Human Gene HACL1 (uc003caf.3)
  Description: Homo sapiens 2-hydroxyacyl-CoA lyase 1 (HACL1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr3:15,602,240-15,643,130 Size: 40,891 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr3:15,602,372-15,642,970 Size: 40,599 Coding Exon Count: 17 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:15,602,240-15,643,130)mRNA (may differ from genome)Protein (578 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
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MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HACL1_HUMAN
DESCRIPTION: RecName: Full=2-hydroxyacyl-CoA lyase 1; EC=4.1.-.-; AltName: Full=2-hydroxyphytanoyl-CoA lyase; Short=2-HPCL; AltName: Full=Phytanoyl-CoA 2-hydroxylase 2;
FUNCTION: Catalyzes a carbon-carbon cleavage reaction; cleaves a 2-hydroxy-3-methylacyl-CoA into formyl-CoA and a 2-methyl-branched fatty aldehyde.
CATALYTIC ACTIVITY: 2-hydroxyphytanoyl-CoA = pristanal + formyl- CoA.
COFACTOR: Binds 1 magnesium ion per subunit.
COFACTOR: Binds 1 thiamine pyrophosphate per subunit.
PATHWAY: Lipid metabolism; fatty acid metabolism.
SUBUNIT: Homotetramer.
INTERACTION: Self; NbExp=2; IntAct=EBI-746580, EBI-746580;
SUBCELLULAR LOCATION: Peroxisome.
TISSUE SPECIFICITY: Expressed in high levels in liver, also expressed in kidney, heart and skeletal muscle.
SIMILARITY: Belongs to the TPP enzyme family.
SEQUENCE CAUTION: Sequence=AAF28957.1; 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: HACL1
Diseases sorted by gene-association score: alpha-methylacyl-coa racemase deficiency (12), beriberi (8), refsum disease (6), hemangiopericytoma, malignant (4)

-  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: 23.30 RPKM in Testis
Total median expression: 429.23 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 -52.31160-0.327 Picture PostScript Text
3' UTR -22.10132-0.167 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
IPR012000 - Thiamin_PyroP_enz_cen_dom
IPR012001 - Thiamin_PyroP_enz_TPP-bd_dom
IPR011766 - TPP_enzyme-bd_C

Pfam Domains:
PF00205 - Thiamine pyrophosphate enzyme, central domain
PF02552 - CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
PF02775 - Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
PF02776 - Thiamine pyrophosphate enzyme, N-terminal TPP binding domain

SCOP Domains:
52467 - DHS-like NAD/FAD-binding domain
52518 - Thiamin diphosphate-binding fold (THDP-binding)

ModBase Predicted Comparative 3D Structure on Q9UJ83
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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 BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0005102 receptor binding
GO:0005515 protein binding
GO:0016829 lyase activity
GO:0016830 carbon-carbon lyase activity
GO:0030976 thiamine pyrophosphate binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0048037 cofactor binding

Biological Process:
GO:0001561 fatty acid alpha-oxidation
GO:0006625 protein targeting to peroxisome
GO:0006631 fatty acid metabolic process
GO:0051259 protein oligomerization

Cellular Component:
GO:0005777 peroxisome
GO:0005782 peroxisomal matrix
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  KJ893515 - Synthetic construct Homo sapiens clone ccsbBroadEn_02909 HACL1 gene, encodes complete protein.
CU674794 - Synthetic construct Homo sapiens gateway clone IMAGE:100017713 5' read HACL1 mRNA.
KJ902411 - Synthetic construct Homo sapiens clone ccsbBroadEn_11805 HACL1 gene, encodes complete protein.
AK299287 - Homo sapiens cDNA FLJ55041 complete cds, highly similar to 2-hydroxyphytanoyl-CoA lyase (EC 4.1.-.-).
AK056977 - Homo sapiens cDNA FLJ32415 fis, clone SKMUS2000724, highly similar to 2-hydroxyphytanoyl-CoA lyase (EC 4.1.-.-).
AJ131753 - Homo sapiens mRNA for 2-hydroxyphytanoyl-CoA lyase.
AF161397 - Homo sapiens HSPC279 mRNA, partial cds.
BC007440 - Homo sapiens 2-hydroxyacyl-CoA lyase 1, mRNA (cDNA clone IMAGE:2959666), complete cds.
AK301990 - Homo sapiens cDNA FLJ54118 complete cds, highly similar to 2-hydroxyphytanoyl-CoA lyase (EC 4.1.-.-).
AK301546 - Homo sapiens cDNA FLJ53672 complete cds, highly similar to 2-hydroxyphytanoyl-CoA lyase (EC 4.1.-.-).
AK302086 - Homo sapiens cDNA FLJ58815 complete cds, highly similar to 2-hydroxyphytanoyl-CoA lyase (EC 4.1.-.-).
BC001627 - Homo sapiens 2-hydroxyacyl-CoA lyase 1, mRNA (cDNA clone MGC:1115 IMAGE:3538159), complete cds.
EU176367 - Synthetic construct Homo sapiens clone IMAGE:100006471; FLH187986.01X; RZPDo839H11251D 2-hydroxyacyl-CoA lyase 1 (HACL1) gene, encodes complete protein.
DQ895558 - Synthetic construct Homo sapiens clone IMAGE:100010018; FLH187979.01L; RZPDo839F03149D 2-hydroxyacyl-CoA lyase 1 (HACL1) gene, encodes complete protein.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04146 - Peroxisome

Reactome (by CSHL, EBI, and GO)

Protein Q9UJ83 (Reactome details) participates in the following event(s):

R-HSA-9033233 PEX5S,L binds cargo proteins containing PTS1
R-HSA-9033236 PEX5S,L:Cargo binds PEX13:PEX14 of PEX13:PEX14:PEX2:PEX10:PEX12 (Docking and Translocation Complex)
R-HSA-389611 2-hydroxyphytanoyl-CoA => pristanal + formyl-CoA
R-HSA-9033241 Peroxisomal protein import
R-HSA-392499 Metabolism of proteins
R-HSA-389599 Alpha-oxidation of phytanate
R-HSA-390918 Peroxisomal lipid metabolism
R-HSA-8978868 Fatty acid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: HACL1_HUMAN, HPCL, HPCL2, HSPC279, NM_012260, NP_036392, PHYH2, Q9BV42, Q9P0A2, Q9UJ83
UCSC ID: uc003caf.3
RefSeq Accession: NM_012260
Protein: Q9UJ83 (aka HACL1_HUMAN)
CCDS: CCDS2627.1, CCDS68360.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_012260.2
exon count: 17CDS single in 3' UTR: no RNA size: 2037
ORF size: 1737CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3350.50frame shift in genome: no % Coverage: 99.61
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: 0# 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.