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; INTERACTS WITH bisphenol A; copper atom; copper(0).
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: LOC366531; RGD1311615; similar to hypothetical protein FLJ33868
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8620,554,991 - 20,563,753 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl620,554,991 - 20,563,753 (-)EnsemblGRCr8
mRatBN7.2614,802,753 - 14,811,516 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl614,786,089 - 14,811,978 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx615,100,773 - 15,109,702 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0615,423,367 - 15,432,127 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0614,919,642 - 14,928,402 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.062,886,764 - 2,895,118 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl62,886,764 - 2,895,118 (+)Ensemblrn6Rnor6.0
Rnor_5.062,863,657 - 2,872,011 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.463,104,742 - 3,113,505 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera614,479,711 - 14,488,464 (-)NCBICelera
RGSC_v3.163,104,741 - 3,113,300 (+)NCBI
Cytogenetic Map6q12NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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
22 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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)6197587946975879Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6197587946975879Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6144788383Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6197587946975879Rat
8693699Alc37Alcohol consumption QTL 372.60.224drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)61371716927053860Rat
2293706Bmd20Bone mineral density QTL 204.30.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6125740059Rat
2292616Ept15Estrogen-induced pituitary tumorigenesis QTL 154.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6144788383Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6197587946975879Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
2301964Bp323Blood pressure QTL 3234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6186868070Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6323998948239989Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6323998948239989Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6140163351Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)61459947363457687Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6323998948239989Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)61608937261967788Rat
1358190Ept1Estrogen-induced pituitary tumorigenesis QTL 14.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6144788383Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6323998948239989Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6197587946975879Rat
8693690Alc35Alcohol consumption QTL 352.20.606drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)61371716927053860Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
3 6 7 46 36 42 14 30 14 1 94 49 3 43 24 46 28 3 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001191906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAXUCZ010000006 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000023114   ⟹   ENSRNOP00000023114
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl620,554,991 - 20,563,753 (-)Ensembl
mRatBN7.2 Ensembl614,786,089 - 14,811,978 (-)Ensembl
Rnor_6.0 Ensembl62,886,764 - 2,895,118 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000117617   ⟹   ENSRNOP00000087266
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
GRCr8620,554,991 - 20,563,753 (-)NCBI
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  
Ensembl Protein ENSRNOP00000023114
  ENSRNOP00000023114.5
RefSeq Acc Id: NP_001178835   ⟸   NM_001191906
- UniProtKB: D4A7N7 (UniProtKB/TrEMBL),   A6H9R5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000023114   ⟸   ENSRNOT00000023114
Ensembl 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 Transcript ENSRNOT00000023114 ENTREZGENE
  ENSRNOT00000023114.8 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
  TETRATRICOPEPTIDE REPEAT DOMAIN 39D UniProtKB/TrEMBL
Pfam Deme6 UniProtKB/TrEMBL
PhenoGen Ttc39d PhenoGen
RatGTEx ENSRNOG00000027343 RatGTEx
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
UniProt A6H9R5 ENTREZGENE, UniProtKB/TrEMBL
  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