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FDFT1 farnesyl-diphosphate farnesyltransferase 1 [ Homo sapiens (human) ]

Gene ID: 2222, updated on 20-Dec-2019

Summary

Official Symbol
FDFT1provided by HGNC
Official Full Name
farnesyl-diphosphate farnesyltransferase 1provided by HGNC
Primary source
HGNC:HGNC:3629
See related
Ensembl:ENSG00000079459 MIM:184420
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SS; SQS; DGPT; ERG9; SQSD
Summary
This gene encodes a membrane-associated enzyme located at a branch point in the mevalonate pathway. The encoded protein is the first specific enzyme in cholesterol biosynthesis, catalyzing the dimerization of two molecules of farnesyl diphosphate in a two-step reaction to form squalene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 32.6), colon (RPKM 26.2) and 25 other tissues See more
Orthologs

Genomic context

See FDFT1 in Genome Data Viewer
Location:
8p23.1
Exon count:
14
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (11795573..11839309)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (11653467..11696818)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379243 Neighboring gene Sharpr-MPRA regulatory region 11637 Neighboring gene SUB1 pseudogene 1 Neighboring gene cathepsin B Neighboring gene CRISPRi-validated cis-regulatory element chr8.428

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
SQUALENE SYNTHASE DEFICIENCY
MedGen: C4748427 OMIM: 618156 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
A genome-wide search for quantitative trait loci affecting the cortical surface area and thickness of Heschl's gyrus.
NHGRI GWA Catalog
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
NHGRI GWA Catalog
Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
farnesyl-diphosphate farnesyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
squalene synthase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
cholesterol biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cholesterol biosynthetic process TAS
Traceable Author Statement
more info
 
ergosterol biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
farnesyl diphosphate metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of cholesterol biosynthetic process TAS
Traceable Author Statement
more info
 
regulation of lipid metabolic process TAS
Traceable Author Statement
more info
 
steroid biosynthetic process TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 
endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
squalene synthase
Names
FPP:FPP farnesyltransferase
presqualene-di-diphosphate synthase
squalene synthetase
NP_001274671.1
NP_001274672.1
NP_001274673.1
NP_001274674.1
NP_001274676.1
NP_001274677.1
NP_001274678.1
NP_001274679.1
NP_001274680.1
NP_001274685.1
NP_004453.3

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001287742.1NP_001274671.1  squalene synthase isoform 1

    See identical proteins and their annotated locations for NP_001274671.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript (1) and encodes the longest isoform (1). Variants 1-3 encode the same isoform.
    Source sequence(s)
    AA679352, AC069185, AK057726, BI765996, X69141
    Consensus CDS
    CCDS5985.1
    UniProtKB/Swiss-Prot
    P37268
    UniProtKB/TrEMBL
    Q6IAX1
    Related
    ENSP00000480828.1, ENST00000618539.4
    Conserved Domains (1) summary
    TIGR01559
    Location:38370
    squal_synth; farnesyl-diphosphate farnesyltransferase
  2. NM_001287743.1NP_001274672.1  squalene synthase isoform 1

    See identical proteins and their annotated locations for NP_001274672.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks a 5' non-coding exon compared to variant 1. Variants 1-3 encode the same isoform (1).
    Source sequence(s)
    AA679352, AC069185, AK057726, BG752446, X69141
    Consensus CDS
    CCDS5985.1
    UniProtKB/Swiss-Prot
    P37268
    UniProtKB/TrEMBL
    Q6IAX1
    Related
    ENSP00000481481.1, ENST00000615631.4
    Conserved Domains (1) summary
    TIGR01559
    Location:38370
    squal_synth; farnesyl-diphosphate farnesyltransferase
  3. NM_001287744.1NP_001274673.1  squalene synthase isoform 2

    See identical proteins and their annotated locations for NP_001274673.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks 2 exons in the 5' region and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 4-8 encode the same isoform.
    Source sequence(s)
    AA679352, AC069185, AK057726, X69141
    Consensus CDS
    CCDS75696.1
    UniProtKB/Swiss-Prot
    P37268
    Related
    ENSP00000444248.2, ENST00000538689.4
    Conserved Domains (1) summary
    cl00210
    Location:1306
    Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
  4. NM_001287745.1NP_001274674.1  squalene synthase isoform 2

    See identical proteins and their annotated locations for NP_001274674.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs at the 5' end and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 4-8 encode the same isoform.
    Source sequence(s)
    AA679352, AK315993, DC314061, DC396859, X69141
    Consensus CDS
    CCDS75696.1
    UniProtKB/Swiss-Prot
    P37268
    Related
    ENSP00000485229.1, ENST00000623368.3
    Conserved Domains (1) summary
    cl00210
    Location:1306
    Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
  5. NM_001287747.1NP_001274676.1  squalene synthase isoform 2

    See identical proteins and their annotated locations for NP_001274676.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs at the 5' end and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 4-8 encode the same isoform.
    Source sequence(s)
    AA679352, AK057726, AK316033, BE384903, X69141
    Consensus CDS
    CCDS75696.1
    UniProtKB/Swiss-Prot
    P37268
    UniProtKB/TrEMBL
    B7Z9R8
    Related
    ENSP00000431749.1, ENST00000528812.5
    Conserved Domains (1) summary
    cl00210
    Location:1306
    Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
  6. NM_001287748.1NP_001274677.1  squalene synthase isoform 2

    See identical proteins and their annotated locations for NP_001274677.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) differs at the 5' end and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 4-8 encode the same isoform.
    Source sequence(s)
    AA679352, AK057726, AK316351, DC387479, X69141
    Consensus CDS
    CCDS75696.1
    UniProtKB/Swiss-Prot
    P37268
    Related
    ENSP00000484122.1, ENST00000622850.2
    Conserved Domains (1) summary
    cl00210
    Location:1306
    Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
  7. NM_001287749.1NP_001274678.1  squalene synthase isoform 2

    See identical proteins and their annotated locations for NP_001274678.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) differs at the 5' end and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 4-8 encode the same isoform.
    Source sequence(s)
    AA679352, AC069185, AK293545, AK316531, X69141
    Consensus CDS
    CCDS75696.1
    UniProtKB/Swiss-Prot
    P37268
    Related
    ENSP00000432331.1, ENST00000530664.5
    Conserved Domains (1) summary
    cl00210
    Location:1306
    Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
  8. NM_001287750.1NP_001274679.1  squalene synthase isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (9) lacks several exons from the 5' end, contains an alternate 5' terminal exon, and initiates translation from an alternate in-frame start codon compared to variant 1. The resulting longer isoform (3) has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AA679352, AC069185, AK316182, DC387127, X69141
    Consensus CDS
    CCDS87579.1
    UniProtKB/Swiss-Prot
    P37268
    UniProtKB/TrEMBL
    A0A1W2PQ47, B4DND3
    Related
    ENSP00000491537.1, ENST00000525954.5
    Conserved Domains (1) summary
    TIGR01559
    Location:97429
    squal_synth; farnesyl-diphosphate farnesyltransferase
  9. NM_001287751.1NP_001274680.1  squalene synthase isoform 4

    See identical proteins and their annotated locations for NP_001274680.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (10) lacks several exons from the 5' end, contains an alternate 5' terminal exon, and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (4) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AA679352, AK057726, AK300059, AK316534, X69141
    Consensus CDS
    CCDS75697.1
    UniProtKB/Swiss-Prot
    P37268
    Related
    ENSP00000431649.1, ENST00000528643.5
    Conserved Domains (1) summary
    cl00210
    Location:1285
    Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
  10. NM_001287756.1NP_001274685.1  squalene synthase isoform 5

    See identical proteins and their annotated locations for NP_001274685.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (11) differs at the 5' end, lacks several internal exons, uses alternate donor and acceptor splice sites, and initiates translation from an alternate start codon compared to variant 1. The resulting shorter isoform (5) has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AA679352, AK301617, DC314061, DC396859, X69141
    UniProtKB/Swiss-Prot
    P37268
    UniProtKB/TrEMBL
    B4DWP0
    Conserved Domains (1) summary
    cl00210
    Location:22203
    Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
  11. NM_004462.5NP_004453.3  squalene synthase isoform 1

    See identical proteins and their annotated locations for NP_004453.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-3 encode the same isoform (1).
    Source sequence(s)
    AC069185
    Consensus CDS
    CCDS5985.1
    UniProtKB/Swiss-Prot
    P37268
    UniProtKB/TrEMBL
    Q6IAX1
    Related
    ENSP00000220584.4, ENST00000220584.9
    Conserved Domains (1) summary
    TIGR01559
    Location:38370
    squal_synth; farnesyl-diphosphate farnesyltransferase

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

    Range
    11795573..11839309
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 PATCHES

Genomic

  1. NW_018654717.1 Reference GRCh38.p13 PATCHES

    Range
    1508763..1552526 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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