LOCUS       NM_001013619            4197 bp    mRNA    linear   PRI 08-JUN-2024
DEFINITION  Homo sapiens hydroxylysine kinase (HYKK), transcript variant 1,
            mRNA.
ACCESSION   NM_001013619 XM_058719
VERSION     NM_001013619.4
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 4197)
  AUTHORS   Sun,H., Pan,Y., He,B., Deng,Q., Ying,H., Chen,J., Liu,X. and
            Wang,S.
  TITLE     Different effects of the three polymorphisms on 15q25.1 onlung
            cancer risk: Evidence from published literatures
  JOURNAL   J Cancer Res Ther 12 (1), 12-19 (2016)
   PUBMED   27072204
  REMARK    GeneRIF: CHRNA3 rs1051730 (G > A) and AGPHD1 rs8034191 (A > G) were
            more susceptible to lung cancers than noncarriers.
REFERENCE   2  (bases 1 to 4197)
  AUTHORS   Zhang,L., Jin,T.B., Gao,Y., Wang,H.J., Yang,H., Feng,T., Chen,C.,
            Kang,L.L. and Chen,C.
  TITLE     Meta-analysis of the association between the rs8034191 polymorphism
            in AGPHD1 and lung cancer risk
  JOURNAL   Asian Pac J Cancer Prev 16 (7), 2713-2717 (2015)
   PUBMED   25854352
  REMARK    GeneRIF: The association between AGPHD1 single nucleotide
            polymorphism rs8034191 and lung cancer risk was significant using
            multiple genetic models, suggesting that AGPHD1 single nucleotide
            polymorphism rs8034191 is a risk factor for lung cancer.
REFERENCE   3  (bases 1 to 4197)
  AUTHORS   Wang,H. and Liu,Z.D.
  TITLE     Genetic association between AGPHD1 variant and lung cancer risk
  JOURNAL   Cell Biochem Biophys 70 (3), 1963-1968 (2014)
   PUBMED   25074529
  REMARK    GeneRIF: The variant rs8034191 in the AGPHD1 gene may not modify
            the genetic risk of lung cancer in Asian populations.
REFERENCE   4  (bases 1 to 4197)
  AUTHORS   Castaldi,P.J., Cho,M.H., San Jose Estepar,R., McDonald,M.L.,
            Laird,N., Beaty,T.H., Washko,G., Crapo,J.D. and Silverman,E.K.
  CONSRTM   COPDGene Investigators
  TITLE     Genome-wide association identifies regulatory Loci associated with
            distinct local histogram emphysema patterns
  JOURNAL   Am J Respir Crit Care Med 190 (4), 399-409 (2014)
   PUBMED   25006744
REFERENCE   5  (bases 1 to 4197)
  AUTHORS   Wilk,J.B., Shrine,N.R., Loehr,L.R., Zhao,J.H., Manichaikul,A.,
            Lopez,L.M., Smith,A.V., Heckbert,S.R., Smolonska,J., Tang,W.,
            Loth,D.W., Curjuric,I., Hui,J., Cho,M.H., Latourelle,J.C.,
            Henry,A.P., Aldrich,M., Bakke,P., Beaty,T.H., Bentley,A.R.,
            Borecki,I.B., Brusselle,G.G., Burkart,K.M., Chen,T.H., Couper,D.,
            Crapo,J.D., Davies,G., Dupuis,J., Franceschini,N., Gulsvik,A.,
            Hancock,D.B., Harris,T.B., Hofman,A., Imboden,M., James,A.L.,
            Khaw,K.T., Lahousse,L., Launer,L.J., Litonjua,A., Liu,Y.,
            Lohman,K.K., Lomas,D.A., Lumley,T., Marciante,K.D., McArdle,W.L.,
            Meibohm,B., Morrison,A.C., Musk,A.W., Myers,R.H., North,K.E.,
            Postma,D.S., Psaty,B.M., Rich,S.S., Rivadeneira,F., Rochat,T.,
            Rotter,J.I., Soler Artigas,M., Starr,J.M., Uitterlinden,A.G.,
            Wareham,N.J., Wijmenga,C., Zanen,P., Province,M.A., Silverman,E.K.,
            Deary,I.J., Palmer,L.J., Cassano,P.A., Gudnason,V., Barr,R.G.,
            Loos,R.J., Strachan,D.P., London,S.J., Boezen,H.M.,
            Probst-Hensch,N., Gharib,S.A., Hall,I.P., O'Connor,G.T., Tobin,M.D.
            and Stricker,B.H.
  TITLE     Genome-wide association studies identify CHRNA5/3 and HTR4 in the
            development of airflow obstruction
  JOURNAL   Am J Respir Crit Care Med 186 (7), 622-632 (2012)
   PUBMED   22837378
REFERENCE   6  (bases 1 to 4197)
  AUTHORS   Pillai,S.G., Ge,D., Zhu,G., Kong,X., Shianna,K.V., Need,A.C.,
            Feng,S., Hersh,C.P., Bakke,P., Gulsvik,A., Ruppert,A., Lodrup
            Carlsen,K.C., Roses,A., Anderson,W., Rennard,S.I., Lomas,D.A.,
            Silverman,E.K. and Goldstein,D.B.
  CONSRTM   ICGN Investigators
  TITLE     A genome-wide association study in chronic obstructive pulmonary
            disease (COPD): identification of two major susceptibility loci
  JOURNAL   PLoS Genet 5 (3), e1000421 (2009)
   PUBMED   19300482
REFERENCE   7  (bases 1 to 4197)
  AUTHORS   Liu,P., Vikis,H.G., Wang,D., Lu,Y., Wang,Y., Schwartz,A.G.,
            Pinney,S.M., Yang,P., de Andrade,M., Petersen,G.M., Wiest,J.S.,
            Fain,P.R., Gazdar,A., Gaba,C., Rothschild,H., Mandal,D., Coons,T.,
            Lee,J., Kupert,E., Seminara,D., Minna,J., Bailey-Wilson,J.E.,
            Wu,X., Spitz,M.R., Eisen,T., Houlston,R.S., Amos,C.I.,
            Anderson,M.W. and You,M.
  TITLE     Familial aggregation of common sequence variants on 15q24-25.1 in
            lung cancer
  JOURNAL   J Natl Cancer Inst 100 (18), 1326-1330 (2008)
   PUBMED   18780872
REFERENCE   8  (bases 1 to 4197)
  AUTHORS   Amos,C.I., Wu,X., Broderick,P., Gorlov,I.P., Gu,J., Eisen,T.,
            Dong,Q., Zhang,Q., Gu,X., Vijayakrishnan,J., Sullivan,K.,
            Matakidou,A., Wang,Y., Mills,G., Doheny,K., Tsai,Y.Y., Chen,W.V.,
            Shete,S., Spitz,M.R. and Houlston,R.S.
  TITLE     Genome-wide association scan of tag SNPs identifies a
            susceptibility locus for lung cancer at 15q25.1
  JOURNAL   Nat Genet 40 (5), 616-622 (2008)
   PUBMED   18385676
REFERENCE   9  (bases 1 to 4197)
  AUTHORS   Hung,R.J., McKay,J.D., Gaborieau,V., Boffetta,P., Hashibe,M.,
            Zaridze,D., Mukeria,A., Szeszenia-Dabrowska,N., Lissowska,J.,
            Rudnai,P., Fabianova,E., Mates,D., Bencko,V., Foretova,L.,
            Janout,V., Chen,C., Goodman,G., Field,J.K., Liloglou,T.,
            Xinarianos,G., Cassidy,A., McLaughlin,J., Liu,G., Narod,S.,
            Krokan,H.E., Skorpen,F., Elvestad,M.B., Hveem,K., Vatten,L.,
            Linseisen,J., Clavel-Chapelon,F., Vineis,P.,
            Bueno-de-Mesquita,H.B., Lund,E., Martinez,C., Bingham,S.,
            Rasmuson,T., Hainaut,P., Riboli,E., Ahrens,W., Benhamou,S.,
            Lagiou,P., Trichopoulos,D., Holcatova,I., Merletti,F.,
            Kjaerheim,K., Agudo,A., Macfarlane,G., Talamini,R., Simonato,L.,
            Lowry,R., Conway,D.I., Znaor,A., Healy,C., Zelenika,D., Boland,A.,
            Delepine,M., Foglio,M., Lechner,D., Matsuda,F., Blanche,H., Gut,I.,
            Heath,S., Lathrop,M. and Brennan,P.
  TITLE     A susceptibility locus for lung cancer maps to nicotinic
            acetylcholine receptor subunit genes on 15q25
  JOURNAL   Nature 452 (7187), 633-637 (2008)
   PUBMED   18385738
REFERENCE   10 (bases 1 to 4197)
  AUTHORS   Oh,J.H., Yang,J.O., Hahn,Y., Kim,M.R., Byun,S.S., Jeon,Y.J.,
            Kim,J.M., Song,K.S., Noh,S.M., Kim,S., Yoo,H.S., Kim,Y.S. and
            Kim,N.S.
  TITLE     Transcriptome analysis of human gastric cancer
  JOURNAL   Mamm Genome 16 (12), 942-954 (2005)
   PUBMED   16341674
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BM045979.1, DN831396.1, AC027228.16 and AW327432.1.
            
            On Nov 23, 2018 this sequence version replaced NM_001013619.3.
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the longer isoform (1).
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data because no single transcript was available
            for the full length of the gene. The extent of this transcript is
            supported by orthologous mouse and Xenopus data.
            
            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 :: SRR1803617.154262.1,
                                           SRR1660805.162945.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1968189
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000388988.9/ ENSP00000373640.4
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-295               BM045979.1         15-309
            296-727             DN831396.1         50-481              c
            728-730             AC027228.16        69482-69484         c
            731-776             DN831396.1         1-46                c
            777-4016            AC027228.16        60550-63789         c
            4017-4197           AW327432.1         72-252
FEATURES             Location/Qualifiers
     source          1..4197
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="15"
                     /map="15q25.1"
     gene            1..4197
                     /gene="HYKK"
                     /gene_synonym="AGPHD1"
                     /note="hydroxylysine kinase"
                     /db_xref="GeneID:123688"
                     /db_xref="HGNC:HGNC:34403"
                     /db_xref="MIM:614681"
     exon            1..95
                     /gene="HYKK"
                     /gene_synonym="AGPHD1"
                     /inference="alignment:Splign:2.1.0"
     exon            96..437
                     /gene="HYKK"
                     /gene_synonym="AGPHD1"
                     /inference="alignment:Splign:2.1.0"
     CDS             101..1222
                     /gene="HYKK"
                     /gene_synonym="AGPHD1"
                     /EC_number="2.7.1.81"
                     /note="isoform 1 is encoded by transcript variant 1;
                     aminoglycoside phosphotransferase domain-containing
                     protein 1; 5-hydroxylysine kinase; 5-hydroxy-L-lysine
                     kinase"
                     /codon_start=1
                     /product="hydroxylysine kinase isoform 1"
                     /protein_id="NP_001013641.2"
                     /db_xref="CCDS:CCDS42063.1"
                     /db_xref="GeneID:123688"
                     /db_xref="HGNC:HGNC:34403"
                     /db_xref="MIM:614681"
                     /translation="MSSGNYQQSEALSKPTFSEEQASALVESVFGLKVSKVRPLPSYD
                     DQNFHVYVSKTKDGPTEYVLKISNTKASKNPDLIEVQNHIIMFLKAAGFPTASVCHTK
                     GDNTASLVSVDSGSEIKSYLVRLLTYLPGRPIAELPVSPQLLYEIGKLAAKLDKTLQR
                     FHHPKLSSLHRENFIWNLKNVPLLEKYLYALGQNRNREIVEHVIHLFKEEVMTKLSHF
                     RECINHGDLNDHNILIESSKSASGNAEYQVSGILDFGDMSYGYYVFEVAITIMYMMIE
                     SKSPIQVGGHVLAGFESITPLTAVEKGALFLLVCSRFCQSLVMAAYSCQLYPENKDYL
                     MVTAKTGWKHLQQMFDMGQKAVEEIWFETAKSYESGISM"
     exon            438..577
                     /gene="HYKK"
                     /gene_synonym="AGPHD1"
                     /inference="alignment:Splign:2.1.0"
     exon            578..761
                     /gene="HYKK"
                     /gene_synonym="AGPHD1"
                     /inference="alignment:Splign:2.1.0"
     exon            762..4197
                     /gene="HYKK"
                     /gene_synonym="AGPHD1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4178..4183
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HYKK"
                     /gene_synonym="AGPHD1"
                     /note="hexamer: ATTACA"
     polyA_site      4197
                     /gene="HYKK"
                     /gene_synonym="AGPHD1"
                     /note="major polyA site"
ORIGIN      
        1 cccctgctct acctcctagc gccggtgcgc ggccgaggcc gcactacctg tctgcgggaa
       61 agcgggatcc accccaggac gtcgggtcgc tgccgacata atgtcaagtg gaaactatca
      121 gcagtcagag gctcttagca aacccacttt cagtgaggaa caagcctctg cgttagtgga
      181 gtcagtgttt gggttgaaag tttccaaggt ccggccactt cctagctatg atgaccaaaa
      241 ctttcatgtc tacgtttcaa aaaccaaaga tggcccaact gaatatgtcc tcaaaataag
      301 caacaccaag gctagcaaaa atccagacct gattgaagtg cagaatcaca tcatcatgtt
      361 tctgaaagcc gctggatttc caacagcctc tgtgtgtcac actaaaggag acaacacagc
      421 ttctctcgtg tctgtagata gtggctctga aatcaaaagc tacttggtga ggctgctgac
      481 ttacctccca ggaagaccca tcgctgagct tcccgtcagc ccccagctat tgtatgaaat
      541 tggaaaacta gctgccaaat tggataagac actgcagaga ttccatcacc caaagttaag
      601 tagtcttcat cgggagaact tcatctggaa tctgaaaaat gttcctcttc tggagaaata
      661 cctgtatgcc ctgggccaga atcgaaaccg agagattgtt gagcatgtca ttcatctgtt
      721 caaggaggaa gtaatgacca aattaagtca ttttcgagaa tgtatcaatc acggagatct
      781 taatgaccat aatattttaa tagagtccag caagtcagcc tctggaaatg ctgaatatca
      841 agtgtctggg attttagact ttggtgacat gagctatggc tactatgtgt ttgaagtggc
      901 aattaccatc atgtacatga tgattgagag caagagtcct atacaagtag gaggccatgt
      961 ccttgcaggg tttgaaagca tcaccccact gacagctgta gagaagggtg ctttgttttt
     1021 acttgtatgc agtcgttttt gtcagtcact tgtcatggct gcatactctt gccagctata
     1081 cccagagaac aaagactatc tcatggttac tgcaaaaacc gggtggaaac acttacagca
     1141 aatgtttgac atgggtcaga aagctgtaga agaaatctgg tttgaaactg ccaaatccta
     1201 tgaatctggg atctccatgt gactgagatc tccatgtgac tcaaagttca ctttaacttg
     1261 ggtaattaaa ataggaccca gtcaaatttt aggaaggatt ttcctgcata gttaaaaatc
     1321 aactgatgga atggatcaat tctgaatatg acagagcaca tgaaatccct aaggtcttca
     1381 agcaatctcg tgacaatttt ttaaaattca caaaagtacc acaagcaagc atatttttct
     1441 gtgagtctta cttgccatat ctataaaaca catataatga taccattttg aagcagataa
     1501 tctcacaaga tctattcctg ccctgagatt aatgactatt ttaattttaa aaataatata
     1561 tacatataga tatattgaca tattttaaat atctggacat aacatactga cctagataac
     1621 atactaccag ttctatgaaa cctcctctga tctctccttt ctctagaatc ccagtgcatt
     1681 gtgtcttttt catggcccat cactttgtat aatggatcgt ggttgtgcag tcatcttgcc
     1741 tgagagctac tgagggcgga gaccatgtaa aacttatttt tgtctcctca gcccttcttt
     1801 tttttttttt tttttttttg agacggagtc tcgctctgtc gcccaggctg gagtgcagtg
     1861 gcacgatctc ggctcattgc aagctccgct tctcgagttc acgccattct cctgcctcag
     1921 cctcctgagt agctgggact acaggcgccc accaccacgc ccggctaatt ttttttgtat
     1981 ttttagtaga gacagggttt caccgtgtta gccagaatgg tctcgatctc ctgaccttgt
     2041 gatccacccg cctcgatctc ccaaagtgct gggattacag gcatgagtca ccgtgcccgg
     2101 cctcctcatc ccttcttatc acacctgcta ttatagtgcc tttcctacag agaggtcttt
     2161 aaaaatattt gaaaataaat gcgtgctaga agaagggatg gagaaggcac acactaagat
     2221 gctttaggag aaagcattga cagcattctt ggagaaaaaa ttttaacttg tctgagaggg
     2281 tggttgaaac tggaactcca gagatagatg ctggaagacc ctgggaactg caaggaagca
     2341 aataatgaca tccaggcaag gccactaacc cctgagctac ttaaatataa tggttccttt
     2401 cagactgata ccaggaacct ccttaagcat ataagcatat attttttaat tctctataat
     2461 ctgtttcttt ttggatgact atgaagtaga ttgggtagac tgaagctcac tgtattcttg
     2521 gctgacggta tcccactgtg tttccttcac tggtttctcg tcatgtctcc tttagtatga
     2581 tttagtaaat ggctgtttac tattcttatg atttcaacta ttcattgtct acagatgact
     2641 caagtctaga accctggcca ttcaaatact caatagttat ctttctatat atatgaacag
     2701 gcattgatcc tatctccatc tttctgtcta cctacctagt cttcccaaac tagatatttc
     2761 tctaaattgt cttatatggt tcatttttca cttctttgtc cctcaatttc atttcatttc
     2821 tttttctttt cttttctttt cttttttttt ttttttggtg gtggggcggc agggacaggg
     2881 tttcactgca gcctcaacct cctaggctca ggtgatcctc ccacctcagc ctccctagta
     2941 gctgggactt caggcatgtg ccaccatgtc tggctaattc tttaattttt tgtagagatt
     3001 ggggtaatac ctatctcata gaattaatag agttcattgt gaagatttca taagagaaca
     3061 gtgccaagtg cttaacacag tgtgtggcac atagttagga ctcagtaact atttactcaa
     3121 taaatgaacc atattccagg ttacccaaac tcaaaatatt ggagtaattt tttgcttgcc
     3181 tctcttatat tcagtgagcc ctactggttt ttagaattgt agaattttag gaatctctgt
     3241 ctttactgga ttttttgttt gttttgggct tttttgtttg tttgtttgag atagggtctc
     3301 actccgtcac cgacgctgga gtgcagtggt gtgatcacag ctcactgcaa cctctacctc
     3361 ctgggctcaa gcaatcctcc cacctcagcc tcctgagtag ctgggactac aggcatgtgc
     3421 caccatgccc aactaattta ttttattttg tagagatagg gtctcactat gttgcccagg
     3481 ctggtctcaa acccctggac tcaagcaatc ctcctgcctt ggcctcccta aatgctagga
     3541 ttataggcgt gagctatcat acccagcctg tgttgttttt taacaatata taataaaagc
     3601 caacatttat tcagcactga agtattttat acacattagc tcacttaatt tttacaacaa
     3661 acctgtgtgg gaagtactgt tataattaat cgtcattttc agataagaaa atagcagctg
     3721 aaaaagtaaa aataatttcc tcaaagacag ccagggctta aatcaggcct ttctgatgta
     3781 gaccatgctc ttcactacca cagagttcca tgctactttc tctccctctc cctcctctcc
     3841 tgtccctgct acacacacac acacacacac acacacacac acatgcacac tcactcacac
     3901 acactaggag gaacaaatga gatcattcac atgaaagcac ttatgtttct gaaatttaag
     3961 ggactgtggt ttttatctag gttgacctct caagctaaaa actgggaacc agaataatgg
     4021 actgaaactt gggtttcact tccagaccag tgttgatcct ctgaattgat gaaactgtat
     4081 agatttccct cttgattgcc cctgctaaca tggatttcct ttcactcaat tcctaatgca
     4141 aatattgctg accactgttt agatgtttac atgctgcatt acattgatat tttacta
//
