LOCUS       NM_032830               2188 bp    mRNA    linear   PRI 19-SEP-2024
DEFINITION  Homo sapiens UTP4 small subunit processome component (UTP4),
            transcript variant 1, mRNA.
ACCESSION   NM_032830
VERSION     NM_032830.3
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 2188)
  AUTHORS   Cho,N.H., Cheveralls,K.C., Brunner,A.D., Kim,K., Michaelis,A.C.,
            Raghavan,P., Kobayashi,H., Savy,L., Li,J.Y., Canaj,H., Kim,J.Y.S.,
            Stewart,E.M., Gnann,C., McCarthy,F., Cabrera,J.P., Brunetti,R.M.,
            Chhun,B.B., Dingle,G., Hein,M.Y., Huang,B., Mehta,S.B.,
            Weissman,J.S., Gomez-Sjoberg,R., Itzhak,D.N., Royer,L.A., Mann,M.
            and Leonetti,M.D.
  TITLE     OpenCell: Endogenous tagging for the cartography of human cellular
            organization
  JOURNAL   Science 375 (6585), eabi6983 (2022)
   PUBMED   35271311
REFERENCE   2  (bases 1 to 2188)
  AUTHORS   Singh,S., Vanden Broeck,A., Miller,L., Chaker-Margot,M. and
            Klinge,S.
  TITLE     Nucleolar maturation of the human small subunit processome
  JOURNAL   Science 373 (6560), eabj5338 (2021)
   PUBMED   34516797
REFERENCE   3  (bases 1 to 2188)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   4  (bases 1 to 2188)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Paulo,J.A., Cannon,J.R., Ting,L.,
            Baltier,K., Colby,G., Gebreab,F., Gygi,M.P., Parzen,H., Szpyt,J.,
            Tam,S., Zarraga,G., Pontano-Vaites,L., Swarup,S., White,A.E.,
            Schweppe,D.K., Rad,R., Erickson,B.K., Obar,R.A., Guruharsha,K.G.,
            Li,K., Artavanis-Tsakonas,S., Gygi,S.P. and Harper,J.W.
  TITLE     Architecture of the human interactome defines protein communities
            and disease networks
  JOURNAL   Nature 545 (7655), 505-509 (2017)
   PUBMED   28514442
REFERENCE   5  (bases 1 to 2188)
  AUTHORS   Guo,F., Chen,J.J. and Tang,W.J.
  TITLE     CIRH1A augments the proliferation of RKO colorectal cancer cells
  JOURNAL   Oncol Rep 37 (4), 2375-2381 (2017)
   PUBMED   28350096
  REMARK    GeneRIF: Results show that CIRH1A was highly expressed in carcinoma
            samples and colorectal cancer cells and suggest that CIRH1A plays a
            critical role in the proliferation, cell cycle distribution, and
            apoptosis of human malignant colorectal cells.
REFERENCE   6  (bases 1 to 2188)
  AUTHORS   Yu,B., Mitchell,G.A. and Richter,A.
  TITLE     Nucleolar localization of cirhin, the protein mutated in North
            American Indian childhood cirrhosis
  JOURNAL   Exp Cell Res 311 (2), 218-228 (2005)
   PUBMED   16225863
  REMARK    GeneRIF: Cirhin is a nucleolar protein and the R565W mutation, for
            which all North American Indian childhood cirrhosis patients are
            homozygous, has no effect on subcellular localization.
REFERENCE   7  (bases 1 to 2188)
  AUTHORS   Carlton,V.E., Pawlikowska,L. and Bull,L.N.
  TITLE     Molecular basis of intrahepatic cholestasis
  JOURNAL   Ann Med 36 (8), 606-617 (2004)
   PUBMED   15768832
  REMARK    Review article
REFERENCE   8  (bases 1 to 2188)
  AUTHORS   Chagnon,P., Michaud,J., Mitchell,G., Mercier,J., Marion,J.F.,
            Drouin,E., Rasquin-Weber,A., Hudson,T.J. and Richter,A.
  TITLE     A missense mutation (R565W) in cirhin (FLJ14728) in North American
            Indian childhood cirrhosis
  JOURNAL   Am J Hum Genet 71 (6), 1443-1449 (2002)
   PUBMED   12417987
  REMARK    GeneRIF: A missense mutation (R565W) in cirhin (FLJ14728) in North
            American Indian childhood cirrhosis
REFERENCE   9  (bases 1 to 2188)
  AUTHORS   Drouin,E., Russo,P., Tuchweber,B., Mitchell,G. and Rasquin-Weber,A.
  TITLE     North American Indian cirrhosis in children: a review of 30 cases
  JOURNAL   J Pediatr Gastroenterol Nutr 31 (4), 395-404 (2000)
   PUBMED   11045837
REFERENCE   10 (bases 1 to 2188)
  AUTHORS   Betard,C., Rasquin-Weber,A., Brewer,C., Drouin,E., Clark,S.,
            Verner,A., Darmond-Zwaig,C., Fortin,J., Mercier,J., Chagnon,P.,
            Fujiwara,T.M., Morgan,K., Richter,A., Hudson,T.J. and Mitchell,G.A.
  TITLE     Localization of a recessive gene for North American Indian
            childhood cirrhosis to chromosome region 16q22-and identification
            of a shared haplotype
  JOURNAL   Am J Hum Genet 67 (1), 222-228 (2000)
   PUBMED   10820129
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA277545.1 and BC009348.2.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_032830.2.
            
            Summary: This gene encodes a WD40-repeat-containing protein that is
            localized to the nucleolus. Mutation of this gene causes North
            American Indian childhood cirrhosis, a severe intrahepatic
            cholestasis that results in transient neonatal jaundice, and
            progresses to periportal fibrosis and cirrhosis in childhood and
            adolescence. Alternative splicing results in multiple transcript
            variants. [provided by RefSeq, Jan 2016].
            
            Transcript Variant: This variant (1) represents the longer
            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 :: SRR3476690.1105789.1, AK027675.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000314423.12/ ENSP00000327179.7
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-15                DA277545.1         54-68
            16-2188             BC009348.2         1-2173
FEATURES             Location/Qualifiers
     source          1..2188
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="16"
                     /map="16q22.1"
     gene            1..2188
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /note="UTP4 small subunit processome component"
                     /db_xref="GeneID:84916"
                     /db_xref="HGNC:HGNC:1983"
                     /db_xref="MIM:607456"
     exon            1..41
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            42..202
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     CDS             44..2104
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /note="isoform 1 is encoded by transcript variant 1;
                     testis expressed gene 292; UTP4, small subunit (SSU)
                     processome component, homolog; cirrhosis, autosomal
                     recessive 1A (cirhin); UTP4 small subunit (SSU) processome
                     component; U3 small nucleolar RNA-associated protein 4
                     homolog"
                     /codon_start=1
                     /product="U3 small nucleolar RNA-associated protein 4
                     homolog isoform 1"
                     /protein_id="NP_116219.2"
                     /db_xref="CCDS:CCDS10872.1"
                     /db_xref="GeneID:84916"
                     /db_xref="HGNC:HGNC:1983"
                     /db_xref="MIM:607456"
                     /translation="MGEFKVHRVRFFNYVPSGIRCVAYNNQSNRLAVSRTDGTVEIYN
                     LSANYFQEKFFPGHESRATEALCWAEGQRLFSAGLNGEIMEYDLQALNIKYAMDAFGG
                     PIWSMAASPSGSQLLVGCEDGSVKLFQITPDKIQFERNFDRQKSRILSLSWHPSGTHI
                     AAGSIDYISVFDVKSGSAVHKMIVDRQYMGVSKRKCIVWGVAFLSDGTIISVDSAGKV
                     QFWDSATGTLVKSHLIANADVQSIAVADQEDSFVVGTAEGTVFHFQLVPVTSNSSEKQ
                     WVRTKPFQHHTHDVRTVAHSPTALISGGTDTHLVFRPLMEKVEVKNYDAALRKITFPH
                     RCLISCSKKRQLLLFQFAHHLELWRLGSTVATGKNGDTLPLSKNADHLLHLKTKGPEN
                     IICSCISPCGSWIAYSTVSRFFLYRLNYEHDNISLKRVSKMPAFLRSALQILFSEDST
                     KLFVASNQGALHIVQLSGGSFKHLHAFQPQSGTVEAMCLLAVSPDGNWLAASGTSAGV
                     HVYNVKQLKLHCTVPAYNFPVTAMAIAPNTNNLVIAHSDQQVFEYSIPDKQYTDWSRT
                     VQKQGFHHLWLQRDTPITHISFHPKRPMHILLHDAYMFCIIDKSLPLPNDKTLLYNPF
                     PPTNESDVIRRRTAHAFKISKIYKPLLFMDLLDERTLVAVERPLDDIIAQLPPPIKKK
                     KFGT"
     exon            203..394
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            395..479
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            480..569
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            570..781
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            782..953
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            954..1045
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            1046..1142
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            1143..1207
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            1208..1330
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            1331..1487
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            1488..1594
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            1595..1690
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            1691..1876
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            1877..1987
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     exon            1988..2188
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2168..2173
                     /regulatory_class="polyA_signal_sequence"
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /note="hexamer: AATAAA"
     polyA_site      2188
                     /gene="UTP4"
                     /gene_synonym="CIRH1A; CIRHIN; NAIC; TEX292"
                     /note="major polyA site"
ORIGIN      
        1 ggagagaggc gagcaccggg aaggggagcg tggggccgct ggaatgggtg aatttaaggt
       61 ccatcgagta cgtttcttta attatgttcc atcaggaatc cgctgtgtgg cttacaataa
      121 ccagtcaaac agattggctg tttcacgaac agatggcact gtggaaattt ataacttgtc
      181 agcaaactac tttcaggaga aatttttccc aggtcatgag tctcgggcta cagaagcttt
      241 gtgctgggca gaaggacagc gactctttag tgctgggctc aatggcgaga ttatggagta
      301 tgatttacag gcgttaaaca tcaagtatgc tatggatgcc tttggaggac ctatttggag
      361 catggctgcc agccccagtg gctctcaact tttggttggt tgtgaagatg gatctgtgaa
      421 actatttcaa attaccccag acaaaatcca gtttgaaaga aattttgatc ggcagaaaag
      481 tcgcatcctg agtctcagct ggcatccctc tggtacccac attgcagctg gttccataga
      541 ctacattagt gtgtttgatg tcaaatcagg cagcgctgtt cataagatga ttgtggacag
      601 gcagtatatg ggcgtgtcta agcggaagtg catcgtgtgg ggtgtcgcct tcttgtccga
      661 tggcactatc ataagtgtgg actctgctgg gaaggtgcag ttctgggact cagccactgg
      721 gacgcttgtg aagagccatc tcatcgctaa tgctgacgtg cagtccattg ctgtagctga
      781 ccaagaagac agtttcgtgg tgggcacagc cgagggaaca gtcttccatt ttcagctggt
      841 ccctgtgaca tctaacagca gtgagaagca gtgggtgcgg acaaaaccgt tccagcatca
      901 cactcatgac gtgcgcactg tggcccacag cccaacagcg ctgatatctg gaggcactga
      961 cacccactta gtctttcgtc ctctcatgga gaaggtggaa gtaaagaatt acgatgccgc
     1021 tctccgaaaa atcacctttc cccaccgatg tctcatctcc tgttctaaaa agaggcagct
     1081 tctcctcttc cagtttgctc atcacttaga actttggcga ctgggatcca cagttgcaac
     1141 aggcaagaat ggggatactc ttccactctc taaaaatgca gatcatttac tgcacctaaa
     1201 gacaaagggt cctgagaaca ttatctgtag ctgtatctcc ccatgtggaa gttggatagc
     1261 ctattctaca gtttctcggt tttttctcta tcggctgaat tatgaacatg acaacataag
     1321 cctcaaaagg gtttccaaaa tgccagcatt ccttcgctct gcccttcaga ttttgttttc
     1381 tgaagattca acaaagctct ttgtagcatc aaatcaagga gctctgcata ttgttcagct
     1441 gtcaggagga agcttcaagc acctgcatgc tttccagcct cagtcaggaa cagtggaggc
     1501 catgtgtctt ttggcagtca gtccagatgg gaattggcta gctgcatcag gtaccagtgc
     1561 tggagtccat gtctacaacg taaaacagct aaagcttcac tgcacggtgc ctgcttacaa
     1621 tttcccagtg actgctatgg ctattgcccc caataccaac aaccttgtca tcgctcattc
     1681 ggaccagcag gtatttgagt acagcatccc agacaaacag tatacagatt ggagccggac
     1741 tgtccagaag cagggctttc accacctttg gctccaaagg gatactccta tcacacacat
     1801 cagttttcat cccaagagac cgatgcacat ccttctccat gatgcctaca tgttctgcat
     1861 cattgacaag tcattgcccc ttccaaatga caaaacctta ctctacaatc catttcctcc
     1921 cacgaatgaa tcagatgtca tccggaggcg cacagctcat gcttttaaaa tttctaagat
     1981 atataagcct ctactcttca tggatctttt ggatgaaaga acactcgtgg cagtagaacg
     2041 gcctctggat gacatcattg ctcagctccc accacccatt aaaaagaaga aatttggaac
     2101 ctaaaacagg gcactgtctg tgtccttcct tgaactgtct accctgttgc ttttcacaaa
     2161 tcatggtaat aaaacaagtt attcttga
//
