor_WKY
Rnor_6.062,886,764 - 2,895,118 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl62,886,764 - 2,895,118 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.062,863,657 - 2,872,011 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.463,104,742 - 3,113,505 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.163,104,741 - 3,113,300 (+)NCBI
Celera614,479,711 - 14,488,464 (-)NCBICelera
Cytogenetic Map6q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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

Genomics

Variants

.
Variants in Ttc39d
34 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:146
Count of miRNA genes:116
Interacting mature miRNAs:127
Transcripts:ENSRNOT00000023114
Prediction methods:Microtar, 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
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6127574569Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6127574569Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6127574569Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6127574569Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6127574569Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
2293706Bmd20Bone mineral density QTL 204.30.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6507449719988050Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
1358190Ept1Estrogen-induced pituitary tumorigenesis QTL 14.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6984331220338915Rat
2292616Ept15Estrogen-induced pituitary tumorigenesis QTL 154.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6984331220338915Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat


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 1 7 2 2
Below cutoff 2 3 21 10 12 10 2 3 17 12 13 9 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001191906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JACYVU010000163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000023114   ⟹   ENSRNOP00000023114
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl614,786,089 - 14,811,978 (-)Ensembl
Rnor_6.0 Ensembl62,886,764 - 2,895,118 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117617   ⟹   ENSRNOP00000087266
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl614,800,927 - 14,811,978 (-)Ensembl
RefSeq Acc Id: NM_001191906   ⟹   NP_001178835
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2614,802,753 - 14,811,516 (-)NCBI
Rnor_6.062,886,764 - 2,895,118 (+)NCBI
Rnor_5.062,863,657 - 2,872,011 (+)NCBI
Celera614,479,711 - 14,488,464 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178835 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001178835   ⟸   NM_001191906
- UniProtKB: D4A7N7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000023114   ⟸   ENSRNOT00000023114
RefSeq Acc Id: ENSRNOP00000087266   ⟸   ENSRNOT00000117617

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A7N7-F1-model_v2 AlphaFold D4A7N7 1-604 view protein structure

Transcriptome

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

Promoters
RGD ID:13694365
Promoter ID:EPDNEW_R4890
Type:multiple initiation site
Name:Ttc39d_1
Description:tetratricopeptide repeat domain 39D
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_6.062,886,670 - 2,886,730EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311615 AgrOrtholog
BioCyc Gene G2FUF-38522 BioCyc
Ensembl Genes ENSRNOG00000027343 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000023114.5 UniProtKB/TrEMBL
  ENSRNOP00000087266 ENTREZGENE
  ENSRNOP00000087266.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000023114.7 UniProtKB/TrEMBL
  ENSRNOT00000117617 ENTREZGENE
  ENSRNOT00000117617.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.10 UniProtKB/TrEMBL
InterPro OMP_IML2_mit/TPR_39 UniProtKB/TrEMBL
  TPR-like_helical UniProtKB/TrEMBL
KEGG Report rno:366531 UniProtKB/TrEMBL
NCBI Gene 366531 ENTREZGENE
PANTHER PTHR31859 UniProtKB/TrEMBL
Pfam Deme6 UniProtKB/TrEMBL
PhenoGen Ttc39d PhenoGen
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
UniProt D4A7N7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-06-12 Ttc39d  tetratricopeptide repeat domain 39D  RGD1311615  similar to hypothetical protein FLJ33868   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1311615  similar to hypothetical protein FLJ33868   RGD1311615_predicted  similar to hypothetical protein FLJ33868 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1311615_predicted  similar to hypothetical protein FLJ33868 (predicted)  LOC366531_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC366531_predicted  similar to hypothetical protein FLJ33868 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL