Human Gene SLC27A5 (uc002qtc.2) Description and Page Index
  Description: Homo sapiens solute carrier family 27 (fatty acid transporter), member 5 (SLC27A5), mRNA.
RefSeq Summary (NM_012254): The protein encoded by this gene is an isozyme of very long-chain acyl-CoA synthetase (VLCS). It is capable of activating very long-chain fatty-acids containing 24- and 26-carbons. It is expressed in liver and associated with endoplasmic reticulum but not with peroxisomes. Its primary role is in fatty acid elongation or complex lipid synthesis rather than in degradation. This gene has a mouse ortholog. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AK123036.1, AF064255.2 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000263093.7/ ENSP00000263093.2 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr19:59,009,700-59,023,432 Size: 13,733 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr19:59,009,882-59,023,322 Size: 13,441 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:59,009,700-59,023,432)mRNA (may differ from genome)Protein (690 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: S27A5_HUMAN
DESCRIPTION: RecName: Full=Bile acyl-CoA synthetase; Short=BACS; EC=6.2.1.7; AltName: Full=Bile acid-CoA ligase; Short=BA-CoA ligase; Short=BAL; AltName: Full=Cholate--CoA ligase; AltName: Full=Fatty acid transport protein 5; Short=FATP-5; AltName: Full=Fatty-acid-coenzyme A ligase, very long-chain 3; AltName: Full=Solute carrier family 27 member 5; AltName: Full=Very long-chain acyl-CoA synthetase homolog 2; Short=VLCS-H2; Short=VLCSH2; AltName: Full=Very long-chain acyl-CoA synthetase-related protein; Short=VLACS-related; Short=VLACSR;
FUNCTION: Acyl-CoA synthetase involved in bile acid metabolism. Proposed to catalyze the first step in the conjugation of C24 bile acids (choloneates) to glycine and taurine before excretion into bile canaliculi by activating them to their CoA thioesters. Seems to activate secondary bile acids entering the liver from the enterohepatic circulation. In vitro, also activates 3-alpha,7- alpha,12-alpha-trihydroxy-5-beta-cholestanate (THCA), the C27 precursor of cholic acid deriving from the de novo synthesis from cholesterol.
CATALYTIC ACTIVITY: ATP + cholate + CoA = AMP + diphosphate + choloyl-CoA.
CATALYTIC ACTIVITY: ATP + (25R)-3-alpha,7-alpha,12-alpha- trihydroxy-5-beta-cholestan-26-oate + CoA = AMP + diphosphate + (25R)-3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA.
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Predominantly expressed in liver.
SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SLC27A5
CDC HuGE Published Literature: SLC27A5

-  MalaCards Disease Associations
  MalaCards Gene Search: SLC27A5
Diseases sorted by gene-association score: bile acid coa ligase deficiency and defective amidation* (25), amusia (17), schizophreniform disorder (6)
* = 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: 218.90 RPKM in Liver
Total median expression: 324.50 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 -52.30110-0.475 Picture PostScript Text
3' UTR -56.20182-0.309 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
IPR020845 - AMP-binding_CS
IPR000873 - AMP-dep_Synth/Lig

Pfam Domains:
PF00501 - AMP-binding enzyme
PF13193 - AMP-binding enzyme C-terminal domain

SCOP Domains:
56801 - Acetyl-CoA synthetase-like

ModBase Predicted Comparative 3D Structure on Q9Y2P5
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003824 catalytic activity
GO:0004467 long-chain fatty acid-CoA ligase activity
GO:0005524 ATP binding
GO:0015245 fatty acid transporter activity
GO:0016874 ligase activity
GO:0031957 very long-chain fatty acid-CoA ligase activity
GO:0044877 macromolecular complex binding
GO:0047747 cholate-CoA ligase activity

Biological Process:
GO:0000038 very long-chain fatty acid metabolic process
GO:0001676 long-chain fatty acid metabolic process
GO:0006629 lipid metabolic process
GO:0006631 fatty acid metabolic process
GO:0006642 triglyceride mobilization
GO:0006699 bile acid biosynthetic process
GO:0008152 metabolic process
GO:0008206 bile acid metabolic process
GO:0015721 bile acid and bile salt transport
GO:0015908 fatty acid transport
GO:0015911 plasma membrane long-chain fatty acid transport
GO:0046951 ketone body biosynthetic process

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0009925 basal plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030176 integral component of endoplasmic reticulum membrane
GO:0032991 macromolecular complex
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  AK026640 - Homo sapiens cDNA: FLJ22987 fis, clone KAT11802.
AK123036 - Homo sapiens cDNA FLJ41040 fis, clone LIVER1000017, highly similar to Bile acyl-CoA synthetase (EC 6.2.1.7).
AF064255 - Homo sapiens very long-chain acyl-CoA synthetase homolog 2 mRNA, complete cds.
AK298446 - Homo sapiens cDNA FLJ55741 complete cds, moderately similar to Bile acyl-CoA synthetase (EC 6.2.1.7).
JD159166 - Sequence 140190 from Patent EP1572962.
JD257349 - Sequence 238373 from Patent EP1572962.
JD334387 - Sequence 315411 from Patent EP1572962.
BC146387 - Synthetic construct Homo sapiens clone IMAGE:100015134, MGC:180217 solute carrier family 27 (fatty acid transporter), member 5 (SLC27A5) mRNA, encodes complete protein.
BC148807 - Synthetic construct Homo sapiens clone IMAGE:100015855, MGC:183197 solute carrier family 27 (fatty acid transporter), member 5 (SLC27A5) mRNA, encodes complete protein.
AB527212 - Synthetic construct DNA, clone: pF1KE0364, Homo sapiens SLC27A5 gene for solute carrier family 27 (fatty acid transporter), member 5, without stop codon, in Flexi system.
AB208931 - Homo sapiens mRNA for solute carrier family 27 (fatty acid transporter), member 5 variant protein.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00120 - Primary bile acid biosynthesis
hsa01100 - Metabolic pathways
hsa03320 - PPAR signaling pathway

BioCyc Knowledge Library
FAO-PWY - fatty acid β-oxidation I
PWY-5136 - fatty acid β-oxidation II (core pathway)

Reactome (by CSHL, EBI, and GO)

Protein Q9Y2P5 (Reactome details) participates in the following event(s):

R-HSA-159425 Cytosolic cholate and chenodeoxycholate are conjugated with Coenzyme A (SLC27A5 BACS)
R-HSA-192137 THCA is conjugated with Coenzyme A (SLC27A5 BACS)
R-HSA-193407 DHCA is conjugated with Coenzyme A (SLC27A5 BACS)
R-HSA-193711 3,7,24THCA is conjugated with Coenzyme A (SLC27A5 BACS)
R-HSA-193766 TetraHCA is conjugated with Coenzyme A (SLC27A5 BACS)
R-HSA-159418 Recycling of bile acids and salts
R-HSA-193368 Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol
R-HSA-193775 Synthesis of bile acids and bile salts via 24-hydroxycholesterol
R-HSA-194068 Bile acid and bile salt metabolism
R-HSA-192105 Synthesis of bile acids and bile salts
R-HSA-8957322 Metabolism of steroids
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: ACSB, ACSVL6, B3KVP6, FACVL3, FATP5, NM_012254, NP_036386, Q9Y2P5, S27A5_HUMAN
UCSC ID: uc002qtc.2
RefSeq Accession: NM_012254
Protein: Q9Y2P5 (aka S27A5_HUMAN)
CCDS: CCDS12983.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_012254.2
exon count: 10CDS single in 3' UTR: no RNA size: 2378
ORF size: 2073CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3701.00frame shift in genome: no % Coverage: 99.45
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 161# strange splices: 0
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.