LOCUS       NM_007237               3244 bp    mRNA    linear   PRI 15-OCT-2024
DEFINITION  Homo sapiens SP140 nuclear body protein (SP140), transcript variant
            1, mRNA.
ACCESSION   NM_007237
VERSION     NM_007237.5
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 3244)
  AUTHORS   Nakamura,H., Hikichi,H., Seto,S., Hijikata,M. and Keicho,N.
  TITLE     Transcriptional regulators SP110 and SP140 modulate inflammatory
            response genes in Mycobacterium tuberculosis-infected human
            macrophages
  JOURNAL   Microbiol Spectr 12 (10), e0010124 (2024)
   PUBMED   39162523
  REMARK    GeneRIF: Transcriptional regulators SP110 and SP140 modulate
            inflammatory response genes in Mycobacterium tuberculosis-infected
            human macrophages.
REFERENCE   2  (bases 1 to 3244)
  AUTHORS   Tanagala,K.K.K., Morin-Baxter,J., Carvajal,R., Cheema,M., Dubey,S.,
            Nakagawa,H., Yoon,A., Cheng,Y.L., Taylor,A., Nickerson,J., Mintz,A.
            and Momen-Heravi,F.
  TITLE     SP140 inhibits STAT1 signaling, induces IFN-gamma in
            tumor-associated macrophages, and is a predictive biomarker of
            immunotherapy response
  JOURNAL   J Immunother Cancer 10 (12) (2022)
   PUBMED   36600652
  REMARK    GeneRIF: SP140 inhibits STAT1 signaling, induces IFN-gamma in
            tumor-associated macrophages, and is a predictive biomarker of
            immunotherapy response.
REFERENCE   3  (bases 1 to 3244)
  AUTHORS   Fraschilla,I., Amatullah,H., Rahman,R.U. and Jeffrey,K.L.
  TITLE     Immune chromatin reader SP140 regulates microbiota and risk for
            inflammatory bowel disease
  JOURNAL   Cell Host Microbe 30 (10), 1370-1381 (2022)
   PUBMED   36130593
  REMARK    GeneRIF: Immune chromatin reader SP140 regulates microbiota and
            risk for inflammatory bowel disease.
REFERENCE   4  (bases 1 to 3244)
  AUTHORS   Amatullah,H., Fraschilla,I., Digumarthi,S., Huang,J.,
            Adiliaghdam,F., Bonilla,G., Wong,L.P., Rivard,M.E., Beauchamp,C.,
            Mercier,V., Goyette,P., Sadreyev,R.I., Anthony,R.M., Rioux,J.D. and
            Jeffrey,K.L.
  TITLE     Epigenetic reader SP140 loss of function drives Crohn's disease due
            to uncontrolled macrophage topoisomerases
  JOURNAL   Cell 185 (17), 3232-3247 (2022)
   PUBMED   35952671
  REMARK    GeneRIF: Epigenetic reader SP140 loss of function drives Crohn's
            disease due to uncontrolled macrophage topoisomerases.
REFERENCE   5  (bases 1 to 3244)
  AUTHORS   Zucchelli,C., Tamburri,S., Quilici,G., Palagano,E., Berardi,A.,
            Saare,M., Peterson,P., Bachi,A. and Musco,G.
  TITLE     Structure of human Sp140 PHD finger: an atypical fold interacting
            with Pin1
  JOURNAL   FEBS J 281 (1), 216-231 (2014)
   PUBMED   24267382
REFERENCE   6  (bases 1 to 3244)
  AUTHORS   Granito,A., Yang,W.H., Muratori,L., Lim,M.J., Nakajima,A.,
            Ferri,S., Pappas,G., Quarneti,C., Bianchi,F.B., Bloch,D.B. and
            Muratori,P.
  TITLE     PML nuclear body component Sp140 is a novel autoantigen in primary
            biliary cirrhosis
  JOURNAL   Am J Gastroenterol 105 (1), 125-131 (2010)
   PUBMED   19861957
REFERENCE   7  (bases 1 to 3244)
  AUTHORS   Di Bernardo,M.C., Crowther-Swanepoel,D., Broderick,P., Webb,E.,
            Sellick,G., Wild,R., Sullivan,K., Vijayakrishnan,J., Wang,Y.,
            Pittman,A.M., Sunter,N.J., Hall,A.G., Dyer,M.J., Matutes,E.,
            Dearden,C., Mainou-Fowler,T., Jackson,G.H., Summerfield,G.,
            Harris,R.J., Pettitt,A.R., Hillmen,P., Allsup,D.J., Bailey,J.R.,
            Pratt,G., Pepper,C., Fegan,C., Allan,J.M., Catovsky,D. and
            Houlston,R.S.
  TITLE     A genome-wide association study identifies six susceptibility loci
            for chronic lymphocytic leukemia
  JOURNAL   Nat Genet 40 (10), 1204-1210 (2008)
   PUBMED   18758461
REFERENCE   8  (bases 1 to 3244)
  AUTHORS   Madani,N., Millette,R., Platt,E.J., Marin,M., Kozak,S.L.,
            Bloch,D.B. and Kabat,D.
  TITLE     Implication of the lymphocyte-specific nuclear body protein Sp140
            in an innate response to human immunodeficiency virus type 1
  JOURNAL   J Virol 76 (21), 11133-11138 (2002)
   PUBMED   12368356
  REMARK    GeneRIF: the nuclear body protein Sp140, was found specifically in
            all NP cells (n = 12 cell lines tested; P < or = 0.001), and HIV-1
            infection induced its partial dispersal from nuclear bodies into
            cytosolic colocalization with Vif
REFERENCE   9  (bases 1 to 3244)
  AUTHORS   Bloch,D.B., de la Monte,S.M., Guigaouri,P., Filippov,A. and
            Bloch,K.D.
  TITLE     Identification and characterization of a leukocyte-specific
            component of the nuclear body
  JOURNAL   J Biol Chem 271 (46), 29198-29204 (1996)
   PUBMED   8910577
REFERENCE   10 (bases 1 to 3244)
  AUTHORS   Dent,A.L., Yewdell,J., Puvion-Dutilleul,F., Koken,M.H., de The,H.
            and Staudt,L.M.
  TITLE     LYSP100-associated nuclear domains (LANDs): description of a new
            class of subnuclear structures and their relationship to PML
            nuclear bodies
  JOURNAL   Blood 88 (4), 1423-1426 (1996)
   PUBMED   8695863
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK301267.1, BC038091.1,
            BC105960.1, U36500.1 and AC009949.9.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_007237.4.
            
            Summary: This gene encodes a member of the SP100 family of
            proteins, which are share common domains including an N-terminal
            homogeneously staining region domain followed by a SP100/autoimmune
            regulator/NucP41/P75/deformed epidermal autoregulatory factor
            domain, a plant homeobox zinc finger, and a bromodomain. The
            encoded protein is interferon-inducible and is expressed at high
            levels in the nuclei of leukocytes. Variants of this gene have been
            associated with multiple sclerosis, Crohn's disease, and chronic
            lymphocytic leukemia. Alternative splicing results in multiple
            variants. [provided by RefSeq, Aug 2016].
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (1).
            
            Sequence Note: The RefSeq transcript and protein were derived from
            transcript and genomic sequence to make the sequence consistent
            with the reference genome assembly. The extent of this RefSeq
            transcript is supported by 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 :: U36500.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000392045.8/ ENSP00000375899.3
            RefSeq Select criteria :: based on expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-34                AK301267.1         7-40
            35-950              BC038091.1         12-927
            951-1181            BC105960.1         942-1172
            1182-1654           U36500.1           1189-1661
            1655-1655           AC009949.9         19372-19372
            1656-3099           BC105960.1         1566-3009
            3100-3244           U36500.1           3108-3252
FEATURES             Location/Qualifiers
     source          1..3244
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q37.1"
     gene            1..3244
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /note="SP140 nuclear body protein"
                     /db_xref="GeneID:11262"
                     /db_xref="HGNC:HGNC:17133"
                     /db_xref="MIM:608602"
     exon            1..168
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     CDS             110..2713
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /note="isoform 1 is encoded by transcript variant 1;
                     lymphoid-specific SP100 homolog; speckled 140 kDa; nuclear
                     autoantigen Sp-140; lymphoid-restricted homolog of Sp100"
                     /codon_start=1
                     /product="nuclear body protein SP140 isoform 1"
                     /protein_id="NP_009168.4"
                     /db_xref="CCDS:CCDS42831.1"
                     /db_xref="GeneID:11262"
                     /db_xref="HGNC:HGNC:17133"
                     /db_xref="MIM:608602"
                     /translation="MAQQGQQGQMASGDSNLNFRMVAEIQNVEGQNLQEQVCPEPIFR
                     FFRENKVEIASAITRPFPFLMGLRDRSFISEQMYEHFQEAFRNLVPVTRVMYCVLSEL
                     EKTFGWSHLEALFSRINLMAYPDLNEIYRSFQNVCYEHSPLQMNNVNDLEDRPRLLPY
                     GKQENSNACHEMDDIAVPQEALSSSPRCEPGFSSESCEQLALPKAGGGDAEDAPSLLP
                     GGGVSCKLAIQIDEGESEEMPKLLPYDTEVLESNGMIDAARTYSTAPGEKQGEEEGRN
                     SPRKRNQDKEKYQESPEGRDKETFDLKTPQVTNEGEPEKGLCLLPGEGEEGSDDCSEM
                     CDGEEPQEASSSLARCGSVSCLSAETFDLKTPQVTNEGEPEKELSLLPGEGEEGSDDC
                     SEMCDGEERQEASSSLARRGSVSSELENHPMNEEGESEELASSLLYDNVPGAEQSAYE
                     NEKCSCVMCFSEEVPGSPEARTESDQACGTMDTVDIANNSTLGKPKRKRRKKRGHGWS
                     RMRMRRQENSQQNDNSKADGQVVSSEKKANVNLKDLSKIRGRKRGKPGTRFTQSDRAA
                     QKRVRSRASRKHKDETVDFKAPLLPVTCGGVKGILHKKKLQQGILVKCIQTEDGKWFT
                     PTEFEIKGGHARSKNWRLSVRCGGWPLRWLMENGFLPDPPRIRYRKKKRILKSQNNSS
                     VDPCMRNLDECEVCRDGGELFCCDTCSRVFHEDCHIPPVEAERTPWNCIFCRMKESPG
                     SQQCCQESEVLERQMCPEEQLKCEFLLLKVYCCSESSFFAKIPYYYYIREACQGLKEP
                     MWLDKIKKRLNEHGYPQVEGFVQDMRLIFQNHRASYKYKDFGQMGFRLEAEFEKNFKE
                     VFAIQETNGNN"
     exon            169..346
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            347..515
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            516..599
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            600..680
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            681..773
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            774..851
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            852..1001
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            1002..1085
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            1086..1166
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            1167..1268
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            1269..1349
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            1350..1436
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            1437..1553
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            1554..1607
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            1608..1673
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            1674..1754
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            1755..1829
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            1830..1934
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            1935..2077
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            2078..2125
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            2126..2167
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            2168..2283
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            2284..2392
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            2393..2470
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            2471..2614
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     exon            2615..3244
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3222..3227
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /note="hexamer: ATTAAA"
     polyA_site      3244
                     /gene="SP140"
                     /gene_synonym="LYSP100; LYSP100-A; LYSP100-B"
                     /note="major polyA site"
ORIGIN      
        1 cttttcctct ttgactgagc accgaggggc agttggcagc ttcacctcag agctgcagga
       61 aggaacgggg cagtgaaaat cgaatcgggt gtgatcctag gccaagctca tggcccagca
      121 gggccagcag gggcagatgg caagtggaga cagcaatctc aacttcagga tggtcgcaga
      181 gatccagaac gtagagggtc agaacctgca ggagcaggtt tgccctgagc ccattttcag
      241 gttcttcaga gaaaacaagg tggagattgc aagtgcaata acaaggccat ttcctttcct
      301 tatgggcctc cgagaccgct ccttcatctc cgagcagatg tatgaacatt ttcaagaagc
      361 ttttagaaac ctggtcccag tgacaagagt gatgtattgt gtactcagtg aactggagaa
      421 gacatttggc tggtcacatc tggaagcatt gttcagcagg attaacctga tggcctatcc
      481 tgatttaaac gagatttaca gaagcttcca gaatgtatgc tatgaacact cacctctcca
      541 aatgaataat gtaaacgatt tagaagatag acccagatta ctaccatatg gtaaacaaga
      601 gaacagcaat gcctgtcatg aaatggatga tatagcagtg cctcaggaag ccttgagctc
      661 ctcgccaagg tgtgagccag gtttctcttc agagtcttgt gagcagttag ctctcccaaa
      721 ggctggtgga ggagatgctg aagatgcacc cagcctacta ccaggtgggg gagtgtcctg
      781 taaacttgct atacaaatag atgaaggaga atcagaagaa atgcccaagt tactgcctta
      841 tgatacagaa gttctagaaa gcaacgggat gatagatgcg gcaaggacat acagcacagc
      901 accaggggag aaacagggag aggaggaagg caggaacagt cccagaaaaa gaaaccaaga
      961 caaggagaag taccaagaga gtccagaggg aagagacaaa gagacctttg atctaaaaac
     1021 tccccaagtc actaatgaag gagaaccaga gaaggggctc tgtctactac caggtgaagg
     1081 agaagagggc agtgatgact gttcagaaat gtgtgatgga gaagagcccc aggaagcctc
     1141 tagctcccta gcaagatgtg ggtcagtttc ttgtttatct gcagagacct ttgatctaaa
     1201 gactccccaa gtcactaatg aaggagaacc agagaaggag ctcagtctac taccaggtga
     1261 aggagaagag ggcagtgatg actgttcgga aatgtgtgat ggagaagagc gccaggaagc
     1321 ctctagctcc ctagcaagac gtgggtcagt gtctagtgaa ctagaaaatc acccaatgaa
     1381 tgaagaagga gaatcagaag agcttgcttc tagcctgcta tatgataatg taccaggagc
     1441 ggagcaatca gcatatgaaa atgagaagtg ttcctgtgtc atgtgtttct cagaagaggt
     1501 gccaggaagc ccagaagcaa ggacggaaag tgatcaagcg tgtggcacaa tggatactgt
     1561 ggatattgca aacaactcca ctttgggaaa acccaagagg aaaagaagaa aaaagagggg
     1621 gcatggctgg agcagaatga gaatgagaag gcaggaaaac agccaacaaa atgataatag
     1681 caaagccgac ggccaggtgg tctccagtga aaagaaggcg aacgtgaatc tgaaagacct
     1741 ttccaagatt agggggagaa agagaggcaa acctggaacc cgcttcactc agagtgacag
     1801 agctgcacag aaaagagtcc gatcaagagc ttcaagaaag cacaaagatg aaactgtgga
     1861 ttttaaggct cctttgcttc cagtgacctg tggtggggtg aagggaattt tacataagaa
     1921 gaaattgcag caaggaatct tggtgaagtg tatacagact gaggatggaa aatggttcac
     1981 ccccacggaa tttgaaatca aaggaggcca tgcaagatca aagaactgga ggctgagtgt
     2041 gcgctgtggc gggtggcccc tacgatggct gatggagaat ggatttctgc ctgatcctcc
     2101 aagaatacgt tacaggaaaa aaaagagaat actgaagtct caaaacaata gctcagttga
     2161 cccttgtatg agaaacctgg atgagtgtga ggtgtgccgg gacggagggg agctgttctg
     2221 ttgcgacact tgttcaagag tcttccatga ggactgtcac atcccgcctg tggaagctga
     2281 gaggaccccg tggaattgca tcttctgcag gatgaaggag tctccgggaa gccaacagtg
     2341 ttgtcaggaa tctgaggtcc tggagaggca gatgtgtcct gaggaacagt tgaaatgtga
     2401 gttcctcctc ttgaaagtct attgctgttc tgagagctcc ttttttgcca agattccata
     2461 ctattattat attagagagg cgtgtcaagg cctgaaggag cccatgtggt tggataaaat
     2521 caagaaaagg ctgaatgagc acggttaccc ccaagtggag gggtttgtac aagacatgcg
     2581 cctcatcttc cagaaccaca gggcctctta caagtacaag gattttggcc aaatgggatt
     2641 tagactggag gctgagtttg agaagaattt caaggaagtg tttgctattc aggaaacaaa
     2701 tgggaacaat tgactggatt agtggatgct gaaagcattc agcaaatggc accctaaaat
     2761 atgccgctgg tttgccactg acttcaaaat gaggtcactt gggcacagca catgcaggga
     2821 ggggcttttc tctgagcctc cttcatctgc ccaaagacaa atcctcaaaa ggaaattcaa
     2881 tcatcatgaa tcacaacccc aagtatctca tcagccaggg aagagtaagt gggatcacag
     2941 ggaaggatgt tggcagcgac accatcccat acaggctctt acctcttctc ctgagggctg
     3001 ctccagacaa catttattac ccagaagacc ttttgtctga aaaccagcca agctttattc
     3061 aggacacact tcttgccttc actttcccac ttccgtggcc acctccatgc agaagcccta
     3121 agcccacatt ctttcgatag ctcacggtgg tgcatgagtg tccatcatct gactcttctc
     3181 ggagtctcat attttgtggg actcctgtgc aaacatatgt tattaaaatt tttttcctcc
     3241 tgtt
//
