LOCUS       NM_024598               2248 bp    mRNA    linear   PRI 12-OCT-2024
DEFINITION  Homo sapiens U6 snRNA biogenesis phosphodiesterase 1 (USB1),
            transcript variant 1, mRNA.
ACCESSION   NM_024598
VERSION     NM_024598.4
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 2248)
  AUTHORS   Parajuli,P., Craig,D.B., Gadgeel,M., Bagla,S., Wright,R.E. 3rd,
            Chu,R., Shanti,C.M., Thirunagari,R., Grover,S.K. and
            Ravindranath,Y.
  TITLE     Defective monocyte plasticity and altered cAMP pathway characterize
            USB1-mutated poikiloderma with neutropenia Clericuzio type
  JOURNAL   Br J Haematol 204 (2), 683-693 (2024)
   PUBMED   37779259
  REMARK    GeneRIF: Defective monocyte plasticity and altered cAMP pathway
            characterize USB1-mutated poikiloderma with neutropenia Clericuzio
            type.
REFERENCE   2  (bases 1 to 2248)
  AUTHORS   Yan,C., Zhou,T. and Geng,S.
  TITLE     Chinese nontwin sisters suffer from poikiloderma with neutropenia
            harboring novel compound heterozygous USB1 gene mutations
  JOURNAL   J Dermatol 50 (9), e278-e279 (2023)
   PUBMED   36938655
  REMARK    GeneRIF: Chinese nontwin sisters suffer from poikiloderma with
            neutropenia harboring novel compound heterozygous USB1 gene
            mutations.
REFERENCE   3  (bases 1 to 2248)
  AUTHORS   Jeong,H.C., Shukla,S., Fok,W.C., Huynh,T.N., Batista,L.F.Z. and
            Parker,R.
  TITLE     USB1 is a miRNA deadenylase that regulates hematopoietic
            development
  JOURNAL   Science 379 (6635), 901-907 (2023)
   PUBMED   36862787
  REMARK    GeneRIF: USB1 is a miRNA deadenylase that regulates hematopoietic
            development.
REFERENCE   4  (bases 1 to 2248)
  AUTHORS   Vahidnezhad,H., Youssefian,L., Saeidian,A.H., Boyden,L.M.,
            Touati,A., Harvey,N., Naji,M., Zabihi,M., Barzegar,M., Sotoudeh,S.,
            Liu,L., Guy,A., Kariminejad,A., Zeinali,S., Choate,K.A.,
            McGrath,J.A. and Uitto,J.
  TITLE     Kindler epidermolysis bullosa-like skin phenotype and downregulated
            basement membrane zone gene expression in poikiloderma with
            neutropenia and a homozygous USB1 mutation
  JOURNAL   Matrix Biol 99, 43-57 (2021)
   PUBMED   34004352
  REMARK    GeneRIF: Kindler epidermolysis bullosa-like skin phenotype and
            downregulated basement membrane zone gene expression in
            poikiloderma with neutropenia and a homozygous USB1 mutation.
REFERENCE   5  (bases 1 to 2248)
  AUTHORS   Bishnoi,A., Jamwal,M., Das,R., Scaria,V., Vishwajeet,V., De,D.,
            Saikia,U.N. and Mahajan,R.
  TITLE     Clericuzio-type poikiloderma with neutropenia in a patient from
            India
  JOURNAL   Am J Med Genet A 185 (1), 278-281 (2021)
   PUBMED   33111394
  REMARK    GeneRIF: Clericuzio-type poikiloderma with neutropenia in a patient
            from India.
REFERENCE   6  (bases 1 to 2248)
  AUTHORS   Arnold,A.W., Itin,P.H., Pigors,M., Kohlhase,J.,
            Bruckner-Tuderman,L. and Has,C.
  TITLE     Poikiloderma with neutropenia: a novel C16orf57 mutation and
            clinical diagnostic criteria
  JOURNAL   Br J Dermatol 163 (4), 866-869 (2010)
   PUBMED   20618321
REFERENCE   7  (bases 1 to 2248)
  AUTHORS   Tanaka,A., Morice-Picard,F., Lacombe,D., Nagy,N., Hide,M., Taieb,A.
            and McGrath,J.
  TITLE     Identification of a homozygous deletion mutation in C16orf57 in a
            family with Clericuzio-type poikiloderma with neutropenia
  JOURNAL   Am J Med Genet A 152A (6), 1347-1348 (2010)
   PUBMED   20503306
REFERENCE   8  (bases 1 to 2248)
  AUTHORS   Volpi,L., Roversi,G., Colombo,E.A., Leijsten,N., Concolino,D.,
            Calabria,A., Mencarelli,M.A., Fimiani,M., Macciardi,F., Pfundt,R.,
            Schoenmakers,E.F. and Larizza,L.
  TITLE     Targeted next-generation sequencing appoints c16orf57 as
            clericuzio-type poikiloderma with neutropenia gene
  JOURNAL   Am J Hum Genet 86 (1), 72-76 (2010)
   PUBMED   20004881
  REMARK    GeneRIF: c16orf57 has a role in clericuzio-type poikiloderma with
            neutropenia
            Erratum:[Am J Hum Genet. 2010 Sep 10;87(3):445]
REFERENCE   9  (bases 1 to 2248)
  AUTHORS   Colland,F., Jacq,X., Trouplin,V., Mougin,C., Groizeleau,C.,
            Hamburger,A., Meil,A., Wojcik,J., Legrain,P. and Gauthier,J.M.
  TITLE     Functional proteomics mapping of a human signaling pathway
  JOURNAL   Genome Res 14 (7), 1324-1332 (2004)
   PUBMED   15231748
REFERENCE   10 (bases 1 to 2248)
  AUTHORS   Wang,L., Clericuzio,C., Larizza,L. and Concolino,D.
  TITLE     Poikiloderma with Neutropenia
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   29072891
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DC363309.1, BC004415.1, AC012182.7 and DB364698.1.
            
            On Aug 31, 2019 this sequence version replaced NM_024598.3.
            
            Summary: This gene encodes a protein with several conserved
            domains, however, its exact function is not known. Mutations in
            this gene are associated with poikiloderma with neutropenia (PN),
            which shows phenotypic overlap with Rothmund-Thomson syndrome (RTS)
            caused by mutations in the RECQL4 gene. It is believed that this
            gene product interacts with RECQL4 protein via SMAD4 proteins,
            explaining the partial clinical overlap between PN and RTS.
            Alternatively spliced transcript variants encoding different
            isoforms have been noted for this gene. [provided by RefSeq, Mar
            2011].
            
            Transcript Variant: This variant (1) represents the predominant
            transcript and encodes the longest 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 :: BC004415.1, AK023216.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000219281.8/ ENSP00000219281.3
            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
            1-30                DC363309.1         35-64
            31-1197             BC004415.1         1-1167
            1198-2208           AC012182.7         95777-96787
            2209-2248           DB364698.1         6-45                c
FEATURES             Location/Qualifiers
     source          1..2248
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="16"
                     /map="16q21"
     gene            1..2248
                     /gene="USB1"
                     /gene_synonym="C16orf57; hMpn1; hUsb1; HVSL1; Mpn1; PN"
                     /note="U6 snRNA biogenesis phosphodiesterase 1"
                     /db_xref="GeneID:79650"
                     /db_xref="HGNC:HGNC:25792"
                     /db_xref="MIM:613276"
     exon            1..175
                     /gene="USB1"
                     /gene_synonym="C16orf57; hMpn1; hUsb1; HVSL1; Mpn1; PN"
                     /inference="alignment:Splign:2.1.0"
     CDS             78..875
                     /gene="USB1"
                     /gene_synonym="C16orf57; hMpn1; hUsb1; HVSL1; Mpn1; PN"
                     /EC_number="3.1.4.-"
                     /note="isoform 1 is encoded by transcript variant 1; HVSL
                     motif containing 1; UPF0406 protein C16orf57; U six
                     biogenesis 1; putative U6 snRNA phosphodiesterase; U6
                     snRNA biogenesis 1; mutated in poikiloderma with
                     neutropenia protein 1; mutated in PN protein 1; 3'-5' RNA
                     exonuclease USB1; U6 snRNA phosphodiesterase 1"
                     /codon_start=1
                     /product="U6 snRNA phosphodiesterase 1 isoform 1"
                     /protein_id="NP_078874.2"
                     /db_xref="CCDS:CCDS10791.1"
                     /db_xref="GeneID:79650"
                     /db_xref="HGNC:HGNC:25792"
                     /db_xref="MIM:613276"
                     /translation="MSAAPLVGYSSSGSEDESEDGMRTRPGDGSHRRGQSPLPRQRFP
                     VPDSVLNMFPGTEEGPEDDSTKHGGRVRTFPHERGNWATHVYVPYEAKEEFLDLLDVL
                     LPHAQTYVPRLVRMKVFHLSLSQSVVLRHHWILPFVQALKARMTSFHRFFFTANQVKI
                     YTNQEKTRTFIGLEVTSGHAQFLDLVSEVDRVMEEFNLTTFYQDPSFHLSLAWCVGDA
                     RLQLEGQCLQELQAIVDGFEDAEVLLRVHTEQVRCKSGNKFFSMPLK"
     exon            176..342
                     /gene="USB1"
                     /gene_synonym="C16orf57; hMpn1; hUsb1; HVSL1; Mpn1; PN"
                     /inference="alignment:Splign:2.1.0"
     exon            343..526
                     /gene="USB1"
                     /gene_synonym="C16orf57; hMpn1; hUsb1; HVSL1; Mpn1; PN"
                     /inference="alignment:Splign:2.1.0"
     exon            527..580
                     /gene="USB1"
                     /gene_synonym="C16orf57; hMpn1; hUsb1; HVSL1; Mpn1; PN"
                     /inference="alignment:Splign:2.1.0"
     exon            581..686
                     /gene="USB1"
                     /gene_synonym="C16orf57; hMpn1; hUsb1; HVSL1; Mpn1; PN"
                     /inference="alignment:Splign:2.1.0"
     exon            687..770
                     /gene="USB1"
                     /gene_synonym="C16orf57; hMpn1; hUsb1; HVSL1; Mpn1; PN"
                     /inference="alignment:Splign:2.1.0"
     exon            771..2248
                     /gene="USB1"
                     /gene_synonym="C16orf57; hMpn1; hUsb1; HVSL1; Mpn1; PN"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2222..2227
                     /regulatory_class="polyA_signal_sequence"
                     /gene="USB1"
                     /gene_synonym="C16orf57; hMpn1; hUsb1; HVSL1; Mpn1; PN"
                     /note="hexamer: AATAAA"
     polyA_site      2248
                     /gene="USB1"
                     /gene_synonym="C16orf57; hMpn1; hUsb1; HVSL1; Mpn1; PN"
                     /note="major polyA site"
ORIGIN      
        1 gcttccggca cagcggaact ccgggtgccg gttgaggttg ctggtggacc tgctctggtg
       61 gtcttggatg aggccccatg agcgcggcgc ccctggtggg ctacagcagc agcggctccg
      121 aggatgagtc cgaggacggg atgcggacca ggccggggga tgggagccac cgtcgtggcc
      181 agagccccct tcccaggcag agatttccag tacctgacag tgtgctgaac atgttcccgg
      241 gcaccgagga ggggcctgaa gatgacagca caaaacacgg gggacgggtg cgcaccttcc
      301 cccacgagcg aggcaactgg gccacccacg tctatgtacc atatgaagcc aaggaggagt
      361 tcctggatct gcttgatgtg ttgctgcccc atgcccagac atatgtcccc cggctggtaa
      421 ggatgaaggt gttccacctc agcctgtccc agagtgtggt tctgcgccac cactggatcc
      481 tccccttcgt gcaggctctg aaagcccgta tgacctcctt ccacagattc ttctttactg
      541 ccaaccaggt aaagatttac accaatcaag agaaaaccag gacctttatt gggcttgagg
      601 tcacttcagg gcatgcccag ttcctggacc tggtttcaga ggtggacaga gtcatggagg
      661 aattcaacct caccactttc taccaggatc cttctttcca cctcagcctg gcctggtgtg
      721 tgggtgatgc acgtctccag ctggaggggc agtgcctgca ggaactacag gcaatcgtgg
      781 atgggtttga agatgctgag gtgctgctgc gcgtgcacac tgagcaagtc cgctgcaagt
      841 ctgggaacaa gttcttctcg atgcctttga agtgagcacc agaggccttc ctcctccagg
      901 gccctctgca gaccaggctg agatggagga acctgctaaa atcgatggag atgcttctag
      961 cctcccagta ggaggcccca gccatgcctt caacctggca ggaggtgtag ccactcctca
     1021 tcctccctga gtgctgatat tctctctctc tctttctctt cctcttcttt ctctctcttc
     1081 tcctctcttt ctctcctctg tctctcttcc tctcctctct tcctctcttc tctcttcctc
     1141 tcctctctct cttcctcttc tctctcttcc cctcctgtct ctcctcccct cctctcttcc
     1201 tctcctctct cttcctctcc tctctctacc cctcctgtct ctcctcccct cctctctctt
     1261 cctctcctct ctctcttcct ctcctctctc ttcccttcct gtctctcttc ccctcctctc
     1321 tctcttcctg tcctctatct cttcccctcc tctatctctt cctctcctct ctctcttcct
     1381 ctcctctctc tctcttgctt tcttctctct ctcctgtctc ggctgttgtg ggttgcaggt
     1441 tgggtgctgc tgttgtggtc cttcccagaa actgccagta gagggcagcc tgggcatcct
     1501 aatgcttact ctggttgtta cacaaagaaa atattggggt cactggcgag cccacccaca
     1561 ctcaccagaa tctccactgt agtcccccta acaaacagcc cttcacttcc tctcccactt
     1621 cagcaatttg tattttgatg ccattggcct cagatcagag tgttttaaat catcacgccc
     1681 tggcttatcc ctggtcgagc caggacacgg ggtgcttcag tgggtctgtc accctctctc
     1741 cttgaagcat gttgctttta tttatttact tttactctca ccctgctcct gtaccagcag
     1801 gggccacttc aaagccaagg tacagggtga taacttgtgg tccagcatca gttttctcca
     1861 cttctttctc ccactcaccc ccagcaaggt gcctggggag acttgagcag atgtttcatt
     1921 ttggcctggc cagtggctga aagccaggcc tccaatgcac tgtgacctct ggcttcccca
     1981 gcagctttcc cagagaggca gaggggcctt ccacagcccg ggttctcctg ctgcctcctg
     2041 cctgctgcag ctgcaggcat tctgaggggc aacgtggagg aagggccagg gatgcatggg
     2101 attttaattg tttcatcaca ccttccccgt ggcaaagaaa cagtcagtcc tcttcaggtg
     2161 tcttctggat ttctggtgat ggacagagaa atctttttac agtttcaaat tatgttcaac
     2221 aaataaaaat tgcatttttt attttgga
//
