LOCUS       NM_025236               2084 bp    mRNA    linear   PRI 20-FEB-2025
DEFINITION  Homo sapiens ring finger protein 39 (RNF39), transcript variant 1,
            mRNA.
ACCESSION   NM_025236
VERSION     NM_025236.4
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 2084)
  AUTHORS   Wang,W., Li,Q., Jia,M., Wang,C., Liang,W., Liu,Y., Kong,H., Qin,Y.,
            Zhao,C., Zhao,W. and Song,H.
  TITLE     RNF39 facilitates antiviral immune responses by promoting
            K63-linked ubiquitination of STING
  JOURNAL   Int Immunopharmacol 142 (Pt A), 113091 (2024)
   PUBMED   39255680
REFERENCE   2  (bases 1 to 2084)
  AUTHORS   Wang,W., Jia,M., Zhao,C., Yu,Z., Song,H., Qin,Y. and Zhao,W.
  TITLE     RNF39 mediates K48-linked ubiquitination of DDX3X and inhibits
            RLR-dependent antiviral immunity
  JOURNAL   Sci Adv 7 (10) (2021)
   PUBMED   33674311
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2084)
  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   4  (bases 1 to 2084)
  AUTHORS   Maltby,V.E., Lea,R.A., Sanders,K.A., White,N., Benton,M.C.,
            Scott,R.J. and Lechner-Scott,J.
  TITLE     Differential methylation at MHC in CD4+ T cells is associated with
            multiple sclerosis independently of HLA-DRB1
  JOURNAL   Clin Epigenetics 9, 71 (2017)
   PUBMED   28729889
  REMARK    GeneRIF: The findings provide evidence that hypermethylation in an
            independent MHC locus, RNF39, is also associated with
            relapsing-remitting multiple sclerosis.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2084)
  AUTHORS   Morin,A., Laviolette,M., Pastinen,T., Boulet,L.P. and Laprise,C.
  TITLE     Combining omics data to identify genes associated with allergic
            rhinitis
  JOURNAL   Clin Epigenetics 9, 3 (2017)
   PUBMED   28149331
  REMARK    GeneRIF: Results identified RNF39 as cis methylation quantitative
            trait loci in both allergic rhinitis and asthma.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2084)
  AUTHORS   Mungall,A.J., Palmer,S.A., Sims,S.K., Edwards,C.A., Ashurst,J.L.,
            Wilming,L., Jones,M.C., Horton,R., Hunt,S.E., Scott,C.E.,
            Gilbert,J.G., Clamp,M.E., Bethel,G., Milne,S., Ainscough,R.,
            Almeida,J.P., Ambrose,K.D., Andrews,T.D., Ashwell,R.I.,
            Babbage,A.K., Bagguley,C.L., Bailey,J., Banerjee,R., Barker,D.J.,
            Barlow,K.F., Bates,K., Beare,D.M., Beasley,H., Beasley,O.,
            Bird,C.P., Blakey,S., Bray-Allen,S., Brook,J., Brown,A.J.,
            Brown,J.Y., Burford,D.C., Burrill,W., Burton,J., Carder,C.,
            Carter,N.P., Chapman,J.C., Clark,S.Y., Clark,G., Clee,C.M.,
            Clegg,S., Cobley,V., Collier,R.E., Collins,J.E., Colman,L.K.,
            Corby,N.R., Coville,G.J., Culley,K.M., Dhami,P., Davies,J.,
            Dunn,M., Earthrowl,M.E., Ellington,A.E., Evans,K.A., Faulkner,L.,
            Francis,M.D., Frankish,A., Frankland,J., French,L., Garner,P.,
            Garnett,J., Ghori,M.J., Gilby,L.M., Gillson,C.J., Glithero,R.J.,
            Grafham,D.V., Grant,M., Gribble,S., Griffiths,C., Griffiths,M.,
            Hall,R., Halls,K.S., Hammond,S., Harley,J.L., Hart,E.A.,
            Heath,P.D., Heathcott,R., Holmes,S.J., Howden,P.J., Howe,K.L.,
            Howell,G.R., Huckle,E., Humphray,S.J., Humphries,M.D., Hunt,A.R.,
            Johnson,C.M., Joy,A.A., Kay,M., Keenan,S.J., Kimberley,A.M.,
            King,A., Laird,G.K., Langford,C., Lawlor,S., Leongamornlert,D.A.,
            Leversha,M., Lloyd,C.R., Lloyd,D.M., Loveland,J.E., Lovell,J.,
            Martin,S., Mashreghi-Mohammadi,M., Maslen,G.L., Matthews,L.,
            McCann,O.T., McLaren,S.J., McLay,K., McMurray,A., Moore,M.J.,
            Mullikin,J.C., Niblett,D., Nickerson,T., Novik,K.L., Oliver,K.,
            Overton-Larty,E.K., Parker,A., Patel,R., Pearce,A.V., Peck,A.I.,
            Phillimore,B., Phillips,S., Plumb,R.W., Porter,K.M., Ramsey,Y.,
            Ranby,S.A., Rice,C.M., Ross,M.T., Searle,S.M., Sehra,H.K.,
            Sheridan,E., Skuce,C.D., Smith,S., Smith,M., Spraggon,L.,
            Squares,S.L., Steward,C.A., Sycamore,N., Tamlyn-Hall,G., Tester,J.,
            Theaker,A.J., Thomas,D.W., Thorpe,A., Tracey,A., Tromans,A.,
            Tubby,B., Wall,M., Wallis,J.M., West,A.P., White,S.S.,
            Whitehead,S.L., Whittaker,H., Wild,A., Willey,D.J., Wilmer,T.E.,
            Wood,J.M., Wray,P.W., Wyatt,J.C., Young,L., Younger,R.M.,
            Bentley,D.R., Coulson,A., Durbin,R., Hubbard,T., Sulston,J.E.,
            Dunham,I., Rogers,J. and Beck,S.
  TITLE     The DNA sequence and analysis of human chromosome 6
  JOURNAL   Nature 425 (6960), 805-811 (2003)
   PUBMED   14574404
REFERENCE   7  (bases 1 to 2084)
  AUTHORS   Matsuo,R., Asada,A., Fujitani,K. and Inokuchi,K.
  TITLE     LIRF, a gene induced during hippocampal long-term potentiation as
            an immediate-early gene, encodes a novel RING finger protein
  JOURNAL   Biochem Biophys Res Commun 289 (2), 479-484 (2001)
   PUBMED   11716498
REFERENCE   8  (bases 1 to 2084)
  AUTHORS   Coriton,O., Lepourcelet,M., Hampe,A., Galibert,F. and Mosser,J.
  TITLE     Transcriptional analysis of the 69-kb sequence centromeric to
            HLA-J: a dense and complex structure of five genes
  JOURNAL   Mamm Genome 11 (12), 1127-1131 (2000)
   PUBMED   11130983
REFERENCE   9  (bases 1 to 2084)
  AUTHORS   Orimo,A., Yamagishi,T., Tominaga,N., Yamauchi,Y., Hishinuma,T.,
            Okada,K., Suzuki,M., Sato,M., Nogi,Y., Suzuki,H., Inoue,S.,
            Yoshimura,K., Shimizu,Y. and Muramatsu,M.
  TITLE     Molecular cloning of testis-abundant finger Protein/Ring finger
            protein 23 (RNF23), a novel RING-B box-coiled coil-B30.2 protein on
            the class I region of the human MHC
  JOURNAL   Biochem Biophys Res Commun 276 (1), 45-51 (2000)
   PUBMED   11006080
REFERENCE   10 (bases 1 to 2084)
  AUTHORS   Hidaka,M., Caruana,G., Stanford,W.L., Sam,M., Correll,P.H. and
            Bernstein,A.
  TITLE     Gene trapping of two novel genes, Hzf and Hhl, expressed in
            hematopoietic cells
  JOURNAL   Mech Dev 90 (1), 3-15 (2000)
   PUBMED   10585558
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL669914.2.
            
            On Aug 10, 2020 this sequence version replaced NM_025236.3.
            
            Summary: This gene lies within the major histocompatibility complex
            class I region on chromosome 6. Studies of a similar rat protein
            suggest that this gene encodes a protein that plays a role in an
            early phase of synaptic plasticity. Multiple transcript variants
            encoding different isoforms have been found for this gene.
            [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1), also known as HZFw1,
            represents the longer transcript and encodes the longer isoform
            (1).
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on 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 :: AF238315.1, SRR14038191.3593421.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2154405 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000244360.8/ ENSP00000244360.7
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-547               AL669914.2         69856-70402         c
            548-570             AL669914.2         68089-68111         c
            571-662             AL669914.2         67790-67881         c
            663-2084            AL669914.2         64903-66324         c
FEATURES             Location/Qualifiers
     source          1..2084
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6p22.1"
     gene            1..2084
                     /gene="RNF39"
                     /gene_synonym="FAP216; HZF; HZFW; LIRF"
                     /note="ring finger protein 39"
                     /db_xref="GeneID:80352"
                     /db_xref="HGNC:HGNC:18064"
                     /db_xref="MIM:607524"
     exon            1..547
                     /gene="RNF39"
                     /gene_synonym="FAP216; HZF; HZFW; LIRF"
                     /inference="alignment:Splign:2.1.0"
     CDS             185..1243
                     /gene="RNF39"
                     /gene_synonym="FAP216; HZF; HZFW; LIRF"
                     /EC_number="2.3.2.27"
                     /note="isoform 1 is encoded by transcript variant 1; LTP
                     (long-term potentiation) induced RING finger protein;
                     protein HZFw"
                     /codon_start=1
                     /product="RING finger protein 39 isoform 1"
                     /protein_id="NP_079512.3"
                     /db_xref="CCDS:CCDS4673.2"
                     /db_xref="GeneID:80352"
                     /db_xref="HGNC:HGNC:18064"
                     /db_xref="MIM:607524"
                     /translation="MDAPELGPGLVERLEQLATCPLCGGSFEDPVLLACEHSFCRACL
                     ARRWGTPPATGTEASPTACPCCGLPCPRRSLRSNVRLAVEVRISRELREKLAEPGARA
                     GRRRGGRIPTMGCLDLPGEDMRKTWRRFEVPTSKSSNSEDDLPEDYPVVKKMLHRLTA
                     DLTLDPGTAHRRLLISADRRSVQLAPPGTPAPPDGPKRFDQLPAVLGAQGFGAGRHCW
                     EVETADAASCRDSSGEDADDEESHYAVGAAGESVQRKGCVRLCPAGAVWAVEGRGGRL
                     WALTAPEPTLLGGVEPPPRRIRVDLDWERGRVAFYDGRSLDLLYAFQAPGPLGERIFP
                     LFCTCDPRAPLRIVPAES"
     exon            548..570
                     /gene="RNF39"
                     /gene_synonym="FAP216; HZF; HZFW; LIRF"
                     /inference="alignment:Splign:2.1.0"
     exon            571..662
                     /gene="RNF39"
                     /gene_synonym="FAP216; HZF; HZFW; LIRF"
                     /inference="alignment:Splign:2.1.0"
     exon            663..2084
                     /gene="RNF39"
                     /gene_synonym="FAP216; HZF; HZFW; LIRF"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2060..2065
                     /regulatory_class="polyA_signal_sequence"
                     /gene="RNF39"
                     /gene_synonym="FAP216; HZF; HZFW; LIRF"
                     /note="hexamer: AATAAA"
     polyA_site      2084
                     /gene="RNF39"
                     /gene_synonym="FAP216; HZF; HZFW; LIRF"
                     /note="major polyA site"
ORIGIN      
        1 gagactgaga ctctggttga agagagaggc aatcccagga gaggggcgga aagcggcaaa
       61 agttaatgcg ggagtcggag agaagggcat ctacacagca agcagcaggg gcggcccgcc
      121 atctgcgcgc tcgaaggcgg tcacggtggt cgcggaaggg gcggcgtcca gatcctggct
      181 ttccatggat gcgcccgagc tgggcccggg gctggtggag cgtctggagc agctggcgac
      241 gtgtcctctg tgcgggggct ccttcgagga cccggtgctt ctggcgtgcg agcacagctt
      301 ctgccgcgcg tgtctggccc gccgctgggg gactccgccg gcgaccggca ccgaggcttc
      361 ccccaccgcc tgtccctgct gcggcctgcc gtgtccccgc cgcagcctga ggtctaatgt
      421 gcggctggcg gtggaggtgc gaatcagccg cgagctgcga gagaagctgg ctgagcctgg
      481 ggcccgtgcg gggagacgcc gaggggggcg catccccacc atgggctgcc tggacctgcc
      541 cggagaggat atgaggaaga catggagacg atttgaagtc ccaacatcca agtcatctaa
      601 ttcagaggat gatctccctg aagattatcc agtggtcaaa aaaatgcttc atagactgac
      661 agccgacctg accctggacc ctgggaccgc acaccgccgc ctgctcatct ccgccgaccg
      721 ccgcagcgta caactggccc caccagggac gcccgcgccc cctgacggcc ccaagcgctt
      781 cgatcagctc ccagctgtgc tgggtgcgca gggcttcggg gccggccgcc actgctggga
      841 ggtggagact gcggacgccg cctcctgcag agactcttct ggggaggatg cggacgacga
      901 ggagagccac tatgcagtgg gcgcggccgg ggaatcagtg caacgcaagg gctgcgtaag
      961 gctgtgccct gcgggggccg tgtgggccgt ggagggccgc ggcggccgcc tgtgggccct
     1021 cacggcaccc gaacccaccc tgctgggcgg tgttgagccc ccgccgcggc gcattcgcgt
     1081 ggacctggac tgggagcggg gccgcgtggc cttctacgac ggccgctcac tcgacctgct
     1141 ttacgccttc caggcgcctg gccccctggg ggagcgcatc ttcccgctgt tctgcacctg
     1201 cgaccctcgt gctccgctcc gcattgtacc agcggaaagc tgagtctcgt ctccaactag
     1261 aagtttggcc cggccactgg ccctgcagct gctttttggg ggtggaattc cccactcatt
     1321 tctgggaaca cattcacacg cccattgcag gagtattaat agcaacccac attttcgccc
     1381 caaaataatg agacctcacc tggtctccac gtttccacgt ccctgctcaa aaccaaatcc
     1441 attcctgcct tctggctctc agaatcttct ctcccctaca gctactacag tacttcctga
     1501 cttctcccat tcaaaccatt ctaggcctgc aatggggaac aggccctccc catcagtatt
     1561 ggtaaagtga ccatgattcc tacatagagg ctctgctggt caaatacttg actcccactc
     1621 ttgccactcc tagctccaga agggctcagg gccttcccca cagatctaag gactgggcta
     1681 ccctgcctgt ccactgaggt ttctcctaaa acaagaggct tgactctggt ctgggccctg
     1741 tggccctctg ggaagctttg tacctctttt gcaggatctg ggggtgggga gggacaagct
     1801 agttccccaa cctcctatga ctgctttcta tgctcacagc cttttttcca taagaacctt
     1861 cttgaaactt ctccccgcac atactcacgg aaaggaacca atggtgctat ttcccctctc
     1921 tcctcctcaa cctgggaata cttcagacat ctccaaactc atccttgtgt atagtctcac
     1981 acccttcccc ataagtataa atgggcccat atttaacaca ttttgtgatt ttgggttatt
     2041 tattttgtgc atctgtggca ataaatgaga tctcagtggt ggta
//
