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HACL1 Gene

protein-coding   GIFtS: 53

GC03M015579
2-hydroxyacyl-CoA lyase 1
(Previous name: 2-hydroxyphytanoyl-CoA lyase )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: HPCL)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
1600020H07Rik 2
2-HPCL 1, 2, 3
EC 4.1.-.- 3
FLJ55041 2
HPCL 2, 3
HPCL2 2, 3
PHYH2 1, 2, 3
Descriptions
2-hydroxyacyl-CoA lyase 1 2
2-hydroxyphytanol-CoA lyase 2
2-hydroxyphytanoyl-CoA lyase 1, 2, 3
Phytanoyl-CoA 2-hydroxylase 2 2, 3
phytanoyl-CoA hydroxylase 2 2
External Ids
HGNC: 178561
Entrez Gene: 260612
UniProtKB: Q9UJ833
Ensembl: ENSG000001313737
Search outside databases for aliases for HACL1 gene

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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UniProtKB/Swiss-Prot: HACL1_HUMAN, Q9UJ83
Function: Catalyzes a carbon-carbon cleavage reaction; cleaves a 2-hydroxy-3-methylacyl-CoA into
formyl-CoA and a 2-methyl-branched fatty aldehyde

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the HACL1 gene  

Entrez Gene cytogenetic band: 3p24.3   Ensembl cytogenetic band:  3p24.3   HGNC cytogenetic band: 3p24.3

HACL1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M015579:     (about GC identifiers)

Start:
15,577,243 bp from pter
End:
15,618,134 bp from pter
Size:
40,892 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000003.10  NT_022517.17  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: HACL1_HUMAN, Q9UJ83 (See protein sequence)
Recommended Name: 2-hydroxyacyl-CoA lyase 1  
Size: 578 amino acids; 63729 Da
Cofactor: Binds 1 magnesium ion per subunit
Cofactor: Binds 1 thiamine pyrophosphate per subunit
Subunit: Homotetramer
Subcellular location: Peroxisome
Secondary accessions: Q9BV42 Q9P0A2

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_036392.2  

    ENSEMBL proteins: 
    ENSP00000373289 ENSP00000323811 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (2 Hydroxy phytanoyl CoA lyase )
    Human Recombinant Proteins from Abnova (PHYH2)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    1 Gene Ontology (GO) cellular component term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005777 peroxisome IDA10468558 14561759
    About this table

    Antibodies for HACL1: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for HACL1
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (2 Hydroxy phytanoyl CoA lyase ), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (PHYH2)
    Novus Biologicals Antibody for HACL1

    Assays for HACL1: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    4 InterPro domains/families:
     IPR012001 TPP_bd_enzyme_N
     IPR011766 TPP_enzyme_bd_C
     IPR000399 TPP_bd_CS
     IPR012000 TPP_enzyme_M


       GeneDecks  HACL1 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q9UJ83

    ProtoNet protein and cluster: Q9UJ83

    2 Blocks protein families:
    IPB000399 Pyruvate decarboxylase
    IPB011766 Thiamine pyrophosphate enzyme


    UniProtKB/Swiss-Prot: HACL1_HUMAN, Q9UJ83
    Similarity: Belongs to the TPP enzyme family

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (HACL1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (PHYH2)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_012260

                  Applied Biosystems Silencer® siRNAs for HACL1

                  Sigma-Aldrich siRNA for HACL1  
                         Sigma-Aldrich shRNA for HACL1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for HACL1
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_012260
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_012260
                                     untagged cDNA clone in CMV expression vector: NM_012260 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_012260

    UniProtKB/Swiss-Prot: HACL1_HUMAN, Q9UJ83
    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
    Enzyme Number (IUBMB): EC 4.1.-.- 

    4 Gene Ontology (GO) molecular function terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000287 magnesium ion binding IEA--
    GO:0016830 carbon-carbon lyase activity IDA10468558
    GO:0030976 thiamin pyrophosphate binding IDA10468558
    GO:0042802 identical protein binding IPI16189514
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


    UniProtKB/Swiss-Prot: HACL1_HUMAN, Q9UJ83
    Pathway: Lipid metabolism; fatty acid metabolism


    2 Interacting proteins for HACL1 (Q9UJ831, 2) via UniProtKB, MINT, and/or STRING

    InteractantInteraction Details
    GeneCardExternal ID(s)
    HACL1Q9UJ831, 2EBI-746580, EBI-746580 MINT-67228 EBI-746580, EBI-746580 MINT-67228
    HACL1Q9UJ831, 2EBI-746580, EBI-746580 MINT-67228 EBI-746580, EBI-746580 MINT-67228
    ZMYND19Q96E352MINT-66872
    About this table

    2 Gene Ontology (GO) biological process terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001561 fatty acid alpha-oxidation IDA10468558
    GO:0006629 lipid metabolic process IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for HACL1
    3 Novoseek chemical compound relationships for HACL1 gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    2-hydroxyphytanoyl-coa 99.50 15 10521701 (3), 10468558 (2), 10754307 (1), 16796018 (1) (see all 9)
    formyl-coa 97.18 2 16796018 (1)
    phytanic acid 95.18 5 16786225 (1), 10521701 (1), 10896309 (1), 11948235 (1)
    About this table


    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (HACL1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (PHYH2)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_012260

                  Sigma-Aldrich siRNA for HACL1  
                         Sigma-Aldrich shRNA for HACL1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_012260  

    REFSEQ mRNAs for HACL1 gene: 

    NM_012260.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_012260  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_012260
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_012260
                                     untagged cDNA clone in CMV expression vector: NM_012260 

    Additional cDNA sequence: 

    AF161397.1 AJ131753.1 AK056977.1 AK301546.1 AK301990.1 AK302086.1 BC001627.1 BC007440.2 
    CR608246.1 CR609501.1 

    21 DOTS entries:

    DT.416311  DT.100804747  DT.92442759  DT.101974633  DT.120886761  DT.315966  DT.120886740  DT.416313 
    DT.100804752  DT.120886833  DT.40193790  DT.120886839  DT.100737498  DT.101962225  DT.100762559  DT.120886731 
    DT.120886743  DT.75192882  DT.91684326  DT.95130837  DT.97846094 

    24/264 AceView cDNA sequences (see all 264 ):

    CN479599 BM694820 AA039835 CA441883 BM017121 AA564217 CF243126 BU527364 
    BF434073 AF161397 AA298294 BM670044 BU182873 AL043205 BM759883 CB145879 
    BM675556 BM126759 CR608246 AI636915 AV647242 BI820732 H10428 AI741764 

    highest scoring ESTs for HACL1:

    AA071233 AF161397 AJ131753 AK056977 AL043205 AL600281 AL601151 BC001627 BC007440 BE249896 

    Unigene Cluster for HACL1:

    2-hydroxyacyl-CoA lyase 1
    Hs.63290  [show with all ESTs]
    Unigene Representative Sequence: NM_012260


    GeneLoc Exon Structure

    5/20 Alternative Splicing Database (ASD) splice patterns (SP) for HACL1 (see all 20 )

    ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c · 2d ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14a · 14b ^
    SP1:                          -     -           -           -                                                                             -           -         
    SP2:                          -     -           -           -           -                                         -                       -           -         
    SP3:                          -     -           -     -     -     -     -     -     -     -     -     -     -     -                       -           -         
    SP4:                          -     -           -           -                 -     -                                                                           
    SP5:                          -     -           -           -                 -                                                                                 

    ExUns: 15a · 15b ^ 16a · 16b ^ 17 ^ 18a · 18b · 18c
    SP1:                          -                     
    SP2:                          -                     
    SP3:                          -                     
    SP4:                                                
    SP5:                                                

    About this scheme

    ECgene alternative splicing isoforms for HACL1

    2 Ensembl transcripts including schematic representations:
    ENST00000383779  ENST00000321169  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    HACL1 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for HACL1

    1 / 2 / 3

    3 probe-sets matching HACL1 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    53979_at2, 3 U95-B 1 1.00 1.00 1.00 1.00 AL043205 0.80 1.00 0.91 1

    223211_at2, 3 U133-B 1 1.00 1.00 -- -- BC001627 0.80 1.00 0.91 1

    223211_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: ATTGAGCCAC

    SOURCE GeneReport for Unigene cluster: Hs.63290

    UniProtKB/Swiss-Prot: HACL1_HUMAN, Q9UJ83
    Tissue specificity: Expressed in high levels in liver, also expressed in kidney, heart and skeletal
    muscle

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for HACL1 gene from 5/18 species (see all 18 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    HACL11   -- 2-hydroxyacyl-CoA lyase 1 89.68(n)
    88.93(a)
    477060  XM_534256.2  XP_534256.2 
    chimpanzee
    (Pan troglodytes)
    HACL11   -- 2-hydroxyacyl-CoA lyase 1 99.65(n)
    99.48(a)
    743738  XM_001160528.1  XP_001160528.1 
    cow
    (Bos taurus)
    HACL11   -- 2-hydroxyacyl-CoA lyase 1 89.39(n)
    89.1(a)
    512676  XM_590233.3  XP_590233.3 
    rat
    (Rattus norvegicus)
    Hacl11   -- 2-hydroxyacyl-CoA lyase 1 85.58(n)
    85.99(a)
    85255  NM_053493.1  NP_445945.1 
    mouse
    (Mus musculus)
    Hacl11, 5 145
    2-hydroxyacyl-CoA lyase 11, 5 85.7(n)1
    87.89(a)1
    567941  NM_019975.21  NP_064359.21 
     AA7344745  AJ1321395  (see all 10)
    About this table        Species with no ortholog for HACL1

    ENSEMBL Gene Tree for HACL1
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for HACL1 gene
    ILVBL2  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/174 NCBI SNPs in HACL1 are shown (see all 174 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 51)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 3 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs9056501,2
    C,F,H,O15585074(-) TCCCTG/ACCTAT 1 L/L syn1 ese320Minor allele frequency- A:0.17NA EA MN EU WA 3049
    rs22710201,2
    C,F,H15584423(-) GGGCAA/GTGGAT 1 Q/Q syn1 ese39Minor allele frequency- G:0.01EA EU WA 2304
    rs67848441,2
    A,C,F,H15614448(+) CAACAC/TGTAAC 1 -- int16Minor allele frequency- T:0.40EU EA WA NA 600
    rs67971191,2
    A,C,F,H15598766(+) atataC/Tactaa 1 -- int14Minor allele frequency- T:0.45EU EA WA 412
    rs76489581,2
    A,C,F,H15596147(+) tccagG/Acacat 1 -- int18Minor allele frequency- A:0.40EU EA WA NA 780
    rs98271941,2
    C,F,H15582085(+) GAATGT/GAGGTT 1 -- int17Minor allele frequency- G:0.04EU EA WA NA 560
    rs21347841,2
    C,F,H15613264(-) ATAAAC/TCCCTC 1 -- int111Minor allele frequency- T:0.05NA EU EA WA 980
    rs105104401,2
    C,F,H15582006(+) AAAGGA/GGTATT 1 -- int1 trp320Minor allele frequency- G:0.19NS EU EA WA NA 1500
    rs19798961,2
    A,C,H15602265(+) AGCTAA/CAATGT 1 -- int11Minor allele frequency- C:0.01EU 120
    rs174853901,2
    C,F,H15587217(+) AGTAGT/CAGACA 1 -- int116Minor allele frequency- C:0.18NA EU EA WA 1474
    About this table

    HapMap Linkage Disequilibrium images for HACL1 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 604300

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/17 PubMed articles for HACL1 gene (see all 17 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 26061 HGNC: 17856 AceView: HPCL2 Ensembl:ENSG00000131373 euGenes: HUgn26061
    ECgene: HACL1 H-InvDB: HACL1
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

      --
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for HACL1:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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