Human Gene CPT1C (ENST00000598293.6_7) from GENCODE V47lift37
  Description: carnitine palmitoyltransferase 1C, transcript variant 11 (from RefSeq NM_001378488.1)
Gencode Transcript: ENST00000598293.6_7
Gencode Gene: ENSG00000169169.15_11
Transcript (Including UTRs)
   Position: hg19 chr19:50,194,373-50,216,988 Size: 22,616 Total Exon Count: 20 Strand: +
Coding Region
   Position: hg19 chr19:50,195,510-50,216,862 Size: 21,353 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:50,194,373-50,216,988)mRNA (may differ from genome)Protein (803 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CPT1C_HUMAN
DESCRIPTION: RecName: Full=Carnitine O-palmitoyltransferase 1, brain isoform; Short=CPT1-B; EC=2.3.1.21; AltName: Full=CPT IC; AltName: Full=Carnitine O-palmitoyltransferase I, brain isoform; Short=CPTI-B; AltName: Full=Carnitine palmitoyltransferase 1C;
CATALYTIC ACTIVITY: Palmitoyl-CoA + L-carnitine = CoA + L- palmitoylcarnitine.
PATHWAY: Lipid metabolism; fatty acid beta-oxidation.
SUBCELLULAR LOCATION: Mitochondrion outer membrane; Multi-pass membrane protein (By similarity).
TISSUE SPECIFICITY: Expressed predominantly in brain and testis.
SIMILARITY: Belongs to the carnitine/choline acetyltransferase family.
SEQUENCE CAUTION: Sequence=BAB85068.1; Type=Erroneous initiation; Sequence=CAD38561.2; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CPT1C
Diseases sorted by gene-association score: spastic paraplegia 73, autosomal dominant* (1630)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 32.90 RPKM in Brain - Cerebellum
Total median expression: 341.37 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -115.80308-0.376 Picture PostScript Text
3' UTR -40.20126-0.319 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000542 - Carn_acyl_trans

Pfam Domains:
PF00755 - Choline/Carnitine o-acyltransferase
PF16484 - Carnitine O-palmitoyltransferase N-terminus

SCOP Domains:
52777 - CoA-dependent acyltransferases

ModBase Predicted Comparative 3D Structure on Q8TCG5
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004095 carnitine O-palmitoyltransferase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0016746 transferase activity, transferring acyl groups

Biological Process:
GO:0006629 lipid metabolic process
GO:0006631 fatty acid metabolic process
GO:0006635 fatty acid beta-oxidation
GO:0009437 carnitine metabolic process

Cellular Component:
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030424 axon
GO:0030425 dendrite
GO:0032281 AMPA glutamate receptor complex
GO:0042995 cell projection
GO:0045202 synapse


-  Descriptions from all associated GenBank mRNAs
  LF384258 - JP 2014500723-A/191761: Polycomb-Associated Non-Coding RNAs.
AK096516 - Homo sapiens cDNA FLJ39197 fis, clone OCBBF2005077, highly similar to Carnitine O-palmitoyltransferase I, brain isoform (EC 2.3.1.21).
AK309087 - Homo sapiens cDNA, FLJ99128.
AK289713 - Homo sapiens cDNA FLJ75003 complete cds, highly similar to Homo sapiens carnitine palmitoyltransferase IC mRNA.
AK290092 - Homo sapiens cDNA FLJ78699 complete cds, highly similar to Homo sapiens carnitine palmitoyltransferase 1C (CPT1C), mRNA.
BC029104 - Homo sapiens carnitine palmitoyltransferase 1C, mRNA (cDNA clone MGC:9391 IMAGE:3872727), complete cds.
AF357970 - Homo sapiens carnitine palmitoyltransferase IC mRNA, complete cds.
AK299866 - Homo sapiens cDNA FLJ60346 complete cds, highly similar to Carnitine O-palmitoyltransferase I, brain isoform (EC 2.3.1.21).
DQ891552 - Synthetic construct clone IMAGE:100004182; FLH177998.01X; RZPDo839G03126D carnitine palmitoyltransferase 1C (CPT1C) gene, encodes complete protein.
DQ894739 - Synthetic construct Homo sapiens clone IMAGE:100009199; FLH177994.01L; RZPDo839G03125D carnitine palmitoyltransferase 1C (CPT1C) gene, encodes complete protein.
MA619835 - JP 2018138019-A/191761: Polycomb-Associated Non-Coding RNAs.
JD221461 - Sequence 202485 from Patent EP1572962.
JD495543 - Sequence 476567 from Patent EP1572962.
AB208884 - Homo sapiens mRNA for carnitine palmitoyltransferase 1C variant protein.
AK074389 - Homo sapiens cDNA FLJ23809 fis, clone HRC06614.
AL831876 - Homo sapiens mRNA; cDNA DKFZp547H1310 (from clone DKFZp547H1310).
JD264018 - Sequence 245042 from Patent EP1572962.
JD098422 - Sequence 79446 from Patent EP1572962.
JD107019 - Sequence 88043 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-6111 - mitochondrial L-carnitine shuttle

-  Other Names for This Gene
  Alternate Gene Symbols: A8K0Z8, CATL1, CPT1C , CPT1C_HUMAN, ENST00000598293.1, ENST00000598293.2, ENST00000598293.3, ENST00000598293.4, ENST00000598293.5, NM_001378488, Q5K6N5, Q8N6Q9, Q8NDS6, Q8TCG5, Q8TE84, uc327cys.1, uc327cys.2
UCSC ID: ENST00000598293.6_7
RefSeq Accession: NM_001199753.2
Protein: Q8TCG5 (aka CPT1C_HUMAN or CPTC_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CPT1C:
hsp (Hereditary Spastic Paraplegia Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.