LOCUS       NM_005831               3635 bp    mRNA    linear   PRI 12-NOV-2024
DEFINITION  Homo sapiens calcium binding and coiled-coil domain 2 (CALCOCO2),
            transcript variant 3, mRNA.
ACCESSION   NM_005831
VERSION     NM_005831.5
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 3635)
  AUTHORS   Lu,J., Zhang,J., Jiang,H., Hu,Z., Zhang,Y., He,L., Yang,J., Xie,Y.,
            Wu,D., Li,H., Zeng,K., Tan,P., Xiao,Q., Song,Z., Pan,C., Bai,X. and
            Yu,X.
  TITLE     Vangl2 suppresses NF-kappaB signaling and ameliorates sepsis by
            targeting p65 for NDP52-mediated autophagic degradation
  JOURNAL   Elife 12, 87935 (2024)
   PUBMED   39269442
  REMARK    GeneRIF: Vangl2 suppresses NF-kappaB signaling and ameliorates
            sepsis by targeting p65 for NDP52-mediated autophagic degradation.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3635)
  AUTHORS   Cui,S., Faure,M. and Wei,Y.
  TITLE     CALCOCO2/NDP52 associates with RAB9 to initiate an antiviral
            response to hepatitis B virus infection through a lysosomal
            degradation pathway
  JOURNAL   Autophagy 20 (9), 2109-2111 (2024)
   PUBMED   38752371
  REMARK    GeneRIF: CALCOCO2/NDP52 associates with RAB9 to initiate an
            antiviral response to hepatitis B virus infection through a
            lysosomal degradation pathway.
REFERENCE   3  (bases 1 to 3635)
  AUTHORS   Gao,A., Wang,M., Tang,X., Shi,G., Hou,K., Fang,J., Zhou,L.,
            Zhou,H., Jiang,W., Li,Y. and Ouyang,F.
  TITLE     NDP52 SUMOylation contributes to low-dose X-rays-induced cardiac
            hypertrophy through PINK1/Parkin-mediated mitophagy via MUL1/SUMO2
            signalling
  JOURNAL   J Cell Physiol 239 (1), 79-96 (2024)
   PUBMED   37942585
  REMARK    GeneRIF: NDP52 SUMOylation contributes to low-dose X-rays-induced
            cardiac hypertrophy through PINK1/Parkin-mediated mitophagy via
            MUL1/SUMO2 signalling.
REFERENCE   4  (bases 1 to 3635)
  AUTHORS   Mu,N., Wang,Y., Li,X., Du,Z., Wu,Y., Su,M., Wang,Y., Sun,X., Su,L.
            and Liu,X.
  TITLE     Crotonylated BEX2 interacts with NDP52 and enhances mitophagy to
            modulate chemotherapeutic agent-induced apoptosis in non-small-cell
            lung cancer cells
  JOURNAL   Cell Death Dis 14 (9), 645 (2023)
   PUBMED   37777549
  REMARK    GeneRIF: Crotonylated BEX2 interacts with NDP52 and enhances
            mitophagy to modulate chemotherapeutic agent-induced apoptosis in
            non-small-cell lung cancer cells.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 3635)
  AUTHORS   Kataura,T., Otten,E.G., Rabanal-Ruiz,Y., Adriaenssens,E.,
            Urselli,F., Scialo,F., Fan,L., Smith,G.R., Dawson,W.M., Chen,X.,
            Yue,W.W., Bronowska,A.K., Carroll,B., Martens,S., Lazarou,M. and
            Korolchuk,V.I.
  TITLE     NDP52 acts as a redox sensor in PINK1/Parkin-mediated mitophagy
  JOURNAL   EMBO J 42 (5), e111372 (2023)
   PUBMED   36514953
  REMARK    GeneRIF: NDP52 acts as a redox sensor in PINK1/Parkin-mediated
            mitophagy.
REFERENCE   6  (bases 1 to 3635)
  AUTHORS   Everett,R.D., Sourvinos,G., Leiper,C., Clements,J.B. and Orr,A.
  TITLE     Formation of nuclear foci of the herpes simplex virus type 1
            regulatory protein ICP4 at early times of infection: localization,
            dynamics, recruitment of ICP27, and evidence for the de novo
            induction of ND10-like complexes
  JOURNAL   J Virol 78 (4), 1903-1917 (2004)
   PUBMED   14747555
  REMARK    GeneRIF: interacts with ICP4 regulatory protein of HSV-1 during
            early stage of infection
REFERENCE   7  (bases 1 to 3635)
  AUTHORS   Di,Y., Li,J., Zhang,Y., He,X., Lu,H., Xu,D., Ling,J., Huo,K.,
            Wan,D., Li,Y.Y. and Gu,J.
  TITLE     HCC-associated protein HCAP1, a variant of GEMIN4, interacts with
            zinc-finger proteins
  JOURNAL   J Biochem 133 (6), 713-718 (2003)
   PUBMED   12869526
REFERENCE   8  (bases 1 to 3635)
  AUTHORS   Florin,L., Schafer,F., Sotlar,K., Streeck,R.E. and Sapp,M.
  TITLE     Reorganization of nuclear domain 10 induced by papillomavirus
            capsid protein l2
  JOURNAL   Virology 295 (1), 97-107 (2002)
   PUBMED   12033769
REFERENCE   9  (bases 1 to 3635)
  AUTHORS   Sternsdorf,T., Jensen,K., Zuchner,D. and Will,H.
  TITLE     Cellular localization, expression, and structure of the nuclear dot
            protein 52
  JOURNAL   J Cell Biol 138 (2), 435-448 (1997)
   PUBMED   9230084
REFERENCE   10 (bases 1 to 3635)
  AUTHORS   Korioth,F., Gieffers,C., Maul,G.G. and Frey,J.
  TITLE     Molecular characterization of NDP52, a novel protein of the nuclear
            domain 10, which is redistributed upon virus infection and
            interferon treatment
  JOURNAL   J Cell Biol 130 (1), 1-13 (1995)
   PUBMED   7540613
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from U22897.1 and AC068531.9.
            
            On Jun 2, 2019 this sequence version replaced NM_005831.4.
            
            Summary: This gene encodes a coiled-coil domain-containing protein.
            The encoded protein functions as a receptor for ubiquitin-coated
            bacteria and plays an important role in innate immunity by
            mediating macroautophagy. Alternatively spliced transcript variants
            encoding multiple isoforms have been observed for this gene.
            [provided by RefSeq, May 2012].
            
            Transcript Variant: This variant (3) lacks an exon in the 5' coding
            region, but maintains the reading frame, compared to variant 1. The
            encoded isoform (3) is shorter than isoform 1.
            
            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 :: U22897.1, AK314796.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000258947.8/ ENSP00000258947.3
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-2387              U22897.1           1-2387
            2388-3635           AC068531.9         159226-160473
FEATURES             Location/Qualifiers
     source          1..3635
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="17"
                     /map="17q21.32"
     gene            1..3635
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /note="calcium binding and coiled-coil domain 2"
                     /db_xref="GeneID:10241"
                     /db_xref="HGNC:HGNC:29912"
                     /db_xref="MIM:604587"
     exon            1..44
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /inference="alignment:Splign:2.1.0"
     exon            45..234
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /inference="alignment:Splign:2.1.0"
     CDS             55..1395
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /note="isoform 3 is encoded by transcript variant 3;
                     calcium-binding and coiled-coil domain-containing protein
                     2; nuclear dot protein 52; nuclear domain 10 protein 52;
                     nuclear domain 10 protein NDP52; antigen nuclear dot 52
                     kDa protein"
                     /codon_start=1
                     /product="calcium-binding and coiled-coil
                     domain-containing protein 2 isoform 3"
                     /protein_id="NP_005822.1"
                     /db_xref="CCDS:CCDS11538.1"
                     /db_xref="GeneID:10241"
                     /db_xref="HGNC:HGNC:29912"
                     /db_xref="MIM:604587"
                     /translation="MEETIKDPPTSAVLLDHCHFSQVIFNSVEKFYIPGGDVTCHYTF
                     TQHFIPRRKDWIGIFRVGWKTTREYYTFMWVTLPIDLNNKSAKQQEVQFKAYYLPKDD
                     EYYQFCYVDEDGVVRGASIPFQFRPENEEDILVVTTQGEVEEIEQHNKELCKENQELK
                     DSCISLQKQNSDMQAELQKKQEELETLQSINKKLELKVKEQKDYWETELLQLKEQNQK
                     MSSENEKMGIRVDQLQAQLSTQEKEMEKLVQGDQDKTEQLEQLKKENDHLFLSLTEQR
                     KDQKKLEQTVEQMKQNETTAMKKQQELMDENFDLSKRLSENEIICNALQRQKERLEGE
                     NDLLKRENSRLLSYMGLDFNSLPYQVPTSDEGGARQNPGLAYGNPYSGIQESSSPSPL
                     SIKKCPICKADDICDHTLEQQQMQPLCFNCPICDKIFPATEKQIFEDHVFCHSL"
     exon            235..337
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /inference="alignment:Splign:2.1.0"
     exon            338..471
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /inference="alignment:Splign:2.1.0"
     exon            472..597
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /inference="alignment:Splign:2.1.0"
     exon            598..686
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /inference="alignment:Splign:2.1.0"
     exon            687..756
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /inference="alignment:Splign:2.1.0"
     exon            757..879
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /inference="alignment:Splign:2.1.0"
     exon            880..966
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /inference="alignment:Splign:2.1.0"
     exon            967..1062
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /inference="alignment:Splign:2.1.0"
     exon            1063..1198
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /inference="alignment:Splign:2.1.0"
     exon            1199..1227
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /inference="alignment:Splign:2.1.0"
     exon            1228..3635
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2207..2212
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /note="hexamer: AATAAA"
     polyA_site      2232
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /note="major polyA site"
     regulatory      2247..2252
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /note="hexamer: AATAAA"
     polyA_site      2268
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /note="major polyA site"
     regulatory      2362..2367
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /note="hexamer: AATAAA"
     polyA_site      2383
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
     regulatory      3237..3242
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
                     /note="hexamer: AATAAA"
     polyA_site      3257
                     /gene="CALCOCO2"
                     /gene_synonym="NDP52"
ORIGIN      
        1 actctgccct gttgctgtcg cgccgctgct ggttgctgtc cctggacccc taccatggag
       61 gagaccatca aagatccccc cacatcagct gtcttgctgg atcactgtca tttctctcag
      121 gtcatcttta acagtgtgga gaagttctac atccctggag gggacgtcac atgtcattat
      181 accttcaccc agcatttcat ccctcgtcga aaggattgga ttggcatctt tagagtgggg
      241 tggaagacaa cccgtgagta ttacaccttc atgtgggtta ctttgcccat tgacctaaac
      301 aacaaatcag ctaaacagca ggaagtccaa ttcaaagctt actacctgcc caaggatgat
      361 gagtattacc agttctgcta tgtggatgag gatggtgtgg tccggggagc aagtattcct
      421 ttccaattcc gtccagaaaa tgaggaagac atcctggttg ttaccactca gggagaggtg
      481 gaagagattg agcagcacaa caaggagctt tgcaaagaaa accaggagct gaaggacagc
      541 tgtatcagcc tccagaagca gaactcagac atgcaggctg agctccaaaa gaagcaggag
      601 gagctagaaa ccctacagag catcaataag aagttggaac tgaaagtgaa agaacagaag
      661 gactattggg agacagagct gcttcaactg aaagaacaaa accagaagat gtcctcagaa
      721 aatgagaaga tgggaatcag agtggatcag cttcaggccc agctgtcaac tcaagagaaa
      781 gaaatggaga agcttgttca gggagatcaa gataagacag agcagttaga gcagctgaaa
      841 aaggaaaatg accacctctt tctcagttta actgaacaga ggaaggacca gaagaagctc
      901 gagcagacag tggagcaaat gaagcagaat gaaactactg caatgaagaa acaacaggaa
      961 ttaatggatg aaaactttga cctgtcaaaa agactgagtg agaacgaaat tatatgtaat
     1021 gctctgcaga gacagaaaga gagattggaa ggagaaaatg atcttttgaa gagggagaac
     1081 agcagattgc tcagttacat gggtctggat tttaattctt tgccgtatca agtacctact
     1141 tcagatgaag gaggcgcaag acaaaatcca ggacttgcct atggaaaccc atattctggt
     1201 atccaagaaa gttcttcccc cagcccgctc tccatcaaga aatgccctat ctgcaaagca
     1261 gatgatattt gtgatcacac cttggagcaa cagcagatgc agcccctttg tttcaattgt
     1321 ccaatttgtg acaagatctt cccagctaca gagaagcaga tctttgaaga ccacgtgttc
     1381 tgccactctc tctgagtatc ccaacctctt ggatgtatac agagatttta tagaatagaa
     1441 cctatagctt ctaccatgag ttatatgagt caagatcctg cctaacctga aattattagg
     1501 gatttactca gccctgctgc cgctaacagt ggagttatgt cactgatctg aaggtcactg
     1561 ttaagggctt ctgctgccat ccttgtgggt tgctaccttt aagtcgcata actctagctg
     1621 tatcatcctc tcacctgtca ttcttctgag ggtctcagta caagggccct gggatggagc
     1681 caacctgggt attcacaaca ggcctgactt gatactaagt gattagtttt ccaagttgtc
     1741 ccactgccat tcaaagtcag cccttgagtg tatttgttct cagtcctaac cctggggcca
     1801 gagattggtc cgaggttgag aattccttcc tcctcatcct tggtgttgct ttctccaaat
     1861 gattgtttta gactagccaa aaatgccgtg gcaaagagct cagaaatcca atttggatac
     1921 caaaggtttc tcatgttaat ttctcagccc ccaaagaagc atcttactcc tgaaccttag
     1981 acaggaagta ttgtttcagt cacagaaagc ttttctgggt acctctggtt agcactttct
     2041 actctctgat atttcctatg tacatagctt ttattgttgt aaatcctttc ttaatggtta
     2101 aataggattg ttagcaacta tgggtttgca gttttctgag taggtgagtt ttgaatatgg
     2161 gtaaatcaga ataatgagac aacttgttaa tctctttaat actaaaaata aattactctt
     2221 ctatttcagg gacttaggta atttaaaata aaccttcaat ttatggtctt ctgttttgaa
     2281 gctcatggga aaattgtgat caaaagggct atgggaaggg cagaccccgc caatgatttc
     2341 tcttcacctg tcttaagatt aaataaaaaa gagtgtcctg gcagttatct tgaggtgggg
     2401 aaggaggtga tgaaacatta gtttgtgaaa tccaaggccc tggcttgctt tctttctttt
     2461 tttttttttt tttttgaaac agtctctctc tgtcacccag gctggcgtgc aatggcgcag
     2521 ttgactcact acagcctctg cctcccaggt tcaagcgatt ctcatgcctt agcctcccaa
     2581 gtagctggga ttacaggtgt gtgccgcaat gcccagctaa tttttgtgtt tttagtagag
     2641 acagggtttc actatgttgg ccaggctggt ctcgaactcc tggcctcacg tgatctgtcc
     2701 acttcagccg tccaaagtgc tgggattaca agcgtgagcc actgtgctgg gcccgaggcc
     2761 ctgacttctt gctgtaactt tccatgcatt ttttttaaaa ggagcagtgt ggattttcgc
     2821 accctttgtg aactaagttc aatgcgctct atccaaattt gcctaattga actataagaa
     2881 agtaataatt ccattttcta tcccctcagg gactgaacaa atggaaataa ctcccaggca
     2941 gtatcaggtg gtcactacag agacttccac aaaaactttt gaatgatgtg aaacacgatg
     3001 tcatgaataa gggttgagcc aactatagct ctgtgttcct actgggcttt ccctaatgtg
     3061 gttgggagtt atgccctaga ctaactgtat tgtcctagtc acagctcctt gctttgattt
     3121 catccttgat aaaatgaaga tgaaacttac actacttctc caagcctttt gctgtcttaa
     3181 gaataagacc tgagattaac actaacccta gaatagaaat gtaataggga gatggtaata
     3241 aaggagtttt tctggcacat accctcccta cagaatttct gttgctcccc agatccagtg
     3301 aagaattgca gtttcattta ttttgtacca gtcagctctt aattaagtac atgaatggag
     3361 aggaacagtg gtgcacataa tccaaatcag tgaataccat tttctggtga attacccacc
     3421 cctttgcccc tgctaccccg agggttacca tgattgtcaa cagcagcagg agcccttcca
     3481 cagggcttgg taaaaaaacc agttgaggtg ttaatgaccc tttttgctgg gtgtaaaaca
     3541 aagcatcttt aaccactgtt cattatcccc agctgctctt accaaggctt tgaaggggga
     3601 aattatgctc taggcagcca ctagtagtaa acaat
//
