LOCUS       NM_003363               4070 bp    mRNA    linear   PRI 12-NOV-2024
DEFINITION  Homo sapiens ubiquitin specific peptidase 4 (USP4), transcript
            variant 1, mRNA.
ACCESSION   NM_003363
VERSION     NM_003363.4
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 4070)
  AUTHORS   Liu,B., Zhang,X., Zhou,Y., Liu,H., Wang,Z., Fu,Y., Gao,Q.,
            Cheng,X., Sun,Q. and Ju,Z.
  TITLE     USP4 regulates ribosome biogenesis and protein synthesis for
            hematopoietic stem cell regeneration and leukemia progression
  JOURNAL   Leukemia 38 (11), 2466-2478 (2024)
   PUBMED   39266638
  REMARK    GeneRIF: USP4 regulates ribosome biogenesis and protein synthesis
            for hematopoietic stem cell regeneration and leukemia progression.
REFERENCE   2  (bases 1 to 4070)
  AUTHORS   Hu,C., Zhang,W., Jia,Y., Zhao,J., Chen,Q., Hao,C. and Yu,Y.
  TITLE     USP4 promotes PTC progression by stabilizing LDHA and activating
            the MAPK and AKT signaling pathway
  JOURNAL   Aging (Albany NY) 16 (19), 12850-12865 (2024)
   PUBMED   39393052
  REMARK    GeneRIF: USP4 promotes PTC progression by stabilizing LDHA and
            activating the MAPK and AKT signaling pathway.
REFERENCE   3  (bases 1 to 4070)
  AUTHORS   Zhou,Y., Li,H., Zhang,Y., Zhao,E., Huang,C., Pan,X., Shu,F.,
            Liu,Z., Tang,N., Li,F. and Liao,W.
  TITLE     Deubiquitinase USP4 suppresses antitumor immunity by inhibiting
            IRF3 activation and tumor cell-intrinsic interferon response in
            colorectal cancer
  JOURNAL   Cancer Lett 589, 216836 (2024)
   PUBMED   38556105
  REMARK    GeneRIF: Deubiquitinase USP4 suppresses antitumor immunity by
            inhibiting IRF3 activation and tumor cell-intrinsic interferon
            response in colorectal cancer.
REFERENCE   4  (bases 1 to 4070)
  AUTHORS   Kim,J., Taketomi,T., Yamada,A., Uematsu,Y., Ueda,K., Chiba,T. and
            Tsuruta,F.
  TITLE     USP4 regulates TUT1 ubiquitination status in concert with SART3
  JOURNAL   Biochem Biophys Res Commun 701, 149557 (2024)
   PUBMED   38310689
  REMARK    GeneRIF: USP4 regulates TUT1 ubiquitination status in concert with
            SART3.
REFERENCE   5  (bases 1 to 4070)
  AUTHORS   Xu,J., Guo,R., Wen,N., Li,L., Yi,Y., Chen,J., He,Z., Yang,J.,
            Xiao,Z.J. and Niu,M.
  TITLE     FBXO3 stabilizes USP4 and Twist1 to promote PI3K-mediated breast
            cancer metastasis
  JOURNAL   PLoS Biol 21 (12), e3002446 (2023)
   PUBMED   38134227
  REMARK    GeneRIF: FBXO3 stabilizes USP4 and Twist1 to promote PI3K-mediated
            breast cancer metastasis.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 4070)
  AUTHORS   Di Donato,F., Chan,E.K., Askanase,A.D., Miranda-Carus,M. and
            Buyon,J.P.
  TITLE     Interaction between 52 kDa SSA/Ro and deubiquitinating enzyme
            UnpEL: a clue to function
  JOURNAL   Int J Biochem Cell Biol 33 (9), 924-934 (2001)
   PUBMED   11461834
REFERENCE   7  (bases 1 to 4070)
  AUTHORS   Frederick,A., Rolfe,M. and Chiu,M.I.
  TITLE     The human UNP locus at 3p21.31 encodes two tissue-selective,
            cytoplasmic isoforms with deubiquitinating activity that have
            reduced expression in small cell lung carcinoma cell lines
  JOURNAL   Oncogene 16 (2), 153-165 (1998)
   PUBMED   9464533
  REMARK    Erratum:[Oncogene 1998 Apr 30;16(17):2293]
REFERENCE   8  (bases 1 to 4070)
  AUTHORS   D'Andrea,A. and Pellman,D.
  TITLE     Deubiquitinating enzymes: a new class of biological regulators
  JOURNAL   Crit Rev Biochem Mol Biol 33 (5), 337-352 (1998)
   PUBMED   9827704
  REMARK    Review article
REFERENCE   9  (bases 1 to 4070)
  AUTHORS   Gray,D.A., Inazawa,J., Gupta,K., Wong,A., Ueda,R. and Takahashi,T.
  TITLE     Elevated expression of Unph, a proto-oncogene at 3p21.3, in human
            lung tumors
  JOURNAL   Oncogene 10 (11), 2179-2183 (1995)
   PUBMED   7784062
REFERENCE   10 (bases 1 to 4070)
  AUTHORS   Gupta,K., Chevrette,M. and Gray,D.A.
  TITLE     The Unp proto-oncogene encodes a nuclear protein
  JOURNAL   Oncogene 9 (6), 1729-1731 (1994)
   PUBMED   8183569
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BC125131.1, BC125130.1,
            AI887410.1, DB534804.1 and DA267618.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On May 17, 2019 this sequence version replaced NM_003363.3.
            
            Summary: The protein encoded by this gene is a protease that
            deubiquitinates target proteins such as ADORA2A and TRIM21. The
            encoded protein shuttles between the nucleus and cytoplasm and is
            involved in maintaining operational fidelity in the endoplasmic
            reticulum. Three transcript variants encoding different isoforms
            have been found for this gene. [provided by RefSeq, Oct 2011].
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (a).
            
            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 :: AK291795.1, BC125131.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000265560.9/ ENSP00000265560.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1407              BC125131.1         19-1425
            1408-3070           BC125130.1         1429-3091
            3071-3383           AI887410.1         1-313               c
            3384-3650           DB534804.1         149-415
            3651-4070           DA267618.1         65-484
FEATURES             Location/Qualifiers
     source          1..4070
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3p21.31"
     gene            1..4070
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /note="ubiquitin specific peptidase 4"
                     /db_xref="GeneID:7375"
                     /db_xref="HGNC:HGNC:12627"
                     /db_xref="MIM:603486"
     exon            1..130
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     CDS             30..2921
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /EC_number="3.4.19.12"
                     /note="isoform a is encoded by transcript variant 1;
                     ubiquitin specific protease 4 (proto-oncogene); ubiquitin
                     carboxyl-terminal hydrolase 4; ubiquitin thiolesterase 4;
                     ubiquitin-specific processing protease 4; deubiquitinating
                     enzyme 4; ubiquitin carboxyl-terminal esterase 4;
                     ubiquitin thioesterase 4; ubiquitous nuclear protein
                     homolog; ubiquitin specific peptidase 4 (proto-oncogene)"
                     /codon_start=1
                     /product="ubiquitin carboxyl-terminal hydrolase 4 isoform
                     a"
                     /protein_id="NP_003354.2"
                     /db_xref="CCDS:CCDS2793.1"
                     /db_xref="GeneID:7375"
                     /db_xref="HGNC:HGNC:12627"
                     /db_xref="MIM:603486"
                     /translation="MAEGGGCRERPDAETQKSELGPLMRTTLQRGAQWYLIDSRWFKQ
                     WKKYVGFDSWDMYNVGEHNLFPGPIDNSGLFSDPESQTLKEHLIDELDYVLVPTEAWN
                     KLLNWYGCVEGQQPIVRKVVEHGLFVKHCKVEVYLLELKLCENSDPTNVLSCHFSKAD
                     TIATIEKEMRKLFNIPAERETRLWNKYMSNTYEQLSKLDNTVQDAGLYQGQVLVIEPQ
                     NEDGTWPRQTLQSKSSTAPSRNFTTSPKSSASPYSSVSASLIANGDSTSTCGMHSSGV
                     SRGGSGFSASYNCQEPPSSHIQPGLCGLGNLGNTCFMNSALQCLSNTAPLTDYFLKDE
                     YEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQ
                     DSQELLAFLLDGLHEDLNRVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDT
                     FHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKKDRVMEVFLVPADPHCRPTQYRVT
                     VPLMGAVSDLCEALSRLSGIAAENMVVADVYNHRFHKIFQMDEGLNHIMPRDDIFVYE
                     VCSTSVDGSECVTLPVYFRERKSRPSSTSSASALYGQPLLLSVPKHKLTLESLYQAVC
                     DRISRYVKQPLPDEFGSSPLEPGACNGSRNSCEGEDEEEMEHQEEGKEQLSETEGSGE
                     DEPGNDPSETTQKKIKGQPCPKRLFTFSLVNSYGTADINSLAADGKLLKLNSRSTLAM
                     DWDSETRRLYYDEQESEAYEKHVSMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWY
                     CPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVC
                     NLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKA
                     AYVLFYQRRDDEFYKTPSLSSSGSSDGGTRPSSSQQGFGDDEACSMDTN"
     exon            131..258
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            259..389
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            390..516
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            517..662
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            663..724
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            725..865
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            866..983
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            984..1157
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            1158..1316
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            1317..1541
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            1542..1625
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            1626..1720
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            1721..1912
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            1913..2001
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            2002..2229
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            2230..2300
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            2301..2419
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            2420..2569
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            2570..2673
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            2674..2762
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     exon            2763..4070
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3362..3367
                     /regulatory_class="polyA_signal_sequence"
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /note="hexamer: AGTAAA"
     polyA_site      3385
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /note="major polyA site"
     polyA_site      3583
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /note="major polyA site"
     regulatory      3648..3653
                     /regulatory_class="polyA_signal_sequence"
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /note="hexamer: CATAAA"
     polyA_site      3676
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /note="major polyA site"
     regulatory      3763..3768
                     /regulatory_class="polyA_signal_sequence"
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /note="hexamer: AATACA"
     polyA_site      3785
                     /gene="USP4"
                     /gene_synonym="UNP; Unph"
                     /note="major polyA site"
ORIGIN      
        1 gggccggctg ggccggggcc gcggaggaga tggcggaagg tggaggctgc cgtgagcgac
       61 cggatgcgga gactcagaag tccgagcttg gacccttaat gaggaccaca ctccaacgcg
      121 gggcgcagtg gtatcttatt gacagccggt ggttcaagca gtggaagaag tatgtgggct
      181 ttgacagctg ggacatgtac aatgtgggtg aacataacct atttcctggc ccaatagaca
      241 actctgggct attttcagat cctgagagtc agaccttgaa agaacactta attgatgaat
      301 tggactatgt attggtccct accgaggcgt ggaataaact actaaactgg tacggctgtg
      361 tagaaggcca gcaacccatc gtcagaaaag ttgtggagca tggcctgttt gtcaagcact
      421 gcaaagtcga ggtgtatttg ctggaactga agctctgtga gaacagtgac cccaccaatg
      481 tgctgagttg ccatttcagc aaggcagaca ccattgcaac catcgagaaa gagatgcgga
      541 agctattcaa catccctgcg gagcgtgaaa cacggctctg gaacaaatac atgagcaaca
      601 cctacgagca gttgagcaag ctagacaaca ctgtccagga tgctgggcta taccagggtc
      661 aggtgctagt aattgagcct caaaatgaag atggcacatg gcccaggcag accttgcagt
      721 caaaatcaag cactgcgcct agcagaaatt ttactacctc tccaaaatca tcagcaagtc
      781 cctattcctc agtgtctgcc tctctcattg caaatggtga tagcactagc acctgtggga
      841 tgcacagttc cggtgtcagc aggggtggat ctggcttttc tgcttcgtat aattgtcagg
      901 agccaccatc ctctcatata caacctgggc tctgtggact tggaaacctg ggaaacacct
      961 gcttcatgaa ctccgctttg cagtgtttga gcaacactgc accactgact gactactttc
     1021 tcaaagatga gtatgaagcc gaaatcaaca gagacaaccc tctggggatg aaaggggaaa
     1081 ttgcagaagc ctatgctgaa ctcattaagc agatgtggtc tggaagggac gcccatgtgg
     1141 cacctcgcat gttcaaaact caagtaggac gttttgctcc tcaattttct ggctaccagc
     1201 aacaagattc tcaggagctg ctggcctttc ttctagatgg attgcatgaa gatctgaacc
     1261 gggtaaagaa aaagccctac ttggagctga aggatgccaa tgggcggcca gatgcggtgg
     1321 tggcaaagga agcctgggag aatcacaggt tgaggaatga ttctgtgatt gtggatactt
     1381 tccatggcct cttcaaatct actttggttt gcccagaatg tgctaaggtt tctgtgacct
     1441 ttgacccatt ttgctatcta acgctgccac tgcccttgaa gaaagatcga gttatggagg
     1501 ttttcctggt tcctgctgac cctcactgca gacctactca gtaccgtgtg actgtgccgc
     1561 tgatgggggc tgtgtccgac ctgtgcgagg ctctctccag gctgtctggc attgctgcag
     1621 aaaatatggt ggtcgcagat gtgtataatc accgattcca caaaattttc caaatggatg
     1681 aaggtttaaa ccacatcatg cctcgggatg acattttcgt gtacgaggtc tgcagcactt
     1741 ccgtggatgg ctcggaatgt gtcacgcttc cagtctactt cagggagagg aagtccaggc
     1801 catcaagcac ttcctccgca tcagcgctat atgggcagcc actattgctt tctgtcccca
     1861 agcacaagtt aacccttgag tctttgtacc aggctgtttg tgatcgtatc agccgctatg
     1921 tgaaacagcc tttacctgat gagtttggca gctcaccctt ggagccaggg gcctgcaatg
     1981 gctccaggaa cagctgtgaa ggagaagatg aggaagaaat ggagcatcag gaagaaggca
     2041 aagagcagct ttcagaaaca gaaggcagtg gggaagatga gccaggaaat gaccccagtg
     2101 agaccaccca aaagaagatc aaaggccagc cctgcccaaa aaggcttttt accttcagtc
     2161 ttgtgaactc ctatggaaca gctgacataa attcacttgc agctgatgga aaactactta
     2221 aactcaactc tcgatctaca ctggccatgg attgggacag tgaaactcgg agactttact
     2281 atgatgagca agaatctgag gcctacgaga agcatgtgag catgttgcag cctcagaaga
     2341 agaagaagac cacagtggcc ctgagagact gcatcgagct cttcaccacc atggagaccc
     2401 ttggggagca tgacccctgg tactgtccca actgtaagaa gcatcaacag gccacaaaaa
     2461 agtttgacct atggtccttg cccaagatcc tggtggtcca cctcaaacgt ttctcctaca
     2521 acagatactg gagggataag ctcgacacag tcgtagaatt cccaatcaga gggctgaaca
     2581 tgtccgagtt tgtctgtaac ctgtcagcaa ggccttatgt gtacgacctc attgccgtgt
     2641 ccaatcatta tggagccatg ggggttggcc actacactgc atatgcgaag aacaaactga
     2701 atggtaaatg gtattacttt gatgatagca acgtgtccct ggcctctgag gatcagatag
     2761 tgactaaagc agcttatgtg ctattttacc aacgtcgaga tgatgaattt tataagacac
     2821 cttcacttag cagttctggt tcctctgatg gagggacacg accaagcagc tctcagcagg
     2881 gctttgggga tgatgaggct tgcagcatgg acaccaacta atgctgactc cacgatcctg
     2941 ccaccctgta gcgccagtgt aatcccccag gagaacatct ttgacactct gcagactgct
     3001 agtgttctgt ctaaaaacca gacaaggaaa tacccttctt ttatgagcag aaggaaacaa
     3061 aaaaaaaaaa agaagaccgt ttacctagaa gaagctatgt caagaggctg aattattttt
     3121 atttttaaac aggtggtgag aaatttctgt gaaacctgtg aagctgaaaa gggggtggga
     3181 tgggggtact caatggagta tgtctgatgg atcccgaaga atggagagga acacaggcgc
     3241 tgagtatgga gcagcctgga gacccacccc acctgcaggg ctgccctgag cgcctggatt
     3301 tctggttctg atgccaatac tagtcacccc aagtagtctg ctcacagtaa cccaaacctc
     3361 aagtaaactc ccctttccct cgctatgtgc actgatatgg gtttataatt ttctgaaagt
     3421 tacccactga agcccatttc tccgttgagt catcttgtaa tttccagctt tctccccgct
     3481 aaggaagata tctagtgttg gggatcctgg cccctcaacc tcctgtggaa cccagcagtt
     3541 ctgttatatc ccctgctacc ctagatgaat taagacggtt aaatactgtg tggaactttt
     3601 attagataac acacttttta ttagataacg cttaaaggaa gtcagtacat aaaactgccc
     3661 ggtgctgtgt cccgtctagt tgtttccatg ttggcttgag aacagaaatc tttgtgggag
     3721 ttagccggga aagggctcca gttcatggcg atttagggta gtaatacatt ttggtgttac
     3781 ccagatgctt tctagaacgg gttctttcct catccctgcc aagactcttc ccggggcccc
     3841 cattcgaaag ccccgtcccc actcccaccg cggggccagc cgctgcgtgt gggcaaggcc
     3901 ttaaggaacc ggacgtatgg gtccgggatt ttttgtctga ccttcaacct aatccgtggg
     3961 ggtttggggc ctgcgcgggg cacgcgcatg cgatgaccgt tggatgggtc ggcgtcactg
     4021 cgctgcgggt gaggacaagg acgtggctgc cgactcgcca aagggggggt
//
