Human Gene FDFT1 (ENST00000220584.9_6) from GENCODE V47lift37
  Description: farnesyl-diphosphate farnesyltransferase 1, transcript variant 3 (from RefSeq NM_004462.5)
Gencode Transcript: ENST00000220584.9_6
Gencode Gene: ENSG00000079459.14_12
Transcript (Including UTRs)
   Position: hg19 chr8:11,660,250-11,696,807 Size: 36,558 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr8:11,660,342-11,696,118 Size: 35,777 Coding Exon Count: 8 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:11,660,250-11,696,807)mRNA (may differ from genome)Protein (417 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  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: FDFT1
Diseases sorted by gene-association score: smith-lemli-opitz syndrome (18), keratolytic winter erythema (9), phencyclidine abuse (8), sitosterolemia (6), smoldering myeloma (6)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 69.11 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1276.45 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 -34.9092-0.379 Picture PostScript Text
3' UTR -177.80689-0.258 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
IPR002060 - Squ/phyt_synthse
IPR006449 - Squal_synth
IPR019845 - Squalene/phytoene_synthase_CS
IPR008949 - Terpenoid_synth

Pfam Domains:
PF00494 - Squalene/phytoene synthase

SCOP Domains:
48576 - Terpenoid synthases

ModBase Predicted Comparative 3D Structure on Q6IAX1
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    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004310 farnesyl-diphosphate farnesyltransferase activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0051996 squalene synthase activity

Biological Process:
GO:0006695 cholesterol biosynthetic process
GO:0006696 ergosterol biosynthetic process
GO:0008610 lipid biosynthetic process
GO:0009058 biosynthetic process
GO:0045338 farnesyl diphosphate metabolic process

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0016021 integral component of membrane
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  AK057726 - Homo sapiens cDNA FLJ33164 fis, clone UTERU2000542, highly similar to Squalene synthetase (EC 2.5.1.21).
AK098682 - Homo sapiens cDNA FLJ25816 fis, clone TST07502, highly similar to FARNESYL-DIPHOSPHATE FARNESYLTRANSFERASE (EC 2.5.1.21).
LF385001 - JP 2014500723-A/192504: Polycomb-Associated Non-Coding RNAs.
AK296043 - Homo sapiens cDNA FLJ50548 complete cds, highly similar to Squalene synthetase (EC 2.5.1.21).
AK315993 - Homo sapiens cDNA, FLJ78892 complete cds, highly similar to Squalene synthetase (EC 2.5.1.21).
AK311246 - Homo sapiens cDNA, FLJ18288.
X69141 - H.sapiens mRNA for squalene synthase.
AK301617 - Homo sapiens cDNA FLJ53107 complete cds, highly similar to Squalene synthetase (EC 2.5.1.21).
BC003573 - Homo sapiens farnesyl-diphosphate farnesyltransferase 1, mRNA (cDNA clone MGC:2200 IMAGE:3538137), complete cds.
BC009251 - Homo sapiens farnesyl-diphosphate farnesyltransferase 1, mRNA (cDNA clone MGC:4480 IMAGE:2961623), complete cds.
S76822 - squalene synthase=farnesyl diphosphate:farnesyl diphosphate farnesyltransferase [human, liver, mRNA, 1673 nt].
L06105 - Human hepatic squalene synthetase mRNA, complete cds.
BC029641 - Homo sapiens farnesyl-diphosphate farnesyltransferase 1, mRNA (cDNA clone MGC:25135 IMAGE:4514761), complete cds.
BC034440 - Homo sapiens farnesyl-diphosphate farnesyltransferase 1, mRNA (cDNA clone IMAGE:4510069).
L06070 - Human squalene synthetase (ERG9) mRNA, complete cds.
CU688724 - Synthetic construct Homo sapiens gateway clone IMAGE:100019298 5' read FDFT1 mRNA.
CR457033 - Homo sapiens full open reading frame cDNA clone RZPDo834B0218D for gene FDFT1, farnesyl-diphosphate farnesyltransferase 1; complete cds, incl. stopcodon.
AB529133 - Synthetic construct DNA, clone: pF1KB5011, Homo sapiens FDFT1 gene for farnesyl-diphosphate farnesyltransferase 1, without stop codon, in Flexi system.
BT006704 - Homo sapiens farnesyl-diphosphate farnesyltransferase 1 mRNA, complete cds.
DQ890697 - Synthetic construct clone IMAGE:100003327; FLH165235.01X; RZPDo839H08158D farnesyl-diphosphate farnesyltransferase 1 (FDFT1) gene, encodes complete protein.
DQ893882 - Synthetic construct Homo sapiens clone IMAGE:100008342; FLH165231.01L; RZPDo839H08157D farnesyl-diphosphate farnesyltransferase 1 (FDFT1) gene, encodes complete protein.
KJ905745 - Synthetic construct Homo sapiens clone ccsbBroadEn_15415 FDFT1 gene, encodes complete protein.
KJ896810 - Synthetic construct Homo sapiens clone ccsbBroadEn_06204 FDFT1 gene, encodes complete protein.
KJ896811 - Synthetic construct Homo sapiens clone ccsbBroadEn_06205 FDFT1 gene, encodes complete protein.
KR709848 - Synthetic construct Homo sapiens clone CCSBHm_00006802 FDFT1 (FDFT1) mRNA, encodes complete protein.
AK311362 - Homo sapiens cDNA, FLJ18404.
AK316351 - Homo sapiens cDNA, FLJ79250 complete cds, highly similar to Squalene synthetase (EC 2.5.1.21).
AK316033 - Homo sapiens cDNA, FLJ78932 complete cds, highly similar to Squalene synthetase (EC 2.5.1.21).
AK300245 - Homo sapiens cDNA FLJ50669 complete cds, highly similar to Squalene synthetase (EC 2.5.1.21).
MA620578 - JP 2018138019-A/192504: Polycomb-Associated Non-Coding RNAs.
JD019907 - Sequence 931 from Patent EP1572962.
AK293545 - Homo sapiens cDNA FLJ50447 complete cds, highly similar to Squalene synthetase (EC 2.5.1.21).
AK316531 - Homo sapiens cDNA, FLJ79430 complete cds, highly similar to Squalene synthetase (EC 2.5.1.21).
AK316182 - Homo sapiens cDNA, FLJ79081 complete cds, highly similar to Squalene synthetase (EC 2.5.1.21).
AK297868 - Homo sapiens cDNA FLJ55760 complete cds, highly similar to Squalene synthetase (EC 2.5.1.21).
LF332988 - JP 2014500723-A/140491: Polycomb-Associated Non-Coding RNAs.
LF334790 - JP 2014500723-A/142293: Polycomb-Associated Non-Coding RNAs.
AK316534 - Homo sapiens cDNA, FLJ79433 complete cds, highly similar to Squalene synthetase (EC 2.5.1.21).
AK300059 - Homo sapiens cDNA FLJ50660 complete cds, highly similar to Squalene synthetase (EC 2.5.1.21).
LF334784 - JP 2014500723-A/142287: Polycomb-Associated Non-Coding RNAs.
LF332991 - JP 2014500723-A/140494: Polycomb-Associated Non-Coding RNAs.
LF209943 - JP 2014500723-A/17446: Polycomb-Associated Non-Coding RNAs.
LF332992 - JP 2014500723-A/140495: Polycomb-Associated Non-Coding RNAs.
LF334783 - JP 2014500723-A/142286: Polycomb-Associated Non-Coding RNAs.
LF332993 - JP 2014500723-A/140496: Polycomb-Associated Non-Coding RNAs.
LF334782 - JP 2014500723-A/142285: Polycomb-Associated Non-Coding RNAs.
LF332994 - JP 2014500723-A/140497: Polycomb-Associated Non-Coding RNAs.
LF334780 - JP 2014500723-A/142283: Polycomb-Associated Non-Coding RNAs.
LF332995 - JP 2014500723-A/140498: Polycomb-Associated Non-Coding RNAs.
LF334779 - JP 2014500723-A/142282: Polycomb-Associated Non-Coding RNAs.
LF332996 - JP 2014500723-A/140499: Polycomb-Associated Non-Coding RNAs.
LF334778 - JP 2014500723-A/142281: Polycomb-Associated Non-Coding RNAs.
AK098208 - Homo sapiens cDNA FLJ40889 fis, clone UTERU2000925.
LF334777 - JP 2014500723-A/142280: Polycomb-Associated Non-Coding RNAs.
LF332999 - JP 2014500723-A/140502: Polycomb-Associated Non-Coding RNAs.
LF334776 - JP 2014500723-A/142279: Polycomb-Associated Non-Coding RNAs.
LF334775 - JP 2014500723-A/142278: Polycomb-Associated Non-Coding RNAs.
LF333000 - JP 2014500723-A/140503: Polycomb-Associated Non-Coding RNAs.
JD166461 - Sequence 147485 from Patent EP1572962.
JD073478 - Sequence 54502 from Patent EP1572962.
JD561655 - Sequence 542679 from Patent EP1572962.
JD543393 - Sequence 524417 from Patent EP1572962.
LF333001 - JP 2014500723-A/140504: Polycomb-Associated Non-Coding RNAs.
LF334774 - JP 2014500723-A/142277: Polycomb-Associated Non-Coding RNAs.
JD171855 - Sequence 152879 from Patent EP1572962.
JD563511 - Sequence 544535 from Patent EP1572962.
MA568565 - JP 2018138019-A/140491: Polycomb-Associated Non-Coding RNAs.
MA570367 - JP 2018138019-A/142293: Polycomb-Associated Non-Coding RNAs.
MA570361 - JP 2018138019-A/142287: Polycomb-Associated Non-Coding RNAs.
MA568568 - JP 2018138019-A/140494: Polycomb-Associated Non-Coding RNAs.
MA445520 - JP 2018138019-A/17446: Polycomb-Associated Non-Coding RNAs.
MA568569 - JP 2018138019-A/140495: Polycomb-Associated Non-Coding RNAs.
MA570360 - JP 2018138019-A/142286: Polycomb-Associated Non-Coding RNAs.
MA568570 - JP 2018138019-A/140496: Polycomb-Associated Non-Coding RNAs.
MA570359 - JP 2018138019-A/142285: Polycomb-Associated Non-Coding RNAs.
MA568571 - JP 2018138019-A/140497: Polycomb-Associated Non-Coding RNAs.
MA570357 - JP 2018138019-A/142283: Polycomb-Associated Non-Coding RNAs.
MA568572 - JP 2018138019-A/140498: Polycomb-Associated Non-Coding RNAs.
MA570356 - JP 2018138019-A/142282: Polycomb-Associated Non-Coding RNAs.
MA568573 - JP 2018138019-A/140499: Polycomb-Associated Non-Coding RNAs.
MA570355 - JP 2018138019-A/142281: Polycomb-Associated Non-Coding RNAs.
MA570354 - JP 2018138019-A/142280: Polycomb-Associated Non-Coding RNAs.
MA568576 - JP 2018138019-A/140502: Polycomb-Associated Non-Coding RNAs.
MA570353 - JP 2018138019-A/142279: Polycomb-Associated Non-Coding RNAs.
MA570352 - JP 2018138019-A/142278: Polycomb-Associated Non-Coding RNAs.
MA568577 - JP 2018138019-A/140503: Polycomb-Associated Non-Coding RNAs.
MA568578 - JP 2018138019-A/140504: Polycomb-Associated Non-Coding RNAs.
MA570351 - JP 2018138019-A/142277: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-5670 - epoxysqualene biosynthesis
PWY66-3 - cholesterol biosynthesis II (via 24,25-dihydrolanosterol)
PWY66-341 - cholesterol biosynthesis I
PWY66-4 - cholesterol biosynthesis III (via desmosterol)
PWY66-5 - superpathway of cholesterol biosynthesis

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000220584.1, ENST00000220584.2, ENST00000220584.3, ENST00000220584.4, ENST00000220584.5, ENST00000220584.6, ENST00000220584.7, ENST00000220584.8, FDFT1 , hCG_17749 , NM_004462, Q6IAX1, Q6IAX1_HUMAN, uc317cze.1, uc317cze.2
UCSC ID: ENST00000220584.9_6
RefSeq Accession: NM_004462.5
Protein: Q6IAX1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene FDFT1:
ss-def (Squalene Synthase Deficiency)

-  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.