Cpt1c (carnitine palmitoyltransferase 1c) - Rat Genome Database

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Gene: Cpt1c (carnitine palmitoyltransferase 1c) Rattus norvegicus
Analyze
Symbol: Cpt1c
Name: carnitine palmitoyltransferase 1c
RGD ID: 1305384
Description: Enables carnitine O-palmitoyltransferase activity. Involved in carnitine metabolic process. Located in endoplasmic reticulum membrane. Human ortholog(s) of this gene implicated in hereditary spastic paraplegia 73. Orthologous to human CPT1C (carnitine palmitoyltransferase 1C); PARTICIPATES IN forkhead class A signaling pathway; eicosanoid signaling pathway via peroxisome proliferator-activated receptor gamma; fatty acid metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; decabromodiphenyl ether.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: carnitine O-palmitoyltransferase 1, brain isoform; carnitine O-palmitoyltransferase I, brain isoform; CPT IC; CPT1-B; CPTI-B; LOC308579; MGC125142
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2195,442,814 - 95,457,347 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl195,442,817 - 95,457,342 (-)Ensembl
Rnor_6.01100,955,094 - 100,970,579 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1100,955,095 - 100,969,560 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01102,019,483 - 102,034,110 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4195,432,958 - 95,447,485 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1195,511,195 - 95,524,711 (-)NCBI
Celera189,704,373 - 89,718,810 (-)NCBICelera
Cytogenetic Map1q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. CPT1c is localized in endoplasmic reticulum of neurons and has carnitine palmitoyltransferase activity. Sierra AY, etal., J Biol Chem. 2008 Mar 14;283(11):6878-85. Epub 2008 Jan 11.
Additional References at PubMed
PMID:12477932   PMID:18385088   PMID:18614015   PMID:21961029   PMID:22539351   PMID:22632720   PMID:25751282   PMID:26338711  


Genomics

Comparative Map Data
Cpt1c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2195,442,814 - 95,457,347 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl195,442,817 - 95,457,342 (-)Ensembl
Rnor_6.01100,955,094 - 100,970,579 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1100,955,095 - 100,969,560 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01102,019,483 - 102,034,110 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4195,432,958 - 95,447,485 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1195,511,195 - 95,524,711 (-)NCBI
Celera189,704,373 - 89,718,810 (-)NCBICelera
Cytogenetic Map1q22NCBI
CPT1C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381949,690,662 - 49,713,731 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1949,690,898 - 49,713,731 (+)EnsemblGRCh38hg38GRCh38
GRCh371950,194,105 - 50,216,988 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361954,886,219 - 54,908,800 (+)NCBINCBI36hg18NCBI36
Build 341954,886,218 - 54,908,800NCBI
Celera1947,063,733 - 47,086,445 (+)NCBI
Cytogenetic Map19q13.33NCBI
HuRef1946,571,009 - 46,594,220 (+)NCBIHuRef
CHM1_11950,196,164 - 50,218,780 (+)NCBICHM1_1
T2T-CHM13v2.01952,690,916 - 52,713,875 (+)NCBI
Cpt1c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39744,607,907 - 44,624,304 (-)NCBIGRCm39mm39
GRCm39 Ensembl744,608,796 - 44,624,275 (-)Ensembl
GRCm38744,958,483 - 44,974,880 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl744,959,372 - 44,974,851 (-)EnsemblGRCm38mm10GRCm38
MGSCv37752,214,743 - 52,230,144 (-)NCBIGRCm37mm9NCBIm37
MGSCv36744,827,415 - 44,842,816 (-)NCBImm8
Celera740,410,981 - 40,426,356 (-)NCBICelera
Cytogenetic Map7B3NCBI
Cpt1c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555591,187,858 - 1,203,523 (-)NCBIChiLan1.0ChiLan1.0
CPT1C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11955,625,794 - 55,647,520 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1955,626,831 - 55,647,394 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01946,705,711 - 46,727,996 (+)NCBIMhudiblu_PPA_v0panPan3
CPT1C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11106,826,207 - 106,847,117 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1106,826,303 - 106,846,446 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1106,410,071 - 106,430,708 (-)NCBI
ROS_Cfam_1.01107,347,891 - 107,368,574 (-)NCBI
ROS_Cfam_1.0 Ensembl1107,342,847 - 107,373,187 (-)Ensembl
UMICH_Zoey_3.11107,020,193 - 107,040,828 (-)NCBI
UNSW_CanFamBas_1.01106,662,212 - 106,682,894 (-)NCBI
UU_Cfam_GSD_1.01107,502,688 - 107,523,376 (-)NCBI
Cpt1c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934921,886,951 - 21,908,096 (+)NCBI
SpeTri2.0NW_0049366643,505,146 - 3,526,286 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CPT1C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl654,731,557 - 54,749,249 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1654,732,701 - 54,747,706 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2650,462,134 - 50,476,782 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CPT1C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1642,865,706 - 42,885,359 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl642,866,921 - 42,885,185 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607322,810,843 - 22,833,543 (+)NCBIVero_WHO_p1.0
Cpt1c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248324,577,620 - 4,591,550 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046248324,578,400 - 4,592,933 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
BI285876  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2195,458,857 - 95,459,077 (+)MAPPERmRatBN7.2
mRatBN7.21487,551,063 - 87,551,283 (+)MAPPERmRatBN7.2
Rnor_6.01100,971,137 - 100,971,356NCBIRnor6.0
Rnor_6.01493,040,983 - 93,041,202NCBIRnor6.0
Rnor_5.01492,831,791 - 92,832,010UniSTSRnor5.0
Rnor_5.01102,035,577 - 102,035,796UniSTSRnor5.0
RGSC_v3.4195,449,062 - 95,449,281UniSTSRGSC3.4
RGSC_v3.41493,881,141 - 93,881,360UniSTSRGSC3.4
Celera1486,680,959 - 86,681,178UniSTS
Celera189,720,387 - 89,720,606UniSTS
RH 3.4 Map14654.09UniSTS
Cytogenetic Map1q22UniSTS
RH140408  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2195,442,814 - 95,442,962 (+)MAPPERmRatBN7.2
Rnor_6.01100,955,095 - 100,955,242NCBIRnor6.0
Rnor_5.01102,019,484 - 102,019,631UniSTSRnor5.0
RGSC_v3.4195,432,959 - 95,433,106UniSTSRGSC3.4
Celera189,704,374 - 89,704,521UniSTS
RH 3.4 Map1909.79UniSTS
Cytogenetic Map1q22UniSTS
RH139577  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2195,443,063 - 95,443,524 (+)MAPPERmRatBN7.2
Rnor_6.01100,955,344 - 100,955,804NCBIRnor6.0
Rnor_5.01102,019,733 - 102,020,193UniSTSRnor5.0
RGSC_v3.4195,433,208 - 95,433,668UniSTSRGSC3.4
Celera189,704,623 - 89,705,083UniSTS
Cytogenetic Map1q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)15673266898773277Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)156949932101949932Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)165789093115540829Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)166023617118608521Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)177494165122494165Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)177857876122857876Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)177876254106047988Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)178350581123350581Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)178430536123430536Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)178479925123479925Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)180592172125592172Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)182174743118944897Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)183547917128547917Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)185424647100358001Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)187580395150700247Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)190508614173018436Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)190508614180359386Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)190532338123479925Rat
1300153Bp171Blood pressure QTL 1713.37arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)190664883143200202Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192184926137184926Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)192948896144267916Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)194494440117601394Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)194494440172949803Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)194494440181830018Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)194494440198211706Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)194494440198324465Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)194642722214537671Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:144
Count of miRNA genes:112
Interacting mature miRNAs:122
Transcripts:ENSRNOT00000035908
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.


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 68 24
Low 3 43 57 41 19 41 8 11 6 34 17 11 8
Below cutoff 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001034925 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229066 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017589139 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112107 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112124 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005505496 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005505497 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005505498 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC127719 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC105882 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB544967 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB698393 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB802617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473979 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK598550 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000035908   ⟹   ENSRNOP00000032802
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl195,442,817 - 95,457,342 (-)Ensembl
Rnor_6.0 Ensembl1100,955,095 - 100,969,560 (-)Ensembl
RefSeq Acc Id: NM_001034925   ⟹   NP_001030097
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,442,814 - 95,457,281 (-)NCBI
Rnor_6.01100,955,094 - 100,969,560 (-)NCBI
Rnor_5.01102,019,483 - 102,034,110 (-)NCBI
RGSC_v3.4195,432,958 - 95,447,485 (-)RGD
Celera189,704,373 - 89,718,810 (-)RGD
Sequence:
RefSeq Acc Id: XM_006229066   ⟹   XP_006229128
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,442,814 - 95,457,346 (-)NCBI
Rnor_6.01100,955,094 - 100,970,579 (-)NCBI
Rnor_5.01102,019,483 - 102,034,110 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017589139   ⟹   XP_017444628
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,442,814 - 95,456,406 (-)NCBI
Rnor_6.01100,955,094 - 100,968,685 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039112107   ⟹   XP_038968035
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,442,814 - 95,455,519 (-)NCBI
RefSeq Acc Id: XM_039112117   ⟹   XP_038968045
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,442,814 - 95,455,519 (-)NCBI
RefSeq Acc Id: XM_039112124   ⟹   XP_038968052
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,442,814 - 95,449,076 (-)NCBI
RefSeq Acc Id: XR_005505496
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,442,814 - 95,457,346 (-)NCBI
RefSeq Acc Id: XR_005505497
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,444,111 - 95,457,347 (-)NCBI
RefSeq Acc Id: XR_005505498
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2195,444,138 - 95,457,347 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001030097   ⟸   NM_001034925
- UniProtKB: F1LN46 (UniProtKB/Swiss-Prot),   Q3KR63 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229128   ⟸   XM_006229066
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017444628   ⟸   XM_017589139
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000032802   ⟸   ENSRNOT00000035908
RefSeq Acc Id: XP_038968045   ⟸   XM_039112117
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038968035   ⟸   XM_039112107
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968052   ⟸   XM_039112124
- Peptide Label: isoform X5
Protein Domains
Carn_acyltransf

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LN46-F1-model_v2 AlphaFold F1LN46 1-801 view protein structure

Transcriptome

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

Promoters
RGD ID:13690015
Promoter ID:EPDNEW_R540
Type:multiple initiation site
Name:Cpt1c_1
Description:carnitine palmitoyltransferase 1c
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_6.01100,969,573 - 100,969,633EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 102020770 102020771 T C snv BN/SsNSlc (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305384 AgrOrtholog
BioCyc Gene G2FUF-59738 BioCyc
BioCyc Pathway PWY-6111 [mitochondrial L-carnitine shuttle] BioCyc
Ensembl Genes ENSRNOG00000026163 Ensembl, ENTREZGENE
Ensembl Protein ENSRNOP00000032802 ENTREZGENE
Ensembl Transcript ENSRNOT00000035908 ENTREZGENE
Gene3D-CATH 3.30.559.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.559.70 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Carn_acyl_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CAT-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cho/carn_acyl_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cho/carn_acyl_trans_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CPT_N UniProtKB/Swiss-Prot
KEGG Report rno:308579 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 308579 ENTREZGENE
PANTHER PTHR22589 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Carn_acyltransf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CPT_N UniProtKB/Swiss-Prot
PhenoGen Cpt1c PhenoGen
PROSITE ACYLTRANSF_C_1 UniProtKB/Swiss-Prot
  ACYLTRANSF_C_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CPT1C_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q3KR63 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Cpt1c  carnitine palmitoyltransferase 1c  Cpt1c_predicted  carnitine palmitoyltransferase 1c (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Cpt1c_predicted  carnitine palmitoyltransferase 1c (predicted)      Symbol and Name status set to approved 70820 APPROVED