LOCUS       NM_153373               2081 bp    mRNA    linear   PRI 05-APR-2024
DEFINITION  Homo sapiens 5-phosphohydroxy-L-lysine phospho-lyase (PHYKPL),
            transcript variant 2, mRNA.
ACCESSION   NM_153373
VERSION     NM_153373.4
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 2081)
  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 2081)
  AUTHORS   Fragoza,R., Das,J., Wierbowski,S.D., Liang,J., Tran,T.N., Liang,S.,
            Beltran,J.F., Rivera-Erick,C.A., Ye,K., Wang,T.Y., Yao,L., Mort,M.,
            Stenson,P.D., Cooper,D.N., Wei,X., Keinan,A., Schimenti,J.C.,
            Clark,A.G. and Yu,H.
  TITLE     Extensive disruption of protein interactions by genetic variants
            across the allele frequency spectrum in human populations
  JOURNAL   Nat Commun 10 (1), 4141 (2019)
   PUBMED   31515488
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2081)
  AUTHORS   Chen,S., Fragoza,R., Klei,L., Liu,Y., Wang,J., Roeder,K., Devlin,B.
            and Yu,H.
  TITLE     An interactome perturbation framework prioritizes damaging missense
            mutations for developmental disorders
  JOURNAL   Nat Genet 50 (7), 1032-1040 (2018)
   PUBMED   29892012
REFERENCE   4  (bases 1 to 2081)
  AUTHORS   Veiga-da-Cunha,M., Verhoeven-Duif,N.M., de Koning,T.J., Duran,M.,
            Dorland,B. and Van Schaftingen,E.
  TITLE     Mutations in the AGXT2L2 gene cause phosphohydroxylysinuria
  JOURNAL   J Inherit Metab Dis 36 (6), 961-966 (2013)
   PUBMED   23242558
  REMARK    GeneRIF: Phosphohydroxylysinuria is due to mutations in the AGXT2L2
            gene and the resulting lack of activity of phosphohydroxylysine
            phospholyase in vivo.
REFERENCE   5  (bases 1 to 2081)
  AUTHORS   Veiga-da-Cunha,M., Hadi,F., Balligand,T., Stroobant,V. and Van
            Schaftingen,E.
  TITLE     Molecular identification of hydroxylysine kinase and of
            ammoniophospholyases acting on 5-phosphohydroxy-L-lysine and
            phosphoethanolamine
  JOURNAL   J Biol Chem 287 (10), 7246-7255 (2012)
   PUBMED   22241472
REFERENCE   6  (bases 1 to 2081)
  AUTHORS   Lee,O.H., Kim,H., He,Q., Baek,H.J., Yang,D., Chen,L.Y., Liang,J.,
            Chae,H.K., Safari,A., Liu,D. and Songyang,Z.
  TITLE     Genome-wide YFP fluorescence complementation screen identifies new
            regulators for telomere signaling in human cells
  JOURNAL   Mol Cell Proteomics 10 (2), M110.001628 (2011)
   PUBMED   21044950
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BX417194.2, AK292061.1,
            BC037567.1, HY267487.1 and AC136632.3.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_153373.3.
            
            Summary: This is a nuclear gene encoding a mitochondrial enzyme
            that catalyzes the conversion of 5-phosphonooxy-L-lysine to
            ammonia, inorganic phosphate, and 2-aminoadipate semialdehyde.
            Mutations in this gene may cause phosphohydroxylysinuria.
            Alternative splicing results in multiple transcript variants.
            [provided by RefSeq, May 2013].
            
            Transcript Variant: This variant (2) encodes the longer isoform
            (2).
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1163658.221368.1,
                                           SRR1660809.217588.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000308158.10/ ENSP00000310978.5
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-18                BX417194.2         75-92
            19-1561             AK292061.1         1-1543
            1562-1963           BC037567.1         1544-1945
            1964-2078           HY267487.1         3-117               c
            2079-2081           AC136632.3         199735-199737       c
FEATURES             Location/Qualifiers
     source          1..2081
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q35.3"
     gene            1..2081
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /note="5-phosphohydroxy-L-lysine phospho-lyase"
                     /db_xref="GeneID:85007"
                     /db_xref="HGNC:HGNC:28249"
                     /db_xref="MIM:614683"
     exon            1..311
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /inference="alignment:Splign:2.1.0"
     CDS             253..1605
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /EC_number="4.2.3.134"
                     /note="isoform 2 is encoded by transcript variant 2;
                     alanine--glyoxylate aminotransferase 2-like 2;
                     5-phosphonooxy-L-lysine phospho-lyase"
                     /codon_start=1
                     /product="5-phosphohydroxy-L-lysine phospho-lyase isoform
                     2"
                     /protein_id="NP_699204.1"
                     /db_xref="CCDS:CCDS4434.1"
                     /db_xref="GeneID:85007"
                     /db_xref="HGNC:HGNC:28249"
                     /db_xref="MIM:614683"
                     /translation="MAADQRPKADTLALRQRLISSSCRLFFPEDPVKIVRAQGQYMYD
                     EQGAEYIDCISNVAHVGHCHPLVVQAAHEQNQVLNTNSRYLHDNIVDYAQRLSETLPE
                     QLCVFYFLNSGSEANDLALRLARHYTGHQDVVVLDHAYHGHLSSLIDISPYKFRNLDG
                     QKEWVHVAPLPDTYRGPYREDHPNPAMAYANEVKRVVSSAQEKGRKIAAFFAESLPSV
                     GGQIIPPAGYFSQVAEHIRKAGGVFVADEIQVGFGRVGKHFWAFQLQGKDFVPDIVTM
                     GKSIGNGHPVACVAATQPVARAFEATGVEYFNTFGGSPVSCAVGLAVLNVLEKEQLQD
                     HATSVGSFLMQLLGQQKIKHPIVGDVRGVGLFIGVDLIKDEATRTPATEEAAYLVSRL
                     KENYVLLSTDGPGRNILKFKPPMCFSLDNARQVVAKLDAILTDMEEKVRSCETLRLQP
                     "
     exon            312..430
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /inference="alignment:Splign:2.1.0"
     exon            431..590
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /inference="alignment:Splign:2.1.0"
     exon            591..665
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /inference="alignment:Splign:2.1.0"
     exon            666..753
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /inference="alignment:Splign:2.1.0"
     exon            754..870
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /inference="alignment:Splign:2.1.0"
     exon            871..953
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /inference="alignment:Splign:2.1.0"
     exon            954..1179
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /inference="alignment:Splign:2.1.0"
     exon            1180..1334
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /inference="alignment:Splign:2.1.0"
     exon            1335..1424
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /inference="alignment:Splign:2.1.0"
     exon            1425..1555
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /inference="alignment:Splign:2.1.0"
     exon            1556..1636
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /inference="alignment:Splign:2.1.0"
     exon            1637..2081
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1890..1895
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /note="hexamer: AATAAA"
     polyA_site      1913
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /note="major polyA site"
     regulatory      1944..1949
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /note="hexamer: ATTAAA"
     polyA_site      1968
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /note="major polyA site"
     regulatory      1994..1999
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /note="hexamer: ATTAAA"
     polyA_site      2013
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
     regulatory      2032..2037
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /note="hexamer: ATTAAA"
     regulatory      2059..2064
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
                     /note="hexamer: AATATA"
     polyA_site      2060
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
     polyA_site      2081
                     /gene="PHYKPL"
                     /gene_synonym="AGXT2L2; PHLU"
ORIGIN      
        1 agacggggca gcgctcgagt tcctgcgcgg gactgccaag gcacgaccac gggccggaag
       61 gctgccaggc ccagtgggca agcgaagaaa tgaaccaccg caacgcgggc gcttcggggc
      121 ggggccgagt gcgaacctga gccccaaatc ccgacccagg caggggcggg gcccggagcg
      181 gggccttgga ggcccagccc gcgcggcgac gtctccgcgt ggcgtcacgg caccgactga
      241 cggccaccca ccatggccgc agaccagcgc ccgaaggccg acacgctggc cctgaggcaa
      301 cggctcatca gctcttcctg cagactcttt tttcccgagg atcctgttaa gattgtccgg
      361 gcccaagggc agtacatgta cgatgaacag ggggcagaat acatcgattg catcagcaat
      421 gtggcgcacg ttgggcactg ccaccctctc gtggtccaag cagcacatga gcagaaccag
      481 gtgctcaaca ccaacagccg gtacctgcat gacaacatcg tggactatgc gcagaggctg
      541 tcagagaccc tgccggagca gctctgtgtg ttctatttcc tgaattctgg gtcagaagcc
      601 aatgacctgg ccctgaggct ggctcgccac tacacgggac accaggacgt ggtggtatta
      661 gatcatgcgt atcacggcca cctgagctcc ctgattgaca tcagtcccta caagttccgc
      721 aacctggatg gccagaagga gtgggtccac gtggcacctc tcccagacac ctaccggggc
      781 ccctaccggg aggaccaccc caacccagct atggcctatg ccaacgaggt gaaacgtgtg
      841 gtcagcagtg cacaggagaa gggcaggaag attgcagcct tcttcgctga gtctctgccc
      901 agtgtgggag ggcagatcat tccccctgct ggctacttct cccaagtggc agagcacatc
      961 cgcaaggccg gaggggtctt tgttgcagat gagatccagg ttggctttgg ccgggtaggc
     1021 aagcacttct gggccttcca gctccaggga aaagacttcg tccctgacat cgtcaccatg
     1081 ggcaagtcca ttggcaacgg ccaccctgtt gcctgcgtgg ccgcaaccca gcctgtggcg
     1141 agggcatttg aagccaccgg cgttgagtac ttcaacacgt ttgggggcag cccagtgtcc
     1201 tgcgctgtgg ggctggccgt cctgaatgtc ttggagaagg agcagctcca ggatcatgcc
     1261 accagtgtag gcagcttcct gatgcagctc ctcgggcagc aaaaaatcaa acatcccatc
     1321 gtcggggatg tcaggggtgt tgggctcttc attggtgtgg atctgatcaa agatgaggcc
     1381 acaaggacac cagcaactga agaggctgcc tacttggtat caaggctgaa ggagaactac
     1441 gttttgctga gcactgatgg ccctgggagg aacatcctga agtttaagcc cccaatgtgc
     1501 ttcagcctgg acaatgcacg gcaggtggtg gcaaagctgg atgccattct gactgacatg
     1561 gaagagaagg tgagaagttg tgaaacgctg aggctccagc cctaagccag ccctgctctg
     1621 cctaagtgta ctccagaaga aactcatctc atccaaatac acgctattga gaaggcgagc
     1681 ctgacctccc tcttacagat aaagtcagct ttcagaggct cagggtgggg gggcctgccc
     1741 gaggccataa tgctacccac cccctcctcc taaccactgg tctgttggaa taacccagat
     1801 gtctgcatcc cctcaagtca gtcaatttcc tttctgtcca ctgggggtgg aatggggtag
     1861 ggtgggatac tttaaagtgc tcctgcttaa ataaattaga ccagaccagt gtatttctaa
     1921 agaaaatcct gacatgcaca cccattaaaa atagtacatt ttacagtgtc ccagtcatac
     1981 ttttaattgg caaattaaaa taatgcaatc tgatatattc tatcctacta aattaaaaat
     2041 actgaatata accaactaaa tatacttact cctaagactc a
//
