LOCUS       NM_003900               2840 bp    mRNA    linear   PRI 21-MAR-2025
DEFINITION  Homo sapiens sequestosome 1 (SQSTM1), transcript variant 1, mRNA.
ACCESSION   NM_003900
VERSION     NM_003900.5
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 2840)
  AUTHORS   Kramer,N., Mato,U.G., Krauter,S., Buscher,N., Afifi,A., Herhaus,L.,
            Florin,L., Plachter,B. and Zimmermann,C.
  TITLE     The Autophagy Receptor SQSTM1/p62 Is a Restriction Factor of HCMV
            Infection
  JOURNAL   Viruses 16 (9), 1440 (2024)
   PUBMED   39339916
  REMARK    GeneRIF: The Autophagy Receptor SQSTM1/p62 Is a Restriction Factor
            of HCMV Infection.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2840)
  AUTHORS   Dasgupta,N., Lei,X., Shi,C.H., Arnold,R., Teneche,M.G.,
            Miller,K.N., Rajesh,A., Davis,A., Anschau,V., Campos,A.R.,
            Gilson,R., Havas,A., Yin,S., Chua,Z.M., Liu,T., Proulx,J.,
            Alcaraz,M., Rather,M.I., Baeza,J., Schultz,D.C., Yip,K.Y.,
            Berger,S.L. and Adams,P.D.
  TITLE     Histone chaperone HIRA, promyelocytic leukemia protein, and
            p62/SQSTM1 coordinate to regulate inflammation during cell
            senescence
  JOURNAL   Mol Cell 84 (17), 3271-3287 (2024)
   PUBMED   39178863
  REMARK    GeneRIF: Histone chaperone HIRA, promyelocytic leukemia protein,
            and p62/SQSTM1 coordinate to regulate inflammation during cell
            senescence.
REFERENCE   3  (bases 1 to 2840)
  AUTHORS   Martin,S., Scorzoni,S., Cordone,S., Mazzagatti,A.,
            Beznoussenko,G.V., Gunn,A.L., Di Bona,M., Eliezer,Y., Leor,G.,
            Ben-Yishay,T., Loffreda,A., Cancila,V., Rainone,M.C.,
            Ippolito,M.R., Martis,V., Bedin,F., Garre,M., Vaites,L.P.,
            Vasapolli,P., Polo,S., Parazzoli,D., Tripodo,C., Mironov,A.A.,
            Cuomo,A., Ben-David,U., Bakhoum,S.F., Hatch,E.M., Ly,P. and
            Santaguida,S.
  TITLE     A p62-dependent rheostat dictates micronuclei catastrophe and
            chromosome rearrangements
  JOURNAL   Science 385 (6712), eadj7446 (2024)
   PUBMED   39208097
  REMARK    GeneRIF: A p62-dependent rheostat dictates micronuclei catastrophe
            and chromosome rearrangements.
REFERENCE   4  (bases 1 to 2840)
  AUTHORS   Wang,Y., Lyu,L., Vu,T. and McCarty,N.
  TITLE     TRIM44 enhances autophagy via SQSTM1 oligomerization in response to
            oxidative stress
  JOURNAL   Sci Rep 14 (1), 18974 (2024)
   PUBMED   39152142
  REMARK    GeneRIF: TRIM44 enhances autophagy via SQSTM1 oligomerization in
            response to oxidative stress.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2840)
  AUTHORS   Vadlamudi,R.K., Joung,I., Strominger,J.L. and Shin,J.
  TITLE     p62, a phosphotyrosine-independent ligand of the SH2 domain of
            p56lck, belongs to a new class of ubiquitin-binding proteins
  JOURNAL   J Biol Chem 271 (34), 20235-20237 (1996)
   PUBMED   8702753
REFERENCE   6  (bases 1 to 2840)
  AUTHORS   Joung,I., Strominger,J.L. and Shin,J.
  TITLE     Molecular cloning of a phosphotyrosine-independent ligand of the
            p56lck SH2 domain
  JOURNAL   Proc Natl Acad Sci U S A 93 (12), 5991-5995 (1996)
   PUBMED   8650207
REFERENCE   7  (bases 1 to 2840)
  AUTHORS   Devergne,O., Hummel,M., Koeppen,H., Le Beau,M.M., Nathanson,E.C.,
            Kieff,E. and Birkenbach,M.
  TITLE     A novel interleukin-12 p40-related protein induced by latent
            Epstein-Barr virus infection in B lymphocytes
  JOURNAL   J Virol 70 (2), 1143-1153 (1996)
   PUBMED   8551575
  REMARK    Erratum:[J Virol 1996 Apr;70(4):2678]
REFERENCE   8  (bases 1 to 2840)
  AUTHORS   Park,I., Chung,J., Walsh,C.T., Yun,Y., Strominger,J.L. and Shin,J.
  TITLE     Phosphotyrosine-independent binding of a 62-kDa protein to the src
            homology 2 (SH2) domain of p56lck and its regulation by
            phosphorylation of Ser-59 in the lck unique N-terminal region
  JOURNAL   Proc Natl Acad Sci U S A 92 (26), 12338-12342 (1995)
   PUBMED   8618896
REFERENCE   9  (bases 1 to 2840)
  AUTHORS   Siddique,N. and Siddique,T.
  TITLE     Amyotrophic Lateral Sclerosis Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301623
REFERENCE   10 (bases 1 to 2840)
  AUTHORS   Perlman,S.
  TITLE     Hereditary Ataxia Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301317
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DC398116.1, BC000951.2,
            BC017222.1 and AI333228.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_003900.4.
            
            Summary: This gene encodes a multifunctional protein that binds
            ubiquitin and regulates activation of the nuclear factor kappa-B
            (NF-kB) signaling pathway. The protein functions as a
            scaffolding/adaptor protein in concert with TNF receptor-associated
            factor 6 to mediate activation of NF-kB in response to upstream
            signals. Alternatively spliced transcript variants encoding either
            the same or different isoforms have been identified for this gene.
            Mutations in this gene result in sporadic and familial Paget
            disease of bone. [provided by RefSeq, Mar 2009].
            
            Transcript Variant: This variant (1) represents the predominant
            transcript, and encodes the longer 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 :: BC017222.1, SRR1803611.27484.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000389805.9/ ENSP00000374455.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-248               DC398116.1         64-311
            249-2016            BC000951.2         1-1768
            2017-2492           BC017222.1         2027-2502
            2493-2837           AI333228.1         1-345               c
            2838-2840           BC017222.1         2848-2850
FEATURES             Location/Qualifiers
     source          1..2840
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q35.3"
     gene            1..2840
                     /gene="SQSTM1"
                     /gene_synonym="A170; DMRV; EBIAP; FTDALS3; NADGP; OSIL;
                     p60; p62; p62B; PDB3; ZIP3"
                     /note="sequestosome 1"
                     /db_xref="GeneID:8878"
                     /db_xref="HGNC:HGNC:11280"
                     /db_xref="MIM:601530"
     exon            1..237
                     /gene="SQSTM1"
                     /gene_synonym="A170; DMRV; EBIAP; FTDALS3; NADGP; OSIL;
                     p60; p62; p62B; PDB3; ZIP3"
                     /inference="alignment:Splign:2.1.0"
     CDS             33..1355
                     /gene="SQSTM1"
                     /gene_synonym="A170; DMRV; EBIAP; FTDALS3; NADGP; OSIL;
                     p60; p62; p62B; PDB3; ZIP3"
                     /note="isoform 1 is encoded by transcript variant 1;
                     oxidative stress induced like; ubiquitin-binding protein
                     p62; EBI3-associated protein p60; phosphotyrosine
                     independent ligand for the Lck SH2 domain p62;
                     EBI3-associated protein of 60 kDa;
                     phosphotyrosine-independent ligand for the Lck SH2 domain
                     of 62 kDa; autophagy receptor p62"
                     /codon_start=1
                     /product="sequestosome-1 isoform 1"
                     /protein_id="NP_003891.1"
                     /db_xref="CCDS:CCDS34317.1"
                     /db_xref="GeneID:8878"
                     /db_xref="HGNC:HGNC:11280"
                     /db_xref="MIM:601530"
                     /translation="MASLTVKAYLLGKEDAAREIRRFSFCCSPEPEAEAEAAAGPGPC
                     ERLLSRVAALFPALRPGGFQAHYRDEDGDLVAFSSDEELTMAMSYVKDDIFRIYIKEK
                     KECRRDHRPPCAQEAPRNMVHPNVICDGCNGPVVGTRYKCSVCPDYDLCSVCEGKGLH
                     RGHTKLAFPSPFGHLSEGFSHSRWLRKVKHGHFGWPGWEMGPPGNWSPRPPRAGEARP
                     GPTAESASGPSEDPSVNFLKNVGESVAAALSPLGIEVDIDVEHGGKRSRLTPVSPESS
                     STEEKSSSQPSSCCSDPSKPGGNVEGATQSLAEQMRKIALESEGRPEEQMESDNCSGG
                     DDDWTHLSSKEVDPSTGELQSLQMPESEGPSSLDPSQEGPTGLKEAALYPHLPPEADP
                     RLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQYSKHPPPL"
     exon            238..333
                     /gene="SQSTM1"
                     /gene_synonym="A170; DMRV; EBIAP; FTDALS3; NADGP; OSIL;
                     p60; p62; p62B; PDB3; ZIP3"
                     /inference="alignment:Splign:2.1.0"
     exon            334..563
                     /gene="SQSTM1"
                     /gene_synonym="A170; DMRV; EBIAP; FTDALS3; NADGP; OSIL;
                     p60; p62; p62B; PDB3; ZIP3"
                     /inference="alignment:Splign:2.1.0"
     exon            564..705
                     /gene="SQSTM1"
                     /gene_synonym="A170; DMRV; EBIAP; FTDALS3; NADGP; OSIL;
                     p60; p62; p62B; PDB3; ZIP3"
                     /inference="alignment:Splign:2.1.0"
     exon            706..786
                     /gene="SQSTM1"
                     /gene_synonym="A170; DMRV; EBIAP; FTDALS3; NADGP; OSIL;
                     p60; p62; p62B; PDB3; ZIP3"
                     /inference="alignment:Splign:2.1.0"
     exon            787..1001
                     /gene="SQSTM1"
                     /gene_synonym="A170; DMRV; EBIAP; FTDALS3; NADGP; OSIL;
                     p60; p62; p62B; PDB3; ZIP3"
                     /inference="alignment:Splign:2.1.0"
     exon            1002..1197
                     /gene="SQSTM1"
                     /gene_synonym="A170; DMRV; EBIAP; FTDALS3; NADGP; OSIL;
                     p60; p62; p62B; PDB3; ZIP3"
                     /inference="alignment:Splign:2.1.0"
     exon            1198..2840
                     /gene="SQSTM1"
                     /gene_synonym="A170; DMRV; EBIAP; FTDALS3; NADGP; OSIL;
                     p60; p62; p62B; PDB3; ZIP3"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1990..1995
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SQSTM1"
                     /gene_synonym="A170; DMRV; EBIAP; FTDALS3; NADGP; OSIL;
                     p60; p62; p62B; PDB3; ZIP3"
                     /note="hexamer: ATTAAA"
     polyA_site      2016
                     /gene="SQSTM1"
                     /gene_synonym="A170; DMRV; EBIAP; FTDALS3; NADGP; OSIL;
                     p60; p62; p62B; PDB3; ZIP3"
                     /note="major polyA site"
     regulatory      2814..2819
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SQSTM1"
                     /gene_synonym="A170; DMRV; EBIAP; FTDALS3; NADGP; OSIL;
                     p60; p62; p62B; PDB3; ZIP3"
                     /note="hexamer: AATAAA"
     polyA_site      2840
                     /gene="SQSTM1"
                     /gene_synonym="A170; DMRV; EBIAP; FTDALS3; NADGP; OSIL;
                     p60; p62; p62B; PDB3; ZIP3"
ORIGIN      
        1 acggcccgtt ttccgccagc tcgccgctcg ctatggcgtc gctcaccgtg aaggcctacc
       61 ttctgggcaa ggaggacgcg gcgcgcgaga ttcgccgctt cagcttctgc tgcagccccg
      121 agcctgaggc ggaagccgag gctgcggcgg gtccgggacc ctgcgagcgg ctgctgagcc
      181 gggtggccgc cctgttcccc gcgctgcggc ctggcggctt ccaggcgcac taccgcgatg
      241 aggacgggga cttggttgcc ttttccagtg acgaggaatt gacaatggcc atgtcctacg
      301 tgaaggatga catcttccga atctacatta aagagaaaaa agagtgccgg cgggaccacc
      361 gcccaccgtg tgctcaggag gcgccccgca acatggtgca ccccaatgtg atctgcgatg
      421 gctgcaatgg gcctgtggta ggaacccgct acaagtgcag cgtctgccca gactacgact
      481 tgtgtagcgt ctgcgaggga aagggcttgc accgggggca caccaagctc gcattcccca
      541 gccccttcgg gcacctgtct gagggcttct cgcacagccg ctggctccgg aaggtgaaac
      601 acggacactt cgggtggcca ggatgggaaa tgggtccacc aggaaactgg agcccacgtc
      661 ctcctcgtgc aggggaggcc cgccctggcc ccacggcaga atcagcttct ggtccatcgg
      721 aggatccgag tgtgaatttc ctgaagaacg ttggggagag tgtggcagct gcccttagcc
      781 ctctgggcat tgaagttgat atcgatgtgg agcacggagg gaaaagaagc cgcctgaccc
      841 ccgtctctcc agagagttcc agcacagagg agaagagcag ctcacagcca agcagctgct
      901 gctctgaccc cagcaagccg ggtgggaatg ttgagggcgc cacgcagtct ctggcggagc
      961 agatgaggaa gatcgccttg gagtccgagg ggcgccctga ggaacagatg gagtcggata
     1021 actgttcagg aggagatgat gactggaccc atctgtcttc aaaagaagtg gacccgtcta
     1081 caggtgaact ccagtcccta cagatgccag aatccgaagg gccaagctct ctggacccct
     1141 cccaggaggg acccacaggg ctgaaggaag ctgccttgta cccacatctc ccgccagagg
     1201 ctgacccgcg gctgattgag tccctctccc agatgctgtc catgggcttc tctgatgaag
     1261 gcggctggct caccaggctc ctgcagacca agaactatga catcggagcg gctctggaca
     1321 ccatccagta ttcaaagcat cccccgccgt tgtgaccact tttgcccacc tcttctgcgt
     1381 gcccctcttc tgtctcatag ttgtgttaag cttgcgtaga attgcaggtc tctgtacggg
     1441 ccagtttctc tgccttcttc caggatcagg ggttagggtg caagaagcca tttagggcag
     1501 caaaacaagt gacatgaagg gagggtccct gtgtgtgtgt gtgctgatgt ttcctgggtg
     1561 ccctggctcc ttgcagcagg gctgggcctg cgagacccaa ggctcactgc agcgcgctcc
     1621 tgacccctcc ctgcaggggc tacgttagca gcccagcaca tagcttgcct aatggctttc
     1681 actttctctt ttgttttaaa tgactcatag gtccctgaca tttagttgat tattttctgc
     1741 tacagacctg gtacactctg attttagata aagtaagcct aggtgttgtc agcaggcagg
     1801 ctggggaggc cagtgttgtg ggcttcctgc tgggactgag aaggctcacg aagggcatcc
     1861 gcaatgttgg tttcactgag agctgcctcc tggtctcttc accactgtag ttctctcatt
     1921 tccaaaccat cagctgcttt taaaataaga tctctttgta gccatcctgt taaatttgta
     1981 aacaatctaa ttaaatggca tcagcacttt aaccaatgac gtttgcatag agagaaatga
     2041 ttgacagtaa gtttattgtt aatggttctt acagagtatc tttaaaagtg ccttagggga
     2101 accctgtccc tcctaacaag tgtatctcga ttaataacct gccagtccca gatcacacat
     2161 catcatcgaa gtcttcccca gttataaaga ggtcacatag tcgtgtgggt cgaggattct
     2221 gtgcctccag gaccaggggc ccaccctctg cccagggagt ccttgcgtcc catgaggtct
     2281 tcccgcaagg cctctcagac ccagatgtga cggggtgtgt ggcccgagga agctggacag
     2341 cggcagtggg cctgctgagg ccttctcttg aggcctgtgc tctgggggtc ccttgcttag
     2401 cctgtgctgg accagctggc ctggggtccc tctgaagaga ccttggctgc tcactgtcca
     2461 catgtgaact ttttctaggt ggcaggacaa attgcgccca tttagaggat gtggctgtaa
     2521 cctgctggat gggactccat agctccttcc caggacccct cagctccccg gcactgcagt
     2581 ctgcagagtt ctcctggagg caggggctgc tgccttgttt caccttccat gtcaggccag
     2641 cctgtccctg aaagagaaga tggccatgcc ctccatgtgt aagaacaatg ccagggccca
     2701 ggaggaccgc ctgccctgcc tgggccttgg ctgggcctct ggttctgaca ctttctgctg
     2761 gaagctgtca ggctgggaca ggctttgatt ttgagggtta gcaagacaaa gcaaataaat
     2821 gccttccacc tcaccgcaaa
//
