LOCUS       NM_012260               2009 bp    mRNA    linear   PRI 05-APR-2024
DEFINITION  Homo sapiens 2-hydroxyacyl-CoA lyase 1 (HACL1), transcript variant
            1, mRNA.
ACCESSION   NM_012260
VERSION     NM_012260.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2009)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   2  (bases 1 to 2009)
  AUTHORS   Kitamura,T., Seki,N. and Kihara,A.
  TITLE     Phytosphingosine degradation pathway includes fatty acid
            alpha-oxidation reactions in the endoplasmic reticulum
  JOURNAL   Proc Natl Acad Sci U S A 114 (13), E2616-E2623 (2017)
   PUBMED   28289220
REFERENCE   3  (bases 1 to 2009)
  AUTHORS   Zhong,Q., Pevzner,S.J., Hao,T., Wang,Y., Mosca,R., Menche,J.,
            Taipale,M., Tasan,M., Fan,C., Yang,X., Haley,P., Murray,R.R.,
            Mer,F., Gebreab,F., Tam,S., MacWilliams,A., Dricot,A., Reichert,P.,
            Santhanam,B., Ghamsari,L., Calderwood,M.A., Rolland,T.,
            Charloteaux,B., Lindquist,S., Barabasi,A.L., Hill,D.E., Aloy,P.,
            Cusick,M.E., Xia,Y., Roth,F.P. and Vidal,M.
  TITLE     An inter-species protein-protein interaction network across vast
            evolutionary distance
  JOURNAL   Mol Syst Biol 12 (4), 865 (2016)
   PUBMED   27107014
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2009)
  AUTHORS   Mezzar,S., de Schryver,E. and Van Veldhoven,P.P.
  TITLE     RP-HPLC-fluorescence analysis of aliphatic aldehydes: application
            to aldehyde-generating enzymes HACL1 and SGPL1
  JOURNAL   J Lipid Res 55 (3), 573-582 (2014)
   PUBMED   24323699
  REMARK    GeneRIF: Data show that a easy assay for 2-hydroxyacyl-CoA lyase
            (HACL1) and sphingosine-1-phosphate lyase (SGPL1) activities was
            developed.
REFERENCE   5  (bases 1 to 2009)
  AUTHORS   Fraccascia,P., Casteels,M., De Schryver,E. and Van Veldhoven,P.P.
  TITLE     Role of thiamine pyrophosphate in oligomerisation, functioning and
            import of peroxisomal 2-hydroxyacyl-CoA lyase
  JOURNAL   Biochim Biophys Acta 1814 (10), 1226-1233 (2011)
   PUBMED   21708296
  REMARK    GeneRIF: Transport of thiamine pyrophosphate into peroxisomes is
            dependent on HACL1 import, without requirement of a specific solute
            transporter.
REFERENCE   6  (bases 1 to 2009)
  AUTHORS   Ghosh,D. and Berg,J.M.
  TITLE     A proteome-wide perspective on peroxisome targeting signal
            1(PTS1)-Pex5p affinities
  JOURNAL   J Am Chem Soc 132 (11), 3973-3979 (2010)
   PUBMED   20178365
REFERENCE   7  (bases 1 to 2009)
  AUTHORS   Wanders,R.J. and Waterham,H.R.
  TITLE     Biochemistry of mammalian peroxisomes revisited
  JOURNAL   Annu Rev Biochem 75, 295-332 (2006)
   PUBMED   16756494
  REMARK    Review article
REFERENCE   8  (bases 1 to 2009)
  AUTHORS   Foulon,V., Sniekers,M., Huysmans,E., Asselberghs,S., Mahieu,V.,
            Mannaerts,G.P., Van Veldhoven,P.P. and Casteels,M.
  TITLE     Breakdown of 2-hydroxylated straight chain fatty acids via
            peroxisomal 2-hydroxyphytanoyl-CoA lyase: a revised pathway for the
            alpha-oxidation of straight chain fatty acids
  JOURNAL   J Biol Chem 280 (11), 9802-9812 (2005)
   PUBMED   15644336
  REMARK    GeneRIF: 2-hydroxyphytanoyl-CoA lyase has a role in the breakdown
            of long chain 2-hydroxyfatty acids
REFERENCE   9  (bases 1 to 2009)
  AUTHORS   Kikuchi,M., Hatano,N., Yokota,S., Shimozawa,N., Imanaka,T. and
            Taniguchi,H.
  TITLE     Proteomic analysis of rat liver peroxisome: presence of
            peroxisome-specific isozyme of Lon protease
  JOURNAL   J Biol Chem 279 (1), 421-428 (2004)
   PUBMED   14561759
REFERENCE   10 (bases 1 to 2009)
  AUTHORS   Foulon,V., Antonenkov,V.D., Croes,K., Waelkens,E., Mannaerts,G.P.,
            Van Veldhoven,P.P. and Casteels,M.
  TITLE     Purification, molecular cloning, and expression of
            2-hydroxyphytanoyl-CoA lyase, a peroxisomal thiamine
            pyrophosphate-dependent enzyme that catalyzes the carbon-carbon
            bond cleavage during alpha-oxidation of 3-methyl-branched fatty
            acids
  JOURNAL   Proc Natl Acad Sci U S A 96 (18), 10039-10044 (1999)
   PUBMED   10468558
  REMARK    GeneRIF: peroxisomal thiamine-pyrophosphate depending enzyme
            required for the degradation of phytanic acid, catalyzing the
            cleavage of 2-hydroxyphytanoyl-CoA lyase into formyl-CoA and
            pristanal
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DA609383.1, BC001627.1, AJ131753.1, AA643224.1 and AC027129.6.
            
            On May 17, 2019 this sequence version replaced NM_012260.3.
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (a).
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1803614.53132.1,
                                           SRR1803616.32893.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2145122, SAMEA2152474
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000321169.10/ ENSP00000323811.5
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-34                DA609383.1         1-34
            35-1788             BC001627.1         36-1789
            1789-1976           AJ131753.1         1782-1969
            1977-2004           AA643224.1         1-28                c
            2005-2009           AC027129.6         86401-86405
FEATURES             Location/Qualifiers
     source          1..2009
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3p25.1"
     gene            1..2009
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /note="2-hydroxyacyl-CoA lyase 1"
                     /db_xref="GeneID:26061"
                     /db_xref="HGNC:HGNC:17856"
                     /db_xref="MIM:604300"
     exon            1..187
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     CDS             107..1843
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /EC_number="4.1.2.63"
                     /note="isoform a is encoded by transcript variant 1;
                     2-hydroxyphytanol-CoA lyase; phytanoyl-CoA 2-hydroxylase
                     2; 1600020H07Rik; phytanoyl-CoA hydroxylase 2;
                     2-hydroxyphytanoyl-CoA lyase"
                     /codon_start=1
                     /product="2-hydroxyacyl-CoA lyase 1 isoform a"
                     /protein_id="NP_036392.2"
                     /db_xref="CCDS:CCDS2627.1"
                     /db_xref="GeneID:26061"
                     /db_xref="HGNC:HGNC:17856"
                     /db_xref="MIM:604300"
                     /translation="MPDSNFAERSEEQVSGAKVIAQALKTQDVEYIFGIVGIPVTEIA
                     IAAQQLGIKYIGMRNEQAACYAASAIGYLTSRPGVCLVVSGPGLIHALGGMANANMNC
                     WPLLVIGGSSERNQETMGAFQEFPQVEACRLYTKFSARPSSIEAIPFVIEKAVRSSIY
                     GRPGACYVDIPADFVNLQVNVNSIKYMERCMSPPISMAETSAVCTAASVIRNAKQPLL
                     IIGKGAAYAHAEESIKKLVEQYKLPFLPTPMGKGVVPDNHPYCVGAARSRALQFADVI
                     VLFGARLNWILHFGLPPRYQPDVKFIQVDICAEELGNNVKPAVTLLGNIHAVTKQLLE
                     ELDKTPWQYPPESKWWKTLREKMKSNEAASKELASKKSLPMNYYTVFYHVQEQLPRDC
                     FVVSEGANTMDIGRTVLQNYLPRHRLDAGTFGTMGVGLGFAIAAAVVAKDRSPGQWII
                     CVEGDSAFGFSGMEVETICRYNLPIILLVVNNNGIYQGFDTDTWKEMLKFQDATAVVP
                     PMCLLPNSHYEQVMTAFGGKGYFVQTPEELQKSLRQSLADTTKPSLINIMIEPQATRK
                     AQDFHWLTRSNM"
     exon            188..292
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            293..333
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            334..414
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            415..487
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            488..565
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            566..660
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            661..773
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            774..909
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            910..1015
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            1016..1099
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            1100..1201
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            1202..1356
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            1357..1515
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            1516..1623
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            1624..1810
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     exon            1811..2009
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1945..1950
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /note="hexamer: AATAAA"
     polyA_site      1964
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /note="major polyA site"
     regulatory      1984..1989
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
                     /note="hexamer: ATTAAA"
     polyA_site      2009
                     /gene="HACL1"
                     /gene_synonym="2-HPCL; HPCL; HPCL2; PHYH2"
ORIGIN      
        1 agaggtgcag taccagaggt ggcgtgctgc cgatttcgcg tttgccttgc tggatgattc
       61 cgcttgtttg ccggctgcgt gagtgcttag agcttttcgg tggaagatgc cggacagtaa
      121 cttcgcagag cgcagcgagg agcaggtgtc tggtgctaaa gtcatcgctc aggccctgaa
      181 aacgcaagat gtggagtaca tatttggcat cgtaggcatc ccagtgaccg aaatcgccat
      241 tgctgcccag cagctaggca tcaagtacat cgggatgagg aatgagcaag cggcttgtta
      301 tgctgcctcc gcgattggat atctgacaag caggccagga gtctgccttg ttgtttctgg
      361 cccaggtctc atccatgcct tgggcggtat ggcaaatgca aacatgaact gctggccctt
      421 gcttgtgatt ggtggttcct ctgaaagaaa ccaagaaaca atgggagctt tccaggagtt
      481 tcctcaggtt gaagcttgta gattatatac caagttctct gcccgcccaa gcagcataga
      541 agctattcct tttgttattg aaaaggcagt gagaagcagt atctatggtc gtccaggtgc
      601 ttgctatgtt gacataccag cagattttgt gaaccttcag gtgaatgtga attctataaa
      661 gtacatggaa cgctgcatgt cacctcctat tagcatggca gaaacctctg ctgtgtgcac
      721 ggcggcttct gttattagga atgccaaaca accccttctt atcatcggga aaggtgctgc
      781 ttacgctcat gcagaagaga gtatcaagaa attggtggag caatataaac tgccattttt
      841 gcccacccct atggggaagg gtgttgtccc tgacaaccat ccatactgtg taggtgcagc
      901 cagatccagg gctttgcaat ttgctgatgt aattgtgtta tttggtgcca gactaaattg
      961 gattttacat tttggactgc ctccaagata tcagccagat gtgaagttta tccaggttga
     1021 tatctgtgca gaagaattgg ggaataatgt aaagcccgct gttactttgc taggaaacat
     1081 acatgctgtc actaagcagc ttttagagga acttgataaa acaccatggc agtatcctcc
     1141 agagagcaag tggtggaaaa ctctgagaga aaaaatgaag agcaatgaag ctgcatccaa
     1201 ggaactagct tctaaaaaat ccctgcctat gaattattac acagtattct accatgttca
     1261 agaacaacta cctagagact gtttcgtggt aagtgaagga gcaaatacta tggacattgg
     1321 acggactgtg cttcagaact accttcctcg tcacaggctt gatgctggta ctttcggaac
     1381 aatgggagtt ggtttgggat ttgctattgc agctgccgtg gtggctaaag atagaagccc
     1441 tgggcaatgg atcatctgtg tggaaggaga cagtgcattt gggttttctg gcatggaggt
     1501 agaaaccatc tgcaggtaca acttgccaat catactgttg gtagtgaata acaatggaat
     1561 ttaccaaggt tttgatacag atacttggaa agaaatgtta aaatttcaag atgctactgc
     1621 agtggtccct ccaatgtgtt tgctgccaaa ttcacattat gagcaagtca tgactgcatt
     1681 tggaggcaaa gggtattttg tacaaacacc agaagaactc caaaaatccc tgaggcagag
     1741 cctagcagac acaactaaac cttctcttat caacatcatg attgagccac aagccacacg
     1801 gaaggcccag gattttcatt ggctgacccg ctctaatatg taaataaaga cgccagttgg
     1861 tggtcttgag ttttctcttt cttgcaagat gaaattttat tttccacagc aaaattactc
     1921 tactgttaaa attgtgcaaa ataaaataaa catttaaaat gacattttac agtaaaggaa
     1981 ttgattaaaa acagaaaaag ttagaaaaa
//
