LOCUS       NM_016525               2705 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens ubiquitin associated protein 1 (UBAP1), transcript
            variant 1, mRNA.
ACCESSION   NM_016525
VERSION     NM_016525.5
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 2705)
  AUTHORS   Wei,Q., Wang,P.S., Dong,H.L., Luo,W.J., Wu,Z.Y. and Li,H.F.
  TITLE     A novel UBAP1 truncated variant in a Chinese family with hereditary
            spastic paraplegia
  JOURNAL   Mol Genet Genomic Med 10 (5), e1927 (2022)
   PUBMED   35347897
  REMARK    GeneRIF: A novel UBAP1 truncated variant in a Chinese family with
            hereditary spastic paraplegia.
REFERENCE   2  (bases 1 to 2705)
  AUTHORS   Bian,X., Cheng,G., Sun,X., Liu,H., Zhang,X., Han,Y., Li,B. and
            Li,N.
  TITLE     Two novel truncating variants in UBAP1 are responsible for
            hereditary spastic paraplegia
  JOURNAL   PLoS One 16 (6), e0253871 (2021)
   PUBMED   34191852
  REMARK    GeneRIF: Two novel truncating variants in UBAP1 are responsible for
            hereditary spastic paraplegia.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2705)
  AUTHORS   Bourinaris,T., Smedley,D., Cipriani,V., Sheikh,I.,
            Athanasiou-Fragkouli,A., Chinnery,P., Morris,H., Real,R.,
            Harrison,V., Reid,E., Wood,N., Vandrovcova,J., Houlden,H. and
            Tucci,A.
  CONSRTM   Genomics England Research Consortium
  TITLE     Identification of UBAP1 mutations in juvenile hereditary spastic
            paraplegia in the 100,000 Genomes Project
  JOURNAL   Eur J Hum Genet 28 (12), 1763-1768 (2020)
   PUBMED   32934340
  REMARK    GeneRIF: Identification of UBAP1 mutations in juvenile hereditary
            spastic paraplegia in the 100,000 Genomes Project.
REFERENCE   4  (bases 1 to 2705)
  AUTHORS   Flower,T.G., Takahashi,Y., Hudait,A., Rose,K., Tjahjono,N.,
            Pak,A.J., Yokom,A.L., Liang,X., Wang,H.G., Bouamr,F., Voth,G.A. and
            Hurley,J.H.
  TITLE     A helical assembly of human ESCRT-I scaffolds reverse-topology
            membrane scission
  JOURNAL   Nat Struct Mol Biol 27 (6), 570-580 (2020)
   PUBMED   32424346
REFERENCE   5  (bases 1 to 2705)
  AUTHORS   Gu,S., Chen,C.A., Rosenfeld,J.A., Cope,H., Launay,N.,
            Flanigan,K.M., Waldrop,M.A., Schrader,R., Juusola,J.,
            Goker-Alpan,O., Milunsky,A., Schluter,A., Troncoso,M., Pujol,A.,
            Tan,Q.K., Schaaf,C.P. and Meng,L.
  TITLE     Truncating variants in UBAP1 associated with childhood-onset
            nonsyndromic hereditary spastic paraplegia
  JOURNAL   Hum Mutat 41 (3), 632-640 (2020)
   PUBMED   31696996
  REMARK    GeneRIF: Truncating variants in UBAP1 associated with
            childhood-onset nonsyndromic hereditary spastic paraplegia.
REFERENCE   6  (bases 1 to 2705)
  AUTHORS   Humphray,S.J., Oliver,K., Hunt,A.R., Plumb,R.W., Loveland,J.E.,
            Howe,K.L., Andrews,T.D., Searle,S., Hunt,S.E., Scott,C.E.,
            Jones,M.C., Ainscough,R., Almeida,J.P., Ambrose,K.D., Ashwell,R.I.,
            Babbage,A.K., Babbage,S., Bagguley,C.L., Bailey,J., Banerjee,R.,
            Barker,D.J., Barlow,K.F., Bates,K., Beasley,H., Beasley,O.,
            Bird,C.P., Bray-Allen,S., Brown,A.J., Brown,J.Y., Burford,D.,
            Burrill,W., Burton,J., Carder,C., Carter,N.P., Chapman,J.C.,
            Chen,Y., Clarke,G., Clark,S.Y., Clee,C.M., Clegg,S., Collier,R.E.,
            Corby,N., Crosier,M., Cummings,A.T., Davies,J., Dhami,P., Dunn,M.,
            Dutta,I., Dyer,L.W., Earthrowl,M.E., Faulkner,L., Fleming,C.J.,
            Frankish,A., Frankland,J.A., French,L., Fricker,D.G., Garner,P.,
            Garnett,J., Ghori,J., Gilbert,J.G., Glison,C., Grafham,D.V.,
            Gribble,S., Griffiths,C., Griffiths-Jones,S., Grocock,R., Guy,J.,
            Hall,R.E., Hammond,S., Harley,J.L., Harrison,E.S., Hart,E.A.,
            Heath,P.D., Henderson,C.D., Hopkins,B.L., Howard,P.J., Howden,P.J.,
            Huckle,E., Johnson,C., Johnson,D., Joy,A.A., Kay,M., Keenan,S.,
            Kershaw,J.K., Kimberley,A.M., King,A., Knights,A., Laird,G.K.,
            Langford,C., Lawlor,S., Leongamornlert,D.A., Leversha,M., Lloyd,C.,
            Lloyd,D.M., Lovell,J., Martin,S., Mashreghi-Mohammadi,M.,
            Matthews,L., McLaren,S., McLay,K.E., McMurray,A., Milne,S.,
            Nickerson,T., Nisbett,J., Nordsiek,G., Pearce,A.V., Peck,A.I.,
            Porter,K.M., Pandian,R., Pelan,S., Phillimore,B., Povey,S.,
            Ramsey,Y., Rand,V., Scharfe,M., Sehra,H.K., Shownkeen,R.,
            Sims,S.K., Skuce,C.D., Smith,M., Steward,C.A., Swarbreck,D.,
            Sycamore,N., Tester,J., Thorpe,A., Tracey,A., Tromans,A.,
            Thomas,D.W., Wall,M., Wallis,J.M., West,A.P., Whitehead,S.L.,
            Willey,D.L., Williams,S.A., Wilming,L., Wray,P.W., Young,L.,
            Ashurst,J.L., Coulson,A., Blocker,H., Durbin,R., Sulston,J.E.,
            Hubbard,T., Jackson,M.J., Bentley,D.R., Beck,S., Rogers,J. and
            Dunham,I.
  TITLE     DNA sequence and analysis of human chromosome 9
  JOURNAL   Nature 429 (6990), 369-374 (2004)
   PUBMED   15164053
REFERENCE   7  (bases 1 to 2705)
  AUTHORS   Qian,J., Zhang,X.M., Li,X.L., Wang,J.R., Li,W.F., Wang,R. and
            Li,G.Y.
  TITLE     [Identification of digital differential expression patterns of a
            novel human gene (UBAP1) by an expressed sequence tag strategy]
  JOURNAL   Ai Zheng 21 (3), 225-228 (2002)
   PUBMED   12451983
  REMARK    GeneRIF: the identification of differential expression patterns of
            ubap1 in different tumors.
REFERENCE   8  (bases 1 to 2705)
  AUTHORS   Qian,J., Yang,J., Zhang,X., Zhang,B., Wang,J., Zhou,M., Tang,K.,
            Li,W., Zeng,Z., Zhao,X., Shen,S. and Li,G.
  TITLE     Isolation and characterization of a novel cDNA, UBAP1, derived from
            the tumor suppressor locus in human chromosome 9p21-22
  JOURNAL   J Cancer Res Clin Oncol 127 (10), 613-618 (2001)
   PUBMED   11599797
REFERENCE   9  (bases 1 to 2705)
  AUTHORS   Qian,J., Zhang,X.H., Yang,J.B., Wang,J.R., Zhang,B.C., Tang,K. and
            Li,G.Y.
  TITLE     Cloning and Expression Analysis of a Novel Gene, UBAP1, Possibly
            Involved in Ubiquitin Pathway
  JOURNAL   Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 33 (2),
            147-152 (2001)
   PUBMED   12050802
REFERENCE   10 (bases 1 to 2705)
  AUTHORS   Simpson,J.C., Wellenreuther,R., Poustka,A., Pepperkok,R. and
            Wiemann,S.
  TITLE     Systematic subcellular localization of novel proteins identified by
            large-scale cDNA sequencing
  JOURNAL   EMBO Rep 1 (3), 287-292 (2000)
   PUBMED   11256614
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK074812.1 and AL353662.19.
            
            On Nov 22, 2018 this sequence version replaced NM_016525.4.
            
            Summary: This gene is a member of the UBA domain family, whose
            members include proteins having connections to ubiquitin and the
            ubiquitination pathway. The ubiquitin associated domain is thought
            to be a non-covalent ubiquitin binding domain consisting of a
            compact three helix bundle. This particular protein originates from
            a gene locus in a refined region on chromosome 9 undergoing loss of
            heterozygosity in nasopharyngeal carcinoma (NPC). Taking into
            account its cytogenetic location, this UBA domain family member is
            being studies as a putative target for mutation in nasopharyngeal
            carcinomas. Multiple alternatively spliced transcript variants
            encoding different isoforms have been found for this gene.
            [provided by RefSeq, Jan 2010].
            
            Transcript Variant: This variant (1) is the dominant transcript and
            encodes the dominant isoform (1).
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: AK074426.1, AK074812.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000297661.9/ ENSP00000297661.4
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-2310              AK074812.1         39-2348
            2311-2705           AL353662.19        84530-84924
FEATURES             Location/Qualifiers
     source          1..2705
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="9"
                     /map="9p13.3"
     gene            1..2705
                     /gene="UBAP1"
                     /gene_synonym="NAG20; SPG80; UAP; UBAP; UBAP-1"
                     /note="ubiquitin associated protein 1"
                     /db_xref="GeneID:51271"
                     /db_xref="HGNC:HGNC:12461"
                     /db_xref="MIM:609787"
     exon            1..198
                     /gene="UBAP1"
                     /gene_synonym="NAG20; SPG80; UAP; UBAP; UBAP-1"
                     /inference="alignment:Splign:2.1.0"
     exon            199..239
                     /gene="UBAP1"
                     /gene_synonym="NAG20; SPG80; UAP; UBAP; UBAP-1"
                     /inference="alignment:Splign:2.1.0"
     CDS             206..1714
                     /gene="UBAP1"
                     /gene_synonym="NAG20; SPG80; UAP; UBAP; UBAP-1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     nasopharyngeal carcinoma-associated gene 20 protein"
                     /codon_start=1
                     /product="ubiquitin-associated protein 1 isoform 1"
                     /protein_id="NP_057609.2"
                     /db_xref="CCDS:CCDS6550.1"
                     /db_xref="GeneID:51271"
                     /db_xref="HGNC:HGNC:12461"
                     /db_xref="MIM:609787"
                     /translation="MASKKLGADFHGTFSYLDDVPFKTGDKFKTPAKVGLPIGFSLPD
                     CLQVVREVQYDFSLEKKTIEWAEEIKKIEEAEREAECKIAEAEAKVNSKSGPEGDSKM
                     SFSKTHSTATMPPPINPILASLQHNSILTPTRVSSSATKQKVLSPPHIKADFNLADFE
                     CEEDPFDNLELKTIDEKEELRNILVGTTGPIMAQLLDNNLPRGGSGSVLQDEEVLASL
                     ERATLDFKPLHKPNGFITLPQLGNCEKMSLSSKVSLPPIPAVSNIKSLSFPKLDSDDS
                     NQKTAKLASTFHSTSCLRNGTFQNSLKPSTQSSASELNGHHTLGLSALNLDSGTEMPA
                     LTSSQMPSLSVLSVCTEESSPPNTGPTVTPPNFSVSQVPNMPSCPQAYSELQMLSPSE
                     RQCVETVVNMGYSYECVLRAMKKKGENIEQILDYLFAHGQLCEKGFDPLLVEEALEMH
                     QCSEEKMMEFLQLMSKFKEMGFELKDIKEVLLLHNNDQDNALEDLMARAGAS"
     exon            240..364
                     /gene="UBAP1"
                     /gene_synonym="NAG20; SPG80; UAP; UBAP; UBAP-1"
                     /inference="alignment:Splign:2.1.0"
     exon            365..1288
                     /gene="UBAP1"
                     /gene_synonym="NAG20; SPG80; UAP; UBAP; UBAP-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1289..1471
                     /gene="UBAP1"
                     /gene_synonym="NAG20; SPG80; UAP; UBAP; UBAP-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1472..1573
                     /gene="UBAP1"
                     /gene_synonym="NAG20; SPG80; UAP; UBAP; UBAP-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1574..2705
                     /gene="UBAP1"
                     /gene_synonym="NAG20; SPG80; UAP; UBAP; UBAP-1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2600..2605
                     /regulatory_class="polyA_signal_sequence"
                     /gene="UBAP1"
                     /gene_synonym="NAG20; SPG80; UAP; UBAP; UBAP-1"
                     /note="hexamer: ATTAAA"
     polyA_site      2622
                     /gene="UBAP1"
                     /gene_synonym="NAG20; SPG80; UAP; UBAP; UBAP-1"
                     /note="major polyA site"
     regulatory      2687..2692
                     /regulatory_class="polyA_signal_sequence"
                     /gene="UBAP1"
                     /gene_synonym="NAG20; SPG80; UAP; UBAP; UBAP-1"
                     /note="hexamer: AATAAA"
     polyA_site      2705
                     /gene="UBAP1"
                     /gene_synonym="NAG20; SPG80; UAP; UBAP; UBAP-1"
                     /note="major polyA site"
ORIGIN      
        1 gggaagtagg acttcaacat ggcggctgcg gcactggcgg tggctacggt gacggcctgg
       61 cccggagcgg gcagagttgg aggtggtggc gttcgctctc cctaggggct gtcgggagct
      121 cagcggggac cgagcctggg aggccggccg gtgccagcac ctttcggctt ctgagacggc
      181 ggcagcagcg gcattcaggt tctaaatggc ttctaagaag ttgggtgcag attttcatgg
      241 gactttcagt taccttgatg atgtcccatt taagacagga gacaaattca aaacaccagc
      301 taaagttggt ctacctattg gcttctcctt gcctgattgt ttgcaggttg tcagagaagt
      361 acagtatgac ttctctttgg aaaagaaaac cattgagtgg gctgaagaga ttaagaaaat
      421 cgaagaagcc gagcgggaag cagagtgcaa aattgcggaa gcagaagcta aagtgaattc
      481 taagagtggc ccagagggcg atagcaaaat gagcttctcc aagactcaca gtacagccac
      541 aatgccacct cctattaacc ccatcctcgc cagcttgcag cacaacagca tcctcacacc
      601 aactcgggtc agcagtagtg ccacgaaaca gaaagttctc agcccacctc acataaaggc
      661 ggatttcaat cttgctgact ttgagtgtga agaagaccca tttgataatc tggagttaaa
      721 aactattgat gagaaggaag agctgagaaa tattctggta ggaaccactg gacccattat
      781 ggctcagtta ttggacaata acttgcccag gggaggctct gggtctgtgt tacaggatga
      841 ggaggtcctg gcatccttgg aacgggcaac cctagatttc aagcctcttc ataaacccaa
      901 tggctttata accttaccac agttgggcaa ctgtgaaaag atgtcactgt cttccaaagt
      961 gtccctcccc cctatacctg cagtaagcaa tatcaaatcc ctgtctttcc ccaaacttga
     1021 ctctgatgac agcaatcaga agacagccaa gctggcgagc actttccata gcacatcctg
     1081 cctccgcaat ggcacgttcc agaattccct aaagccttcc acccaaagca gtgccagtga
     1141 gctcaatggg catcacactc ttgggctttc agctttgaac ttggacagtg gcacagagat
     1201 gccagccctg acatcctccc agatgccttc cctctctgtt ttgtctgtgt gcacagagga
     1261 atcatcacct ccaaatactg gtcccacggt cacccctcct aatttctcag tgtcacaagt
     1321 gcccaacatg cccagctgtc cccaggccta ttctgaactg cagatgctgt cccccagcga
     1381 gcggcagtgt gtggagacgg tggtcaacat gggctactcg tacgagtgtg tcctcagagc
     1441 catgaagaag aaaggagaga atattgagca gattctcgac tatctctttg cacatggaca
     1501 gctttgtgag aagggcttcg accctctttt agtggaagag gctctggaaa tgcaccagtg
     1561 ttcagaagaa aagatgatgg agtttcttca gttaatgagc aaatttaagg agatgggctt
     1621 tgagctgaaa gacattaagg aagttttgct attacacaac aatgaccagg acaatgcttt
     1681 ggaagacctc atggctcggg caggagccag ctgagaccag gccctgccta ggccctgccg
     1741 cagaaccacc atccctggga ggccctgcag agcccacctg tggggaaaga gaaggggcag
     1801 cttccggatt ttcttttggg ggttagaagg tcaggtgtgg agactgctcg ccagtctctg
     1861 tgagcctagg ccctgagctg gggaggtggg gaagattcgg gcatgtgagt gcccccagaa
     1921 ctgtcctggc tccttccgta ttaaacgcat ttgcattttg agaagtgtcc ttcccacttc
     1981 agccctccgg agagactacc ctagtctttc tggggtgttt atgtcctcag ctgaagcctg
     2041 gcctagttgc tgagaggggc tggggagatg gggcgggagg gccagactca gtgctgctgt
     2101 ggagctaggt gcttccccct tcccctgaga ctggtggact gaactccagt caagttgagt
     2161 tcaagtgaaa gattcttcca gggttttatt ttttcccctc ctaacaaagt ctcatagtgt
     2221 taacactggt tctgcaatat ctctgaggtg caaagaatgc acttttccct atggggccca
     2281 gagtttgcct tttctgccag gcagtcacca tgcttcccta ccccagcctg tttcttttgg
     2341 cttggtttgg accacagtcc tctgctaccc agggttttag agcccctgct ctaggaaaca
     2401 gtttaagaaa tcattggccc cttcccagca cattgaatgg gtaagcagac aggccatgat
     2461 ttagttggcc agcactaact ccacctctgt tctccttgaa cagcttcccc tccagcccac
     2521 tgctttagga tgacacaatg aataacacct agtcatagaa atcagtctct ctggtttgtt
     2581 ttgtattatg ttgtacatca ttaaagatct aaatacaaag gatatacagt cttgaatcta
     2641 aaataatttg ctaactaact attttgattc ttcagagaga actactaata aaaatctaaa
     2701 aggta
//
