LOCUS       NM_016004               1754 bp    mRNA    linear   PRI 11-OCT-2024
DEFINITION  Homo sapiens intraflagellar transport 52 (IFT52), transcript
            variant 1, mRNA.
ACCESSION   NM_016004
VERSION     NM_016004.5
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 1754)
  AUTHORS   Udupa,P. and Ghosh,D.K.
  TITLE     The emerging functions of intraflagellar transport 52 in ciliary
            transport and ciliopathies
  JOURNAL   Traffic 25 (1), e12929 (2024)
   PUBMED   38272449
  REMARK    GeneRIF: The emerging functions of intraflagellar transport 52 in
            ciliary transport and ciliopathies.
            Review article
REFERENCE   2  (bases 1 to 1754)
  AUTHORS   Guleria,V.S., Parit,R., Quadri,N., Das,R. and Upadhyai,P.
  TITLE     The intraflagellar transport protein IFT52 associated with
            short-rib thoracic dysplasia is essential for ciliary function in
            osteogenic differentiation in vitro and for sensory perception in
            Drosophila
  JOURNAL   Exp Cell Res 418 (2), 113273 (2022)
   PUBMED   35839863
  REMARK    GeneRIF: The intraflagellar transport protein IFT52 associated with
            short-rib thoracic dysplasia is essential for ciliary function in
            osteogenic differentiation in vitro and for sensory perception in
            Drosophila.
REFERENCE   3  (bases 1 to 1754)
  AUTHORS   Ishida,Y., Tasaki,K., Katoh,Y. and Nakayama,K.
  TITLE     Molecular basis underlying the ciliary defects caused by IFT52
            variations found in skeletal ciliopathies
  JOURNAL   Mol Biol Cell 33 (9), ar83 (2022)
   PUBMED   35704471
  REMARK    GeneRIF: Molecular basis underlying the ciliary defects caused by
            IFT52 variations found in skeletal ciliopathies.
REFERENCE   4  (bases 1 to 1754)
  AUTHORS   Sorusch,N., Yildirim,A., Knapp,B., Janson,J., Fleck,W., Scharf,C.
            and Wolfrum,U.
  TITLE     SANS (USH1G) Molecularly Links the Human Usher Syndrome Protein
            Network to the Intraflagellar Transport Module by Direct Binding to
            IFT-B Proteins
  JOURNAL   Front Cell Dev Biol 7, 216 (2019)
   PUBMED   31637240
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1754)
  AUTHORS   Girisha,K.M., Shukla,A., Trujillano,D., Bhavani,G.S., Hebbar,M.,
            Kadavigere,R. and Rolfs,A.
  TITLE     A homozygous nonsense variant in IFT52 is associated with a human
            skeletal ciliopathy
  JOURNAL   Clin Genet 90 (6), 536-539 (2016)
   PUBMED   26880018
  REMARK    GeneRIF: Whole-exome sequencing revealed a homozygous nonsense
            variant p.R142* in IFT52 encoding an IFT-B core complex protein as
            the probable cause of her condition. This is the first report of a
            human disease associated with IFT52
REFERENCE   6  (bases 1 to 1754)
  AUTHORS   Zhang,W., Taylor,S.P., Nevarez,L., Lachman,R.S., Nickerson,D.A.,
            Bamshad,M., Krakow,D. and Cohn,D.H.
  CONSRTM   University of Washington Center for Mendelian Genomics Consortium
  TITLE     IFT52 mutations destabilize anterograde complex assembly, disrupt
            ciliogenesis and result in short rib polydactyly syndrome
  JOURNAL   Hum Mol Genet 25 (18), 4012-4020 (2016)
   PUBMED   27466190
  REMARK    GeneRIF: The data identify a new locus for short-rib polydactyly
            syndromes (SRPS) and show that IFT52 mutations result in a
            ciliopathy with primary effects on the skeleton.
REFERENCE   7  (bases 1 to 1754)
  AUTHORS   Katoh,Y., Terada,M., Nishijima,Y., Takei,R., Nozaki,S., Hamada,H.
            and Nakayama,K.
  TITLE     Overall Architecture of the Intraflagellar Transport (IFT)-B
            Complex Containing Cluap1/IFT38 as an Essential Component of the
            IFT-B Peripheral Subcomplex
  JOURNAL   J Biol Chem 291 (21), 10962-10975 (2016)
   PUBMED   26980730
REFERENCE   8  (bases 1 to 1754)
  AUTHORS   Boldt,K., van Reeuwijk,J., Lu,Q., Koutroumpas,K., Nguyen,T.M.,
            Texier,Y., van Beersum,S.E., Horn,N., Willer,J.R., Mans,D.A.,
            Dougherty,G., Lamers,I.J., Coene,K.L., Arts,H.H., Betts,M.J.,
            Beyer,T., Bolat,E., Gloeckner,C.J., Haidari,K., Hetterschijt,L.,
            Iaconis,D., Jenkins,D., Klose,F., Knapp,B., Latour,B.,
            Letteboer,S.J., Marcelis,C.L., Mitic,D., Morleo,M., Oud,M.M.,
            Riemersma,M., Rix,S., Terhal,P.A., Toedt,G., van Dam,T.J., de
            Vrieze,E., Wissinger,Y., Wu,K.M., Apic,G., Beales,P.L.,
            Blacque,O.E., Gibson,T.J., Huynen,M.A., Katsanis,N., Kremer,H.,
            Omran,H., van Wijk,E., Wolfrum,U., Kepes,F., Davis,E.E., Franco,B.,
            Giles,R.H., Ueffing,M., Russell,R.B. and Roepman,R.
  CONSRTM   UK10K Rare Diseases Group
  TITLE     An organelle-specific protein landscape identifies novel diseases
            and molecular mechanisms
  JOURNAL   Nat Commun 7, 11491 (2016)
   PUBMED   27173435
  REMARK    Publication Status: Online-Only
REFERENCE   9  (bases 1 to 1754)
  AUTHORS   Fossey,S.C., Mychaleckyj,J.C., Pendleton,J.K., Snyder,J.R.,
            Bensen,J.T., Hirakawa,S., Rich,S.S., Freedman,B.I. and Bowden,D.W.
  TITLE     A high-resolution 6.0-megabase transcript map of the type 2
            diabetes susceptibility region on human chromosome 20
  JOURNAL   Genomics 76 (1-3), 45-57 (2001)
   PUBMED   11549316
REFERENCE   10 (bases 1 to 1754)
  AUTHORS   Tan,W., Lin,A. and Keppler-Noreuil,K.
  TITLE     Cranioectodermal Dysplasia
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   24027799
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DC358472.1, BP308189.1,
            BC039831.1, AI819589.1 and AL121886.22.
            This sequence is a reference standard in the RefSeqGene project.
            
            On May 17, 2019 this sequence version replaced NM_016004.4.
            
            Summary: This gene encodes a conserved proline-rich protein that is
            a component of the intraflagellar transport-B (IFT-B) core complex.
            The encoded protein is essential for the integrity of the IFT-B
            core complex, and for biosynthesis and maintenance of cilia.
            Mutations in this gene are associated with ciliopathy that affects
            the skeleton. [provided by RefSeq, Oct 2016].
            
            Transcript Variant: This variant (1) encodes the longest isoform
            (1). Both variants 1 and 2 encode the same 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 :: SRR1803615.185277.1,
                                           SRR1660807.29099.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000373030.8/ ENSP00000362121.3
            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
            1-18                DC358472.1         292-309
            19-283              BP308189.1         1-265
            284-1677            BC039831.1         289-1682
            1678-1751           AI819589.1         1-74                c
            1752-1754           AL121886.22        40471-40473
FEATURES             Location/Qualifiers
     source          1..1754
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="20"
                     /map="20q13.12"
     gene            1..1754
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /note="intraflagellar transport 52"
                     /db_xref="GeneID:51098"
                     /db_xref="HGNC:HGNC:15901"
                     /db_xref="MIM:617094"
     exon            1..118
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /inference="alignment:Splign:2.1.0"
     exon            119..243
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /inference="alignment:Splign:2.1.0"
     CDS             125..1438
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /note="isoform 1 is encoded by transcript variant 1;
                     intraflagellar transport protein 52 homolog; protein NGD5
                     homolog"
                     /codon_start=1
                     /product="intraflagellar transport protein 52 homolog
                     isoform 1"
                     /protein_id="NP_057088.2"
                     /db_xref="CCDS:CCDS33470.1"
                     /db_xref="GeneID:51098"
                     /db_xref="HGNC:HGNC:15901"
                     /db_xref="MIM:617094"
                     /translation="MEKELRSTILFNAYKKEIFTTNNGYKSMQKKLRSNWKIQSLKDE
                     ITSEKLNGVKLWITAGPREKFTAAEFEILKKYLDTGGDVFVMLGEGGESRFDTNINFL
                     LEEYGIMVNNDAVVRNVYHKYFHPKEALVSSGVLNREISRAAGKAVPGIIDEESSGNN
                     AQALTFVYPFGATLSVMKPAVAVLSTGSVCFPLNRPILAFYHSKNQGGKLAVLGSCHM
                     FSDQYLDKEENSKIMDVVFQWLTTGDIHLNQIDAEDPEISDYMMLPYTATLSKRNREC
                     LQESDEIPRDFTTLFDLSIFQLDTTSFHSVIEAHEQLNVKHEPLQLIQPQFETPLPTL
                     QPAVFPPSFRELPPPPLELFDLDETFSSEKARLAQITNKCTEEDLEFYVRKCGDILGV
                     TSKLPKDQQDAKHILEHVFFQVVEFKKLNQEHDIDTSETAFQNNF"
     exon            244..331
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /inference="alignment:Splign:2.1.0"
     exon            332..461
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /inference="alignment:Splign:2.1.0"
     exon            462..537
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /inference="alignment:Splign:2.1.0"
     exon            538..609
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /inference="alignment:Splign:2.1.0"
     exon            610..736
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /inference="alignment:Splign:2.1.0"
     exon            737..823
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /inference="alignment:Splign:2.1.0"
     exon            824..892
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /inference="alignment:Splign:2.1.0"
     exon            893..1047
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /inference="alignment:Splign:2.1.0"
     exon            1048..1135
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /inference="alignment:Splign:2.1.0"
     exon            1136..1244
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /inference="alignment:Splign:2.1.0"
     exon            1245..1390
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /inference="alignment:Splign:2.1.0"
     exon            1391..1754
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1641..1646
                     /regulatory_class="polyA_signal_sequence"
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /note="hexamer: ATTAAA"
     polyA_site      1677
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
                     /note="major polyA site"
     polyA_site      1705
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
     polyA_site      1754
                     /gene="IFT52"
                     /gene_synonym="C20orf9; CGI-53; NGD2; NGD5"
ORIGIN      
        1 gcgtcctggg ccacgcctcc cggcgcaccg acgcgcctct ccggttacta agcggccttg
       61 gatacctggc cgcgggatgc tgggcggcgt caggtgagcg gtggtcgctg ggcctcaggt
      121 aaccatggag aaagagctgc ggagcaccat tcttttcaat gcctacaaaa aggagatatt
      181 taccaccaac aatggctaca aatccatgca gaaaaaactt cggagtaatt ggaagattca
      241 gagcttaaaa gatgaaatca catctgagaa gttaaatgga gtgaaactgt ggattacagc
      301 tgggccaagg gaaaaattta ctgcagctga gtttgaaatc ctgaagaaat atcttgacac
      361 tggtggagat gtctttgtga tgctaggaga aggtggagaa tccagatttg acaccaatat
      421 taacttttta ctagaagaat atggaatcat ggttaataat gatgctgtgg ttagaaatgt
      481 atatcacaaa tatttccatc ctaaagaagc tctagtttcc agtggagtct tgaacaggga
      541 aattagccga gctgcaggaa aggctgtgcc tgggatcatt gatgaggaaa gcagtggaaa
      601 caatgcccag gctctcacct ttgtgtatcc ttttggtgcc acattgagtg tcatgaaacc
      661 agcagtggcg gttctgtcta caggttctgt ctgcttccca cttaacagac ccattttggc
      721 tttctatcac tcaaagaacc aaggtgggaa gctggcagtg cttggttcat gtcacatgtt
      781 cagtgatcaa tatttggaca aagaagaaaa cagcaaaatc atggatgttg ttttccagtg
      841 gctcacgaca ggagacatcc acctaaacca gattgatgct gaggacccag agatttctga
      901 ctacatgatg ctgccctaca cagccaccct atcaaagcgg aatcgagagt gtctccagga
      961 gagtgatgag atcccaaggg actttaccac cctcttcgac ctgtccatct tccagctgga
     1021 taccacctcc ttccacagcg tcatcgaggc tcacgagcag ctaaatgtga aacatgaacc
     1081 actccagctc atccagcctc agtttgagac gccgctgcca acccttcagc ctgcggtttt
     1141 tcctcccagt ttccgggagt taccacctcc tcctctggag ctatttgatt tagatgaaac
     1201 gttctcctct gagaaggcac ggctggctca gattaccaat aagtgtactg aagaagacct
     1261 ggaattttat gtcaggaagt gtggtgatat tcttggagta accagtaaac taccaaagga
     1321 ccaacaggat gccaaacata tccttgagca cgtcttcttc caagtggtgg agttcaagaa
     1381 attgaaccag gaacatgaca tcgatacaag tgaaacagca ttccagaaca atttctgaag
     1441 accatgcctc ttgaagcttt ttctgcctcc tgattctctc tttgtaaact attttcaaat
     1501 tgtttttcaa ctccttatca aaattgttta tacactcttt cctccatgag ctctggaagg
     1561 tatatgcatc ttctgtaata ctcagatagg tataagattt ttcacaaaat ccttatgtaa
     1621 gatacattcc atttttaaaa attaaatgta tggttgcatc tgtcttttta taccctatga
     1681 aacagtcttg attttttttt ctcaacccca gttctggatt tgagtctttt atcaaagaca
     1741 taattaactc tcaa
//
