Human Gene FDFT1 (ENST00000220584.9_6) from GENCODE V47lift37

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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 Index	Sequence and Links	Primers	MalaCards	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Pathways	Other Names	GeneReviews	Model Information	Methods

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 Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	UniProtKB
Wikipedia	BioGrid 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 D002945 Cisplatin D003300 Copper D004958 Estradiol D010634 Phenobarbital D019821 Simvastatin D013749 Tetrachlorodibenzodioxin D014635 Valproic Acid C061365 flusilazole C023036 perfluorooctanoic acid C006253 pirinixic acid more ... click here to view the complete list

Common Gene Haplotype Alleles


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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


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-34.90	92	-0.379	Picture	PostScript	Text
3' UTR	-177.80	689	-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


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD	Ensembl

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


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Methods, Credits, and Use Restrictions


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