LOCUS       NM_012080               2103 bp    mRNA    linear   PRI 06-APR-2024
DEFINITION  Homo sapiens pseudouridine 5'-phosphatase (PUDP), transcript
            variant 2, mRNA.
ACCESSION   NM_012080
VERSION     NM_012080.5
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 2103)
  AUTHORS   Park,J., Cho,Y.G., Kim,J.K. and Kim,H.H.
  TITLE     STS and PUDP Deletion Identified by Targeted Panel Sequencing with
            CNV Analysis in X-Linked Ichthyosis: A Case Report and Literature
            Review
  JOURNAL   Genes (Basel) 14 (10), 1925 (2023)
   PUBMED   37895274
  REMARK    GeneRIF: STS and PUDP Deletion Identified by Targeted Panel
            Sequencing with CNV Analysis in X-Linked Ichthyosis: A Case Report
            and Literature Review.
            Review article
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2103)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   3  (bases 1 to 2103)
  AUTHORS   Preumont,A., Rzem,R., Vertommen,D. and Van Schaftingen,E.
  TITLE     HDHD1, which is often deleted in X-linked ichthyosis, encodes a
            pseudouridine-5'-phosphatase
  JOURNAL   Biochem J 431 (2), 237-244 (2010)
   PUBMED   20722631
  REMARK    GeneRIF: HDHD1 is a phosphatase specifically involved in
            dephosphorylation of a modified nucleotide present in RNA.
REFERENCE   4  (bases 1 to 2103)
  AUTHORS   Suzuki,Y., Tsunoda,T., Sese,J., Taira,H., Mizushima-Sugano,J.,
            Hata,H., Ota,T., Isogai,T., Tanaka,T., Nakamura,Y., Suyama,A.,
            Sakaki,Y., Morishita,S., Okubo,K. and Sugano,S.
  TITLE     Identification and characterization of the potential promoter
            regions of 1031 kinds of human genes
  JOURNAL   Genome Res 11 (5), 677-684 (2001)
   PUBMED   11337467
REFERENCE   5  (bases 1 to 2103)
  AUTHORS   Soehnge,H., Huang,X., Becker,M., Conover,D. and Stern,M.
  TITLE     Cloning and sequencing of ribosomal protein L27a and a gene similar
            to human GS1 in Drosophila
  JOURNAL   Gene 185 (2), 257-263 (1997)
   PUBMED   9055824
REFERENCE   6  (bases 1 to 2103)
  AUTHORS   Yen,P.H., Ellison,J., Salido,E.C., Mohandas,T. and Shapiro,L.
  TITLE     Isolation of a new gene from the distal short arm of the human X
            chromosome that escapes X-inactivation
  JOURNAL   Hum Mol Genet 1 (1), 47-52 (1992)
   PUBMED   1284467
REFERENCE   7  (bases 1 to 2103)
  AUTHORS   Salido,E.C., Yen,P.H., Koprivnikar,K., Yu,L.C. and Shapiro,L.J.
  TITLE     The human enamel protein gene amelogenin is expressed from both the
            X and the Y chromosomes
  JOURNAL   Am J Hum Genet 50 (2), 303-316 (1992)
   PUBMED   1734713
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DC388394.1, BC012494.1,
            DA653367.1 and AC073583.19.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Jun 2, 2019 this sequence version replaced NM_012080.4.
            
            Summary: This gene encodes a member of the haloacid
            dehalogenase-like (HAD) hydrolase superfamily. The encoded protein
            has no known biological function. This gene has a pseudogene on
            chromosome 1. Multiple alternatively spliced transcript variants
            encoding different isoforms have been identified. [provided by
            RefSeq, Jul 2010].
            
            Transcript Variant: This variant (2) lacks an alternate in-frame
            exon compared to variant 1. The resulting isoform (b) has the same
            N- and C-termini but is shorter compared to isoform a.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC012494.1, M86934.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000381077.10/ ENSP00000370467.6
            RefSeq Select criteria :: based on manual assertion, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-28                DC388394.1         39-66
            29-382              BC012494.1         1-354
            383-501             DA653367.1         370-488
            502-1050            BC012494.1         474-1022
            1051-1892           AC073583.19        19454-20295         c
            1893-2103           BC012494.1         1865-2075
FEATURES             Location/Qualifiers
     source          1..2103
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xp22.31"
     gene            1..2103
                     /gene="PUDP"
                     /gene_synonym="DXF68S1E; FAM16AX; GS1; HDHD1; HDHD1A"
                     /note="pseudouridine 5'-phosphatase"
                     /db_xref="GeneID:8226"
                     /db_xref="HGNC:HGNC:16818"
                     /db_xref="MIM:306480"
     exon            1..101
                     /gene="PUDP"
                     /gene_synonym="DXF68S1E; FAM16AX; GS1; HDHD1; HDHD1A"
                     /inference="alignment:Splign:2.1.0"
     CDS             41..727
                     /gene="PUDP"
                     /gene_synonym="DXF68S1E; FAM16AX; GS1; HDHD1; HDHD1A"
                     /EC_number="3.1.3.96"
                     /note="isoform b is encoded by transcript variant 2;
                     family with sequence similarity 16, member A, X-linked;
                     haloacid dehalogenase-like hydrolase domain containing 1A;
                     haloacid dehalogenase-like hydrolase domain-containing
                     protein 1; haloacid dehalogenase-like hydrolase
                     domain-containing protein 1A;
                     pseudouridine-5'-monophosphatase; 5'-PsiMPase"
                     /codon_start=1
                     /product="pseudouridine-5'-phosphatase isoform b"
                     /protein_id="NP_036212.3"
                     /db_xref="CCDS:CCDS48075.1"
                     /db_xref="GeneID:8226"
                     /db_xref="HGNC:HGNC:16818"
                     /db_xref="MIM:306480"
                     /translation="MAAPPQPVTHLIFDMDGLLLDTERLYSVVFQEICNRYDKKYSWD
                     VKSLVMGKKALEAAQIIIDVLQLPMSKEELVEESQTKLKEVFPTAALMPGAEKLIIHL
                     RKHGIPFALATSSGSASFDMKTSRHKEFFSLFSHIVLGDDPEVQHGKPDPDIFLACAK
                     RFSPPPAMEKCLVFEDAPNGVEAALAAGMQVVMVPDGNLSRDLTTKATLVLNSLQDFQ
                     PELFGLPSYE"
     exon            102..320
                     /gene="PUDP"
                     /gene_synonym="DXF68S1E; FAM16AX; GS1; HDHD1; HDHD1A"
                     /inference="alignment:Splign:2.1.0"
     exon            321..550
                     /gene="PUDP"
                     /gene_synonym="DXF68S1E; FAM16AX; GS1; HDHD1; HDHD1A"
                     /inference="alignment:Splign:2.1.0"
     exon            551..2103
                     /gene="PUDP"
                     /gene_synonym="DXF68S1E; FAM16AX; GS1; HDHD1; HDHD1A"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2081..2086
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PUDP"
                     /gene_synonym="DXF68S1E; FAM16AX; GS1; HDHD1; HDHD1A"
                     /note="hexamer: AATAAA"
     polyA_site      2103
                     /gene="PUDP"
                     /gene_synonym="DXF68S1E; FAM16AX; GS1; HDHD1; HDHD1A"
                     /note="major polyA site"
ORIGIN      
        1 acttcctcct cgcccccacc cagacccaga aggcgccacc atggcggcgc ccccgcagcc
       61 cgtcacccac ctcatctttg acatggacgg acttcttctg gatactgaac ggctgtattc
      121 agtggtgttt caagaaatat gtaatcgcta tgacaagaaa tacagctggg atgtaaagtc
      181 cctggttatg ggtaagaagg cattagaggc ggcacagatt ataatagacg tcttgcagct
      241 cccgatgtcc aaagaggagc tggtggaaga aagccaaacg aagttaaagg aagtgttccc
      301 cacggctgcg ctcatgccag gggcggagaa actcatcatc cacctgcgga aacatggcat
      361 cccctttgca ctggccacca gctcggggtc cgcgtcgttc gatatgaaga caagccgcca
      421 caaggagttc ttcagcttgt tttcccacat tgtgctggga gatgaccccg aagtgcagca
      481 tggcaagcca gacccggaca tcttcctagc ttgtgccaag aggttctctc cccctcctgc
      541 tatggagaag tgccttgtct ttgaagatgc tcccaatggg gtggaggcgg ccctggcagc
      601 tgggatgcag gtggtcatgg ttcctgacgg aaacttgagc cgagatctga caacaaaggc
      661 caccctggtg ctgaattccc tgcaggactt ccagcccgag ctgtttggtt tgccctccta
      721 tgagtgagag ggagggcctc agtcttccgc ccccagccca ctctcatggt ccacactgct
      781 gggggaaagg gaaaggaaat cagcaactct tcaatcccaa cctgcgctgt gattttagcc
      841 tcctgagatt ggagtttcca tcccatgttg gtttgtccca gtctaacgtg ttgataaaat
      901 gtgacttgac ggttgagaca aaaaatacag tagagacaga aacgaagccc agaacaaaga
      961 tgaaacttga attaccatct cagaagtcaa gctgatggag tatgtgataa agtgaatgta
     1021 catgtatata cacacacacc tccatatata catgtgtgta tcagtttggt aatatgcagg
     1081 taggcattac atgcatatgt atgtagacat atgcatgcat gtatatgtaa aatatatact
     1141 tttccaagac aaaatggaac atcacttctc tcttctagtt tttctgaaca ctggctggga
     1201 aatgtaaact gtgtatgcat ataagtatat gctttatgta tgcatatgta tgtagatatg
     1261 tttatatcta tcgtctgcat cactctcctc agtgttgatg tcaacatgca atgacaactg
     1321 ataaagcgag atggtagttc tgcctggttt gcagtctgag tgggaaagtc ctgtttttga
     1381 tgagcactcc ttgttagcta acatttaaat tctttttgtg acctcagaat gtctctggat
     1441 ctttcctcat tgactgactc tgtgccacgt catccatagt ttattgttag tatgaacaca
     1501 actgtaacat ttacctggta tctacatcct tacctgcatt ggaaaatgtt tgctacctca
     1561 caacaaccat ttgcctcctt taagaacact gatgggctgc actttttgga tagaaataga
     1621 atttgatttc agaatgtatg cttggtgagt ctcagtgccc aggaacactt ttggaataat
     1681 ttatcagaca ttgaacttct gtgattaatc gcttttatag atttactcag tctttaaaat
     1741 tcgtctctga tttgccagag aaaaacggtg gtagccatgg aaatcgggag tgaaggagca
     1801 ctgcttcatt gtggctcagc ccttcctagg ggcctctgcc ctttgatgtc cttgagctac
     1861 tcttcagctc tggaagttgt ggacaaaccg taggaatgta tgtgtgcgtg tggtggagtg
     1921 attgtctgtg aatgacaggc cctggctatt gattgatgtt gcatcaattt agcaaattca
     1981 tttcctcatt cttgatggcc tgaatatatg tctgcacttt taatgctcct cttaaccagt
     2041 tgtaacatct taccatttcc ctaacaaatt gaattagttt aataaaatct tttgacacat
     2101 gtt
//
