LOCUS       NM_033398               1668 bp    mRNA    linear   ROD 02-MAY-2024
DEFINITION  Mus musculus jumonji domain containing 6 (Jmjd6), transcript
            variant 2, mRNA.
ACCESSION   NM_033398
VERSION     NM_033398.3
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 1668)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   2  (bases 1 to 1668)
  AUTHORS   Zhang,F., Zhao,X., Jiang,R., Wang,Y., Wang,X., Gu,Y., Xu,L., Ye,J.,
            Chen,C.D., Guo,S., Zhang,D. and Zhao,D.
  TITLE     Identification of Jmjd3 as an Essential Epigenetic Regulator of Hox
            Gene Temporal Collinear Activation for Body Axial Patterning in
            Mice
  JOURNAL   Front Cell Dev Biol 9, 642931 (2021)
   PUBMED   34368113
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1668)
  AUTHORS   Arva,A., Kasu,Y.A.T., Duncan,J., Alkhatatbeh,M.A. and Brower,C.S.
  TITLE     The Ligand of Ate1 is intrinsically disordered and participates in
            nucleolar phase separation regulated by Jumonji Domain Containing 6
  JOURNAL   Proc Natl Acad Sci U S A 118 (1) (2021)
   PUBMED   33443146
REFERENCE   4  (bases 1 to 1668)
  AUTHORS   Lee,S., Liu,H., Hill,R., Chen,C., Hong,X., Crawford,F.,
            Kingsley,M., Zhang,Q., Liu,X., Chen,Z., Lengeling,A., Bernt,K.M.,
            Marrack,P., Kappler,J., Zhou,Q., Li,C.Y., Xue,Y., Hansen,K. and
            Zhang,G.
  TITLE     JMJD6 cleaves MePCE to release positive transcription elongation
            factor b (P-TEFb) in higher eukaryotes
  JOURNAL   Elife 9, e53930 (2020)
   PUBMED   32048991
  REMARK    GeneRIF: JMJD6 cleaves MePCE to release positive transcription
            elongation factor b (P-TEFb) in higher eukaryotes.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1668)
  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 1668)
  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 1668)
  AUTHORS   Li,M.O., Sarkisian,M.R., Mehal,W.Z., Rakic,P. and Flavell,R.A.
  TITLE     Phosphatidylserine receptor is required for clearance of apoptotic
            cells
  JOURNAL   Science 302 (5650), 1560-1563 (2003)
   PUBMED   14645847
  REMARK    GeneRIF: data demonstrate a critical role for PSR in early stages
            of mammalian organogenesis and suggest that this receptor may be
            involved in respiratory distress syndromes and congenital brain
            malformations
REFERENCE   8  (bases 1 to 1668)
  AUTHORS   Stryke,D., Kawamoto,M., Huang,C.C., Johns,S.J., King,L.A.,
            Harper,C.A., Meng,E.C., Lee,R.E., Yee,A., L'Italien,L.,
            Chuang,P.T., Young,S.G., Skarnes,W.C., Babbitt,P.C. and Ferrin,T.E.
  TITLE     BayGenomics: a resource of insertional mutations in mouse embryonic
            stem cells
  JOURNAL   Nucleic Acids Res 31 (1), 278-281 (2003)
   PUBMED   12520002
REFERENCE   9  (bases 1 to 1668)
  AUTHORS   Todt,J.C., Hu,B., Punturieri,A., Sonstein,J., Polak,T. and
            Curtis,J.L.
  TITLE     Activation of protein kinase C beta II by the stereo-specific
            phosphatidylserine receptor is required for phagocytosis of
            apoptotic thymocytes by resident murine tissue macrophages
  JOURNAL   J Biol Chem 277 (39), 35906-35914 (2002)
   PUBMED   12114511
  REMARK    GeneRIF: protein kinase C beta activation is dependent upon
            phosphatidylserine receptor action
REFERENCE   10 (bases 1 to 1668)
  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     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL645542.13, CX210791.1 and BP769727.1.
            
            On May 17, 2018 this sequence version replaced NM_033398.2.
            
            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
            functions in differentiation of multiple tissues during
            development, and in anti-inflammatory cytokine signaling. It was
            first identified as a putative phosphatidylserine receptor involved
            in phagocytosis of apoptotic cells; however, subsequent studies
            have indicated that this protein does not directly function in the
            clearance of apoptotic cells, and questioned whether it is a true
            phosphatidylserine receptor. [provided by RefSeq, Jul 2008].
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: BC056629.1, AF304118.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849380, SAMN00849382
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-294               AL645542.13        125353-125646       c
            295-1093            CX210791.1         1-799
            1094-1668           BP769727.1         21-595              c
FEATURES             Location/Qualifiers
     source          1..1668
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="11"
                     /map="11 81.49 cM"
     gene            1..1668
                     /gene="Jmjd6"
                     /gene_synonym="5730436I23Rik; D11Ertd195e; mKIAA0585; PSR;
                     PtdSerR; Ptdsr"
                     /note="jumonji domain containing 6"
                     /db_xref="GeneID:107817"
                     /db_xref="MGI:MGI:1858910"
     exon            1..385
                     /gene="Jmjd6"
                     /gene_synonym="5730436I23Rik; D11Ertd195e; mKIAA0585; PSR;
                     PtdSerR; Ptdsr"
                     /inference="alignment:Splign:2.1.0"
     CDS             257..1468
                     /gene="Jmjd6"
                     /gene_synonym="5730436I23Rik; D11Ertd195e; mKIAA0585; PSR;
                     PtdSerR; Ptdsr"
                     /EC_number="1.14.11.-"
                     /note="isoform 2 is encoded by transcript variant 2;
                     phosphatidylserine receptor; bifunctional arginine
                     demethylase and lysyl-hydroxylase JMJD6; apoptotic cell
                     clearance receptor PtdSerR; jmjC domain-containing protein
                     6; histone arginine demethylase JMJD6; peptide-lysine
                     5-dioxygenase JMJD6; jumonji domain-containing protein 6"
                     /codon_start=1
                     /product="bifunctional arginine demethylase and
                     lysyl-hydroxylase JMJD6 isoform 2"
                     /protein_id="NP_203971.2"
                     /db_xref="CCDS:CCDS25678.1"
                     /db_xref="GeneID:107817"
                     /db_xref="MGI:MGI:1858910"
                     /translation="MNHKSKKRIREAKRSARPELKDSLDWTRHNYYESYPLNPAAVPD
                     NVERADALQLSVKEFVERYERPYKPVVLLNAQEGWSAQEKWTLERLKRKYRNQKFKCG
                     EDNDGYSVKMKMKYYIEYMESTRDDSPLYIFDSSYGEHPKRRKLLEDYKVPKFFTDDL
                     FQYAGEKRRPPYRWFVMGPPRSGTGIHIDPLGTSAWNALVQGHKRWCLFPTNTPRELI
                     KVTREEGGNQQDEAITWFNVIYPRTQLPTWPPEFKPLEILQKPGETVFVPGGWWHVVL
                     NLDTTIAITQNFASSTNFPVVWHKTVRGRPKLSRKWYRILKQEHPELAVLADAVDLQE
                     STGIASDSSSDSSSSSSSSSSDSDSECESGSEGDGTTHRRKKRRTCSMVGNGDTTSQD
                     DCVSKERSSSR"
     exon            386..774
                     /gene="Jmjd6"
                     /gene_synonym="5730436I23Rik; D11Ertd195e; mKIAA0585; PSR;
                     PtdSerR; Ptdsr"
                     /inference="alignment:Splign:2.1.0"
     exon            775..1061
                     /gene="Jmjd6"
                     /gene_synonym="5730436I23Rik; D11Ertd195e; mKIAA0585; PSR;
                     PtdSerR; Ptdsr"
                     /inference="alignment:Splign:2.1.0"
     exon            1062..1197
                     /gene="Jmjd6"
                     /gene_synonym="5730436I23Rik; D11Ertd195e; mKIAA0585; PSR;
                     PtdSerR; Ptdsr"
                     /inference="alignment:Splign:2.1.0"
     exon            1198..1336
                     /gene="Jmjd6"
                     /gene_synonym="5730436I23Rik; D11Ertd195e; mKIAA0585; PSR;
                     PtdSerR; Ptdsr"
                     /inference="alignment:Splign:2.1.0"
     exon            1337..1668
                     /gene="Jmjd6"
                     /gene_synonym="5730436I23Rik; D11Ertd195e; mKIAA0585; PSR;
                     PtdSerR; Ptdsr"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1648..1653
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Jmjd6"
                     /gene_synonym="5730436I23Rik; D11Ertd195e; mKIAA0585; PSR;
                     PtdSerR; Ptdsr"
                     /note="hexamer: AATAAA"
     polyA_site      1668
                     /gene="Jmjd6"
                     /gene_synonym="5730436I23Rik; D11Ertd195e; mKIAA0585; PSR;
                     PtdSerR; Ptdsr"
                     /note="major polyA site"
ORIGIN      
        1 ggcgggtctg gcaggtcgct gaggccaatg gcggaccgca tgaggcggtg gggcggggag
       61 gaaggccgct gttcgcccaa cccaaagctc cggtggcggc tgaggagtga atcttctgga
      121 aggcgacttt aaaggcgccg ggccggagcg aagggcgtct cggggccgcg ccagccaggg
      181 agggagggcg cgtttggtgg caggaaacgc gagccgcgtc ggggtcgggg cggaaccgga
      241 cggcgagcgg ctcacgatga accacaagag caagaagcgc atccgcgagg ccaagcgaag
      301 tgcgcggccg gagctcaagg actcgctcga ctggacccgg cacaactact acgagagcta
      361 cccgctgaac cccgcggccg tgccggataa cgtggagaga gctgatgcct tacagctgtc
      421 ggtgaaagag ttcgtggagc gctacgagag gccttacaag cccgtggttc tgctcaatgc
      481 acaagagggc tggtccgcac aggagaaatg gactctggag cgcctcaaaa ggaaataccg
      541 gaaccagaag ttcaagtgcg gcgaggataa tgacggctac tcggttaaga tgaagatgaa
      601 gtactacatc gagtacatgg agagcacccg cgatgacagt cccctttaca tcttcgatag
      661 cagctatggc gaacacccca aaagaaggaa acttttggaa gactacaagg tgcccaagtt
      721 tttcacagat gatcttttcc aatacgcggg ggagaaacgc agaccccctt acaggtggtt
      781 tgtgatgggg ccaccgcgtt ctggaactgg gattcacatc gaccctctgg ggaccagtgc
      841 ctggaatgcc ttagttcagg gtcacaagcg gtggtgcctc ttcccaacaa acacacccag
      901 agaactcatc aaggtgaccc gagaagaagg agggaaccaa caggatgaag caattacctg
      961 gtttaatgtc atctatcccc ggacacagct tccaacctgg ccacctgaat tcaaacccct
     1021 ggagatatta cagaaaccag gagaaactgt ctttgtacca gggggctggt ggcatgttgt
     1081 cctcaacctt gacaccacca ttgccatcac ccagaacttt gccagcagca ccaacttccc
     1141 tgttgtgtgg cacaagacgg taagagggag accaaagtta tcaaggaagt ggtataggat
     1201 cttgaaacag gagcaccctg agctggcagt cctggccgac gcagttgacc tccaggagtc
     1261 cacaggcatt gcctctgaca gctccagcga ctcttctagc tcctctagtt ccagctcgtc
     1321 agactcggac tcagagtgtg aatctgggtc agaaggtgat gggacgacac accgcaggaa
     1381 gaagaggaga acctgcagca tggtgggaaa tggggacact acctcccagg atgactgtgt
     1441 gagcaaagag cgcagctcct ccaggtgacc acatgtggcc gctgtctgtg ccaggatatg
     1501 ctcgcagcca ggcttggggg gctgacaccc agagaacaag gacactcaga tgggagttgg
     1561 tagtacgtgg tacagtggct tttctctgtg gtcatgtctt aggggcaaag gcgtgtggat
     1621 ggtgccaatg aaacccttta cctatttaat aaaaacggat acatttta
//
