LOCUS       NM_015167               1621 bp    mRNA    linear   PRI 07-APR-2024
DEFINITION  Homo sapiens jumonji domain containing 6, arginine demethylase and
            lysine hydroxylase (JMJD6), transcript variant 2, mRNA.
ACCESSION   NM_015167
VERSION     NM_015167.3
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 1621)
  AUTHORS   Pei,R., Zhao,L., Ding,Y., Su,Z., Li,D., Zhu,S., Xu,L., Zhao,W. and
            Zhou,W.
  TITLE     JMJD6-BRD4 complex stimulates lncRNA HOTAIR transcription by
            binding to the promoter region of HOTAIR and induces
            radioresistance in liver cancer stem cells
  JOURNAL   J Transl Med 21 (1), 752 (2023)
   PUBMED   37880710
  REMARK    GeneRIF: JMJD6-BRD4 complex stimulates lncRNA HOTAIR transcription
            by binding to the promoter region of HOTAIR and induces
            radioresistance in liver cancer stem cells.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1621)
  AUTHORS   Chen,S., Wang,M., Lu,T., Liu,Y., Hong,W., He,X., Cheng,Y., Liu,J.,
            Wei,Y. and Wei,X.
  TITLE     JMJD6 in tumor-associated macrophage regulates macrophage
            polarization and cancer progression via STAT3/IL-10 axis
  JOURNAL   Oncogene 42 (37), 2737-2750 (2023)
   PUBMED   37567973
  REMARK    GeneRIF: JMJD6 in tumor-associated macrophage regulates macrophage
            polarization and cancer progression via STAT3/IL-10 axis.
REFERENCE   3  (bases 1 to 1621)
  AUTHORS   Cioni,B., Ratti,S., Piva,A., Tripodi,I., Milani,M., Menichetti,F.,
            Langella,T., Botti,L., De Cecco,L., Chiodoni,C., Lecis,D. and
            Colombo,M.P.
  TITLE     JMJD6 Shapes a Pro-tumor Microenvironment via ANXA1-Dependent
            Macrophage Polarization in Breast Cancer
  JOURNAL   Mol Cancer Res 21 (6), 614-627 (2023)
   PUBMED   36867680
  REMARK    GeneRIF: JMJD6 Shapes a Pro-tumor Microenvironment via
            ANXA1-Dependent Macrophage Polarization in Breast Cancer.
REFERENCE   4  (bases 1 to 1621)
  AUTHORS   Merchant,J.P., Zhu,K., Henrion,M.Y.R., Zaidi,S.S.A., Lau,B.,
            Moein,S., Alamprese,M.L., Pearse,R.V. 2nd, Bennett,D.A.,
            Ertekin-Taner,N., Young-Pearse,T.L. and Chang,R.
  TITLE     Predictive network analysis identifies JMJD6 and other potential
            key drivers in Alzheimer's disease
  JOURNAL   Commun Biol 6 (1), 503 (2023)
   PUBMED   37188718
  REMARK    GeneRIF: Predictive network analysis identifies JMJD6 and other
            potential key drivers in Alzheimer's disease.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1621)
  AUTHORS   Klose,R.J., Kallin,E.M. and Zhang,Y.
  TITLE     JmjC-domain-containing proteins and histone demethylation
  JOURNAL   Nat Rev Genet 7 (9), 715-727 (2006)
   PUBMED   16983801
REFERENCE   6  (bases 1 to 1621)
  AUTHORS   Williamson,P. and Schlegel,R.A.
  TITLE     Hide and seek: the secret identity of the phosphatidylserine
            receptor
  JOURNAL   J Biol 3 (4), 14 (2004)
   PUBMED   15453906
  REMARK    Review article
REFERENCE   7  (bases 1 to 1621)
  AUTHORS   Chan,A., Seguin,R., Magnus,T., Papadimitriou,C., Toyka,K.V.,
            Antel,J.P. and Gold,R.
  TITLE     Phagocytosis of apoptotic inflammatory cells by microglia and its
            therapeutic implications: termination of CNS autoimmune
            inflammation and modulation by interferon-beta
  JOURNAL   Glia 43 (3), 231-242 (2003)
   PUBMED   12898702
REFERENCE   8  (bases 1 to 1621)
  AUTHORS   Ajmone-Cat,M.A., De Simone,R., Nicolini,A. and Minghetti,L.
  TITLE     Effects of phosphatidylserine on p38 mitogen activated protein
            kinase, cyclic AMP responding element binding protein and nuclear
            factor-kappaB activation in resting and activated microglial cells
  JOURNAL   J Neurochem 84 (2), 413-416 (2003)
   PUBMED   12559004
REFERENCE   9  (bases 1 to 1621)
  AUTHORS   Vandivier,R.W., Fadok,V.A., Hoffmann,P.R., Bratton,D.L.,
            Penvari,C., Brown,K.K., Brain,J.D., Accurso,F.J. and Henson,P.M.
  TITLE     Elastase-mediated phosphatidylserine receptor cleavage impairs
            apoptotic cell clearance in cystic fibrosis and bronchiectasis
  JOURNAL   J Clin Invest 109 (5), 661-670 (2002)
   PUBMED   11877474
  REMARK    GeneRIF: Elastase-mediated phosphatidylserine receptor cleavage
            impairs apoptotic cell clearance in cystic fibrosis and
            bronchiectasis.
REFERENCE   10 (bases 1 to 1621)
  AUTHORS   Fadok,V.A., Bratton,D.L., Rose,D.M., Pearson,A., Ezekewitz,R.A. and
            Henson,P.M.
  TITLE     A receptor for phosphatidylserine-specific clearance of apoptotic
            cells
  JOURNAL   Nature 405 (6782), 85-90 (2000)
   PUBMED   10811223
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DB451815.1, BC066654.1 and
            AA226560.1.
            
            On Feb 27, 2020 this sequence version replaced NM_015167.2.
            
            Summary: This gene encodes a nuclear protein with a JmjC domain.
            JmjC domain-containing proteins are predicted to function as
            protein hydroxylases or histone demethylases. This protein was
            first identified as a putative phosphatidylserine receptor involved
            in phagocytosis of apoptotic cells; however, subsequent studies
            have indicated that it does not directly function in the clearance
            of apoptotic cells, and questioned whether it is a true
            phosphatidylserine receptor. Multiple transcript variants encoding
            different isoforms have been found for this gene. [provided by
            RefSeq, Jul 2008].
            
            Transcript Variant: This variant (2) uses an alternate splice site
            in the 3' coding region and an alternate polyadenylation site,
            compared to variant 1. The resulting protein (isoform 2) has a
            shorter C-terminus, compared to isoform 1.
            
            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 :: BC047003.1, AK021780.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1966682, SAMEA2147920
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000397625.9/ ENSP00000380750.4
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-125               DB451815.1         194-318
            126-1615            BC066654.1         1-1490
            1616-1621           AA226560.1         21-26               c
FEATURES             Location/Qualifiers
     source          1..1621
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="17"
                     /map="17q25.1"
     gene            1..1621
                     /gene="JMJD6"
                     /gene_synonym="PSR; PTDSR; PTDSR1"
                     /note="jumonji domain containing 6, arginine demethylase
                     and lysine hydroxylase"
                     /db_xref="GeneID:23210"
                     /db_xref="HGNC:HGNC:19355"
                     /db_xref="MIM:604914"
     exon            1..260
                     /gene="JMJD6"
                     /gene_synonym="PSR; PTDSR; PTDSR1"
                     /inference="alignment:Splign:2.1.0"
     CDS             132..1343
                     /gene="JMJD6"
                     /gene_synonym="PSR; PTDSR; PTDSR1"
                     /EC_number="1.14.11.-"
                     /note="isoform 2 is encoded by transcript variant 2;
                     bifunctional arginine demethylase and lysyl-hydroxylase
                     JMJD6; jmjC domain-containing protein 6; histone arginine
                     demethylase JMJD6; peptide-lysine 5-dioxygenase JMJD6;
                     jumonji domain-containing protein 6; arginine demethylase
                     and lysine hydroxylase; phosphatidylserine receptor"
                     /codon_start=1
                     /product="bifunctional arginine demethylase and
                     lysyl-hydroxylase JMJD6 isoform 2"
                     /protein_id="NP_055982.2"
                     /db_xref="CCDS:CCDS42384.1"
                     /db_xref="GeneID:23210"
                     /db_xref="HGNC:HGNC:19355"
                     /db_xref="MIM:604914"
                     /translation="MNHKSKKRIREAKRSARPELKDSLDWTRHNYYESFSLSPAAVAD
                     NVERADALQLSVEEFVERYERPYKPVVLLNAQEGWSAQEKWTLERLKRKYRNQKFKCG
                     EDNDGYSVKMKMKYYIEYMESTRDDSPLYIFDSSYGEHPKRRKLLEDYKVPKFFTDDL
                     FQYAGEKRRPPYRWFVMGPPRSGTGIHIDPLGTSAWNALVQGHKRWCLFPTSTPRELI
                     KVTRDEGGNQQDEAITWFNVIYPRTQLPTWPPEFKPLEILQKPGETVFVPGGWWHVVL
                     NLDTTIAITQNFASSTNFPVVWHKTVRGRPKLSRKWYRILKQEHPELAVLADSVDLQE
                     STGIASDSSSDSSSSSSSSSSDSDSECESGSEGDGTVHRRKKRRTCSMVGNGDTTSQD
                     DCVSKERSSSR"
     exon            261..649
                     /gene="JMJD6"
                     /gene_synonym="PSR; PTDSR; PTDSR1"
                     /inference="alignment:Splign:2.1.0"
     exon            650..936
                     /gene="JMJD6"
                     /gene_synonym="PSR; PTDSR; PTDSR1"
                     /inference="alignment:Splign:2.1.0"
     exon            937..1072
                     /gene="JMJD6"
                     /gene_synonym="PSR; PTDSR; PTDSR1"
                     /inference="alignment:Splign:2.1.0"
     exon            1073..1211
                     /gene="JMJD6"
                     /gene_synonym="PSR; PTDSR; PTDSR1"
                     /inference="alignment:Splign:2.1.0"
     exon            1212..1621
                     /gene="JMJD6"
                     /gene_synonym="PSR; PTDSR; PTDSR1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1598..1603
                     /regulatory_class="polyA_signal_sequence"
                     /gene="JMJD6"
                     /gene_synonym="PSR; PTDSR; PTDSR1"
                     /note="hexamer: AATAAA"
     polyA_site      1621
                     /gene="JMJD6"
                     /gene_synonym="PSR; PTDSR; PTDSR1"
                     /note="major polyA site"
ORIGIN      
        1 aaaggcgccg ggactgagcg aagggcgttt gggtactgcc gtcgccgccg cccaggccgg
       61 ggaggggtgc gttagtgtca ggaagcgggc tgcgccgagg tcgtagcgga accagctggc
      121 gaccccgcag aatgaaccac aagagcaaga agcgcatccg cgaggccaag cggagtgcgc
      181 ggccggagct caaggactcg ctggattgga cccggcacaa ctactacgag agcttctcgc
      241 tgagcccggc ggccgtggcg gataacgtgg aaagggcaga tgctttacag ctgtctgtgg
      301 aagaatttgt ggagcggtat gaaagacctt acaagcccgt ggttttgttg aatgcgcaag
      361 agggctggtc tgcgcaggag aaatggactc tggagcgcct aaaaaggaaa tatcggaacc
      421 agaagttcaa gtgtggtgag gataacgatg gctactcagt gaagatgaag atgaaatact
      481 acatcgagta catggagagc actcgagatg atagtcccct ttacatcttt gacagcagct
      541 atggtgaaca ccctaaaaga aggaaacttt tggaagacta caaggtgcca aagtttttca
      601 ctgatgacct tttccagtat gctggggaga agcgcaggcc cccttacagg tggtttgtga
      661 tggggccacc acgctccgga actgggattc acatcgaccc tctgggaacc agtgcctgga
      721 atgccttagt tcagggccac aagcgctggt gcctgtttcc taccagcact cccagggaac
      781 tcatcaaagt gacccgagac gaaggaggga accagcaaga cgaagctatt acctggttta
      841 atgttattta tccccggaca cagcttccaa cctggccacc tgaattcaaa cccctggaaa
      901 tcttacaaaa accaggagag actgtctttg taccaggagg ctggtggcat gttgtcctca
      961 atctcgacac tactatcgcc atcacccaaa attttgccag cagcaccaac ttccctgtgg
     1021 tatggcacaa gacggtaaga gggagaccaa agttatcaag gaaatggtat aggattttga
     1081 agcaagagca ccccgagttg gcagtcctcg cagactcggt tgaccttcag gagtccacag
     1141 ggatagcttc cgacagctcc agcgactctt ccagctcctc cagctccagt tcgtcagact
     1201 ccgactcaga gtgcgagtct ggatccgagg gcgatgggac agtgcaccgc aggaagaaga
     1261 ggaggacgtg cagcatggtg ggaaacgggg acaccacctc ccaggacgac tgtgtcagca
     1321 aagagcgcag ctcctccagg tgacccagca aggctgttgt ctgtatggaa ggacacgctc
     1381 gcggcaaggg cagggcctgg ggagggtggc ctgtccagtc ctgcagacaa ggggaggcct
     1441 gacagagccc aagaatgagg acaccctcgg cacgggaacc cattcactta gcgtttgctc
     1501 cagtagcttt ccctctgcta ccaatgcaga taaacgcggc ttgttttact caggcaagag
     1561 aatgtgaata gtgccaagaa aatcctttac attatttaat aaaaattgaa tccattttct
     1621 a
//
