Ttc39b (tetratricopeptide repeat domain 39B) - Rat Genome Database

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Advanced Search (OLGA)
Gene: Ttc39b (tetratricopeptide repeat domain 39B) Rattus norvegicus
Analyze
Symbol: Ttc39b
Name: tetratricopeptide repeat domain 39B
RGD ID: 1305797
Description: Predicted to be involved in several processes, including cholesterol homeostasis; negative regulation of cholesterol storage; and regulation of cholesterol efflux. Orthologous to human TTC39B (tetratricopeptide repeat domain 39B); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; aconitine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC298186; RGD1305797; similar to hypothetical protein FLJ33868; tetratricopeptide repeat protein 39B; TPR repeat protein 39B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85102,649,259 - 102,754,092 (-)NCBIGRCr8
mRatBN7.2597,603,329 - 97,708,103 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl597,609,392 - 97,736,270 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx599,994,732 - 100,093,451 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05101,787,468 - 101,886,060 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05101,805,603 - 101,904,315 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05101,304,982 - 101,405,689 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5101,304,982 - 101,405,656 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05105,325,543 - 105,422,721 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45102,064,300 - 102,162,978 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15102,082,312 - 102,168,201 (-)NCBI
Celera596,161,736 - 96,260,502 (-)NCBICelera
Cytogenetic Map5q31NCBI
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
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-hydroxypropanoic acid  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
4,4'-sulfonyldiphenol  (ISO)
acetamide  (EXP)
aconitine  (EXP)
aflatoxin B1  (ISO)
antirheumatic drug  (ISO)
aristolochic acid A  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzoates  (ISO)
beta-hexachlorocyclohexane  (ISO)
bisphenol A  (EXP,ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
cobalt dichloride  (EXP)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
dicrotophos  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
Enterolactone  (ISO)
entinostat  (ISO)
fenthion  (ISO)
fenvalerate  (EXP)
flutamide  (EXP)
genistein  (EXP)
gentamycin  (EXP)
Heptachlor epoxide  (ISO)
indole-3-methanol  (EXP)
inulin  (ISO)
Licochalcone B  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
methamphetamine  (EXP)
methidathion  (ISO)
naphthalene  (ISO)
paracetamol  (EXP,ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
rac-lactic acid  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sunitinib  (ISO)
temozolomide  (ISO)
thiram  (ISO)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (ISO)
trovafloxacin  (ISO)
valproic acid  (ISO)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. (-)-Epigallocatechin-3-Gallate Ameliorates Atherosclerosis and Modulates Hepatic Lipid Metabolic Gene Expression in Apolipoprotein E Knockout Mice: Involvement of TTC39B. Wang W, etal., Front Pharmacol. 2018 Mar 9;9:195. doi: 10.3389/fphar.2018.00195. eCollection 2018.
Additional References at PubMed
PMID:27383786  


Genomics

Comparative Map Data
Ttc39b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85102,649,259 - 102,754,092 (-)NCBIGRCr8
mRatBN7.2597,603,329 - 97,708,103 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl597,609,392 - 97,736,270 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx599,994,732 - 100,093,451 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05101,787,468 - 101,886,060 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05101,805,603 - 101,904,315 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05101,304,982 - 101,405,689 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5101,304,982 - 101,405,656 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05105,325,543 - 105,422,721 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45102,064,300 - 102,162,978 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15102,082,312 - 102,168,201 (-)NCBI
Celera596,161,736 - 96,260,502 (-)NCBICelera
Cytogenetic Map5q31NCBI
TTC39B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38915,163,622 - 15,307,216 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl915,163,622 - 15,307,360 (-)EnsemblGRCh38hg38GRCh38
GRCh37915,163,620 - 15,307,214 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36915,161,561 - 15,297,244 (-)NCBINCBI36Build 36hg18NCBI36
Build 34915,161,560 - 15,297,244NCBI
Celera915,104,514 - 15,241,039 (-)NCBICelera
Cytogenetic Map9p22.3NCBI
HuRef915,134,002 - 15,270,023 (-)NCBIHuRef
CHM1_1915,171,189 - 15,307,662 (-)NCBICHM1_1
T2T-CHM13v2.0915,175,161 - 15,318,914 (-)NCBIT2T-CHM13v2.0
Ttc39b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39483,138,537 - 83,242,488 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl483,138,537 - 83,242,492 (-)EnsemblGRCm39 Ensembl
GRCm38483,220,300 - 83,324,309 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl483,220,300 - 83,324,255 (-)EnsemblGRCm38mm10GRCm38
MGSCv37482,866,205 - 82,970,093 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36482,698,073 - 82,795,420 (-)NCBIMGSCv36mm8
Celera481,749,116 - 81,852,836 (-)NCBICelera
Cytogenetic Map4C3NCBI
cM Map439.41NCBI
Ttc39b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543418,070,536 - 18,150,858 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543418,063,520 - 18,150,858 (-)NCBIChiLan1.0ChiLan1.0
TTC39B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v211109,186,588 - 109,381,289 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan19109,192,529 - 109,387,237 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0914,994,729 - 15,127,877 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1915,502,811 - 15,633,374 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl915,502,811 - 15,633,374 (-)Ensemblpanpan1.1panPan2
TTC39B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11135,465,198 - 35,557,800 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1135,472,016 - 35,589,835 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1134,114,261 - 34,244,798 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01136,369,628 - 36,498,809 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1136,374,223 - 36,498,902 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11135,073,616 - 35,204,176 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01134,863,606 - 34,994,353 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01135,522,676 - 35,653,287 (-)NCBIUU_Cfam_GSD_1.0
Ttc39b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947150,190,771 - 150,314,021 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365398,646,074 - 8,695,765 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365398,644,456 - 8,766,696 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TTC39B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1207,347,360 - 207,495,965 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11207,347,345 - 207,490,753 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21231,160,107 - 231,280,020 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TTC39B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11264,315,240 - 64,452,161 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1264,372,763 - 64,450,973 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603852,515,449 - 52,659,743 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ttc39b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473619,349,599 - 19,480,039 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473619,304,586 - 19,480,182 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ttc39b
362 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:96
Count of miRNA genes:81
Interacting mature miRNAs:92
Transcripts:ENSRNOT00000058611
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357396Bw44Body weight QTL 444.19body mass (VT:0001259)body weight (CMO:0000012)568984307104251008Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
61380Edpm5Estrogen-dependent pituitary mass QTL 54.50.92pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)568984307104251008Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1298070Scl18Serum cholesterol level QTL 183.7blood LDL cholesterol amount (VT:0000181)calculated plasma low density lipoprotein cholesterol level (CMO:0001245)579584860124584860Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)56029343498603051Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1357402Bw46Body weight QTL 464.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
2302381Bw84Body weight QTL 844.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
1598859Cm66Cardiac mass QTL 662heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)579584860124584860Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)597570330136479578Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)587468046132468046Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
1598846Bp293Blood pressure QTL 2933.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)579584860124584860Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1358909Kidm25Kidney mass QTL 251.87kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)590067849128034027Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)555715622100715622Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)55349671998496719Rat
1298086Bp156Blood pressure QTL 156arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)584132602129132602Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)564719390109719390Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
2312671Scl64Serum cholesterol level QTL 640.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)568984307104251008Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)587765973132765973Rat
1358889Bp261Blood pressure QTL 2612.86arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)590067849128034027Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat

Markers in Region
RH132199  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2597,664,201 - 97,664,387 (+)MAPPERmRatBN7.2
Rnor_6.05101,359,770 - 101,359,956NCBIRnor6.0
Rnor_5.05105,381,225 - 105,381,411UniSTSRnor5.0
RGSC_v3.45102,119,110 - 102,119,295UniSTSRGSC3.4
Celera596,216,558 - 96,216,743UniSTS
RH 3.4 Map5726.2UniSTS
Cytogenetic Map5q31UniSTS
RH133014  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr85102,655,670 - 102,655,887 (+)Marker Load Pipeline
mRatBN7.2597,609,740 - 97,609,957 (+)MAPPERmRatBN7.2
Rnor_6.05101,305,331 - 101,305,547NCBIRnor6.0
Rnor_5.05105,326,786 - 105,327,002UniSTSRnor5.0
RGSC_v3.45102,064,649 - 102,064,865UniSTSRGSC3.4
Celera596,162,085 - 96,162,301UniSTS
RH 3.4 Map5725.81UniSTS
Cytogenetic Map5q31UniSTS


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: ENSRNOT00000058611   ⟹   ENSRNOP00000055409
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl597,609,392 - 97,708,070 (-)Ensembl
Rnor_6.0 Ensembl5101,304,982 - 101,405,656 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000101882   ⟹   ENSRNOP00000094211
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl597,622,291 - 97,708,070 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000105460   ⟹   ENSRNOP00000086184
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl597,609,392 - 97,665,769 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000109075   ⟹   ENSRNOP00000094295
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl597,640,133 - 97,708,070 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000117292   ⟹   ENSRNOP00000080999
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl597,609,392 - 97,736,270 (-)Ensembl
RefSeq Acc Id: NM_001106665   ⟹   NP_001100135
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85102,655,322 - 102,753,999 (-)NCBI
mRatBN7.2597,609,392 - 97,708,070 (-)NCBI
Rnor_6.05101,304,982 - 101,405,656 (-)NCBI
Rnor_5.05105,325,543 - 105,422,721 (-)NCBI
RGSC_v3.45102,064,300 - 102,162,978 (-)RGD
Celera596,161,736 - 96,260,502 (-)RGD
Sequence:
RefSeq Acc Id: XM_006238350   ⟹   XP_006238412
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85102,649,259 - 102,711,455 (-)NCBI
mRatBN7.2597,603,329 - 97,665,527 (-)NCBI
Rnor_6.05101,305,241 - 101,363,791 (-)NCBI
Rnor_5.05105,325,543 - 105,422,721 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039109510   ⟹   XP_038965438
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85102,649,259 - 102,754,092 (-)NCBI
mRatBN7.2597,603,329 - 97,708,102 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100135 (Get FASTA)   NCBI Sequence Viewer  
  XP_006238412 (Get FASTA)   NCBI Sequence Viewer  
  XP_038965438 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D3ZC96 (Get FASTA)   NCBI Sequence Viewer  
  EDM10461 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000055409
  ENSRNOP00000086184
RefSeq Acc Id: NP_001100135   ⟸   NM_001106665
- UniProtKB: D3ZC96 (UniProtKB/Swiss-Prot),   A0A8I5ZU64 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238412   ⟸   XM_006238350
- Peptide Label: isoform X1
- UniProtKB: A0A8I6A1P9 (UniProtKB/TrEMBL),   A0A8I5ZU64 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000055409   ⟸   ENSRNOT00000058611
RefSeq Acc Id: XP_038965438   ⟸   XM_039109510
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZU64 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000080999   ⟸   ENSRNOT00000117292
Ensembl Acc Id: ENSRNOP00000094295   ⟸   ENSRNOT00000109075
Ensembl Acc Id: ENSRNOP00000094211   ⟸   ENSRNOT00000101882
Ensembl Acc Id: ENSRNOP00000086184   ⟸   ENSRNOT00000105460

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZC96-F1-model_v2 AlphaFold D3ZC96 1-617 view protein structure

Transcriptome

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

Promoters
RGD ID:13693817
Promoter ID:EPDNEW_R4342
Type:initiation region
Name:Ttc39b_1
Description:tetratricopeptide repeat domain 39B
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_6.05101,405,611 - 101,405,671EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305797 AgrOrtholog
BioCyc Gene G2FUF-40882 BioCyc
Ensembl Genes ENSRNOG00000042603 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000058611 ENTREZGENE
  ENSRNOT00000105460 ENTREZGENE
Gene3D-CATH 1.25.40.10 UniProtKB/Swiss-Prot
InterPro Iml2/TPR_39 UniProtKB/Swiss-Prot
  TPR-like_helical_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:298186 UniProtKB/Swiss-Prot
NCBI Gene 298186 ENTREZGENE
PANTHER PTHR31859 UniProtKB/Swiss-Prot
  PTHR31859:SF4 UniProtKB/Swiss-Prot
Pfam DUF3808 UniProtKB/Swiss-Prot
PhenoGen Ttc39b PhenoGen
RatGTEx ENSRNOG00000042603 RatGTEx
Superfamily-SCOP SSF48452 UniProtKB/Swiss-Prot
UniProt A0A8I5ZU64 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A1P9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6ALW2_RAT UniProtKB/TrEMBL
  A0A8I6AMM6_RAT UniProtKB/TrEMBL
  A0A8L2QQK4_RAT UniProtKB/TrEMBL
  D3ZC96 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Ttc39b  tetratricopeptide repeat domain 39B  RGD1305797  similar to hypothetical protein FLJ33868   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1305797  similar to hypothetical protein FLJ33868   RGD1305797_predicted  similar to hypothetical protein FLJ33868 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1305797_predicted  similar to hypothetical protein FLJ33868 (predicted)  LOC298186_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC298186_predicted  similar to hypothetical protein FLJ33868 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL