LOCUS       NM_016008               1399 bp    mRNA    linear   PRI 04-OCT-2024
DEFINITION  Homo sapiens dynein cytoplasmic 2 light intermediate chain 1
            (DYNC2LI1), transcript variant 1, mRNA.
ACCESSION   NM_016008
VERSION     NM_016008.4
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 1399)
  AUTHORS   Qiu,H., Tsurumi,Y., Katoh,Y. and Nakayama,K.
  TITLE     Combinations of deletion and missense variations of the dynein-2
            DYNC2LI1 subunit found in skeletal ciliopathies cause ciliary
            defects
  JOURNAL   Sci Rep 12 (1), 31 (2022)
   PUBMED   34997029
  REMARK    GeneRIF: Combinations of deletion and missense variations of the
            dynein-2 DYNC2LI1 subunit found in skeletal ciliopathies cause
            ciliary defects.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1399)
  AUTHORS   Zhang,X., You,Y., Xie,X., Xu,H., Zhou,H., Lei,Y., Sun,P., Meng,Y.,
            Wang,L. and Lu,Y.
  TITLE     Whole-exome sequencing identified two novel mutations of DYNC2LI1
            in fetal skeletal ciliopathy
  JOURNAL   Mol Genet Genomic Med 8 (12), e1524 (2020)
   PUBMED   33030252
  REMARK    GeneRIF: Whole-exome sequencing identified two novel mutations of
            DYNC2LI1 in fetal skeletal ciliopathy.
REFERENCE   3  (bases 1 to 1399)
  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   4  (bases 1 to 1399)
  AUTHORS   Toropova,K., Zalyte,R., Mukhopadhyay,A.G., Mladenov,M., Carter,A.P.
            and Roberts,A.J.
  TITLE     Structure of the dynein-2 complex and its assembly with
            intraflagellar transport trains
  JOURNAL   Nat Struct Mol Biol 26 (9), 823-829 (2019)
   PUBMED   31451806
REFERENCE   5  (bases 1 to 1399)
  AUTHORS   Hamada,Y., Tsurumi,Y., Nozaki,S., Katoh,Y. and Nakayama,K.
  TITLE     Interaction of WDR60 intermediate chain with TCTEX1D2 light chain
            of the dynein-2 complex is crucial for ciliary protein trafficking
  JOURNAL   Mol Biol Cell 29 (13), 1628-1639 (2018)
   PUBMED   29742051
REFERENCE   6  (bases 1 to 1399)
  AUTHORS   Perrone,C.A., Tritschler,D., Taulman,P., Bower,R., Yoder,B.K. and
            Porter,M.E.
  TITLE     A novel dynein light intermediate chain colocalizes with the
            retrograde motor for intraflagellar transport at sites of axoneme
            assembly in chlamydomonas and Mammalian cells
  JOURNAL   Mol Biol Cell 14 (5), 2041-2056 (2003)
   PUBMED   12802074
REFERENCE   7  (bases 1 to 1399)
  AUTHORS   Mikami,A., Tynan,S.H., Hama,T., Luby-Phelps,K., Saito,T.,
            Crandall,J.E., Besharse,J.C. and Vallee,R.B.
  TITLE     Molecular structure of cytoplasmic dynein 2 and its distribution in
            neuronal and ciliated cells
  JOURNAL   J Cell Sci 115 (Pt 24), 4801-4808 (2002)
   PUBMED   12432068
REFERENCE   8  (bases 1 to 1399)
  AUTHORS   Short,B., Preisinger,C., Schaletzky,J., Kopajtich,R. and Barr,F.A.
  TITLE     The Rab6 GTPase regulates recruitment of the dynactin complex to
            Golgi membranes
  JOURNAL   Curr Biol 12 (20), 1792-1795 (2002)
   PUBMED   12401177
REFERENCE   9  (bases 1 to 1399)
  AUTHORS   Grissom,P.M., Vaisberg,E.A. and McIntosh,J.R.
  TITLE     Identification of a novel light intermediate chain (D2LIC) for
            mammalian cytoplasmic dynein 2
  JOURNAL   Mol Biol Cell 13 (3), 817-829 (2002)
   PUBMED   11907264
REFERENCE   10 (bases 1 to 1399)
  AUTHORS   Da Silva,J.D., Tkachenko,N. and Soares,A.R.
  TITLE     Ellis-van Creveld Syndrome
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   37903214
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK223432.1 and AY083346.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_016008.3.
            
            Summary: This gene encodes a protein that is a component of the
            dynein-2 microtubule motor protein complex that plays a role in the
            retrograde transport of cargo in primary cilia via the
            intraflagellar transport system. This gene is ubiquitously
            expressed and its protein, which localizes to the axoneme and Golgi
            apparatus, interacts directly with the cytoplasmic dynein 2 heavy
            chain 1 protein to form part of the multi-protein dynein-2 complex.
            Mutations in this gene produce defects in the dynein-2 complex
            which result in several types of ciliopathy including short-rib
            thoracic dysplasia 15 with polydactyly (SRTD15). Alternative
            splicing results in multiple transcript variants encoding distinct
            isoforms. [provided by RefSeq, Feb 2017].
            
            Transcript Variant: This variant (1) encodes 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 :: AK223432.1, SRR5189655.69418.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000260605.12/ ENSP00000260605.8
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-40                AK223432.1         1-40
            41-1392             AY083346.1         1-1352
            1393-1399           AK223432.1         1393-1399
FEATURES             Location/Qualifiers
     source          1..1399
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2p21"
     gene            1..1399
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /note="dynein cytoplasmic 2 light intermediate chain 1"
                     /db_xref="GeneID:51626"
                     /db_xref="HGNC:HGNC:24595"
                     /db_xref="MIM:617083"
     exon            1..108
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /inference="alignment:Splign:2.1.0"
     CDS             101..1156
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /note="isoform 1 is encoded by transcript variant 1"
                     /codon_start=1
                     /product="cytoplasmic dynein 2 light intermediate chain 1
                     isoform 1"
                     /protein_id="NP_057092.2"
                     /db_xref="CCDS:CCDS1813.1"
                     /db_xref="GeneID:51626"
                     /db_xref="HGNC:HGNC:24595"
                     /db_xref="MIM:617083"
                     /translation="MPSETLWEIAKAEVEKRGINGSEGDGAEIAEKFVFFIGSKNGGK
                     TTIILRCLDRDEPPKPTLALEYTYGRRAKGHNTPKDIAHFWELGGGTSLLDLISIPIT
                     GDTLRTFSLVLVLDLSKPNDLWPTMENLLQATKSHVDKVIMKLGKTNAKAVSEMRQKI
                     WNNMPKDHPDHELIDPFPVPLVIIGSKYDVFQDFESEKRKVICKTLRFVAHYYGASLM
                     FTSKSEALLLKIRGVINQLAFGIDKSKSICVDQNKPLFITAGLDSFGQIGSPPVPEND
                     IGKLHAHSPMELWKKVYEKLFPPKSINTLKDIKDPARDPQYAENEVDEMRIQKDLELE
                     QYKRSSSKSWKQIELDS"
     exon            109..226
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /inference="alignment:Splign:2.1.0"
     exon            227..261
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /inference="alignment:Splign:2.1.0"
     exon            262..331
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /inference="alignment:Splign:2.1.0"
     exon            332..420
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /inference="alignment:Splign:2.1.0"
     exon            421..607
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /inference="alignment:Splign:2.1.0"
     exon            608..676
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /inference="alignment:Splign:2.1.0"
     exon            677..754
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /inference="alignment:Splign:2.1.0"
     exon            755..831
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /inference="alignment:Splign:2.1.0"
     exon            832..902
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /inference="alignment:Splign:2.1.0"
     exon            903..1000
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /inference="alignment:Splign:2.1.0"
     exon            1001..1093
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /inference="alignment:Splign:2.1.0"
     exon            1094..1399
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1369..1374
                     /regulatory_class="polyA_signal_sequence"
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /note="hexamer: AATAAA"
     polyA_site      1399
                     /gene="DYNC2LI1"
                     /gene_synonym="CGI-60; D2LIC; LIC3"
                     /note="major polyA site"
ORIGIN      
        1 agaaggcctc actcccagac tccttgcgga gctcgccgcc tgattctagg ctggtcacta
       61 ctccgagcct gtgacgtttg cggcagccag gccgtcgacg atgcccagtg aaactctctg
      121 ggaaattgca aaagctgaag tggaaaaaag gggaattaat ggaagtgaag gtgatggagc
      181 tgaaattgca gaaaaatttg ttttcttcat tggcagtaaa aatgggggaa agactactat
      241 tattctaagg tgtcttgaca gagatgaacc accaaaacca accttagctt tggaatatac
      301 atatggaaga agagcaaaag ggcacaacac accaaaagat atcgctcact tttgggaact
      361 cggtggagga acctctttat tggacttaat cagcataccc atcacaggtg acaccttacg
      421 gacgttttct cttgttctcg ttctggatct ttcaaaacct aatgatctct ggcccaccat
      481 ggaaaatctc ttgcaagcca caaaaagcca tgtagacaaa gtgataatga aactgggaaa
      541 gacaaatgct aaagcagttt ctgaaatgag acagaagatc tggaataata tgccgaagga
      601 tcatcctgat catgaattaa ttgacccatt tccggtacct ctggtcataa ttggaagtaa
      661 atatgatgtt tttcaggatt ttgagtctga gaagagaaag gtaatatgca agacacttcg
      721 atttgttgca cattattatg gagcatcatt aatgtttacc agtaaatcag aagctctatt
      781 actaaaaata cgtggagtta tcaaccagtt ggcatttggc attgacaaaa gcaaatcaat
      841 atgtgtggat cagaataaac cgctgtttat cacagcagga ttggattctt tcggtcaaat
      901 aggatctcct cctgttcctg aaaatgacat tggaaagctt catgcccact cacctatgga
      961 gttgtggaaa aaagtgtatg aaaagctctt tccaccaaag agtattaaca cgctgaaaga
     1021 tatcaaggac cctgcgagag atcctcagta tgctgaaaat gaagtcgatg agatgagaat
     1081 tcagaaggat ctggaactgg aacagtacaa aagaagttct tccaagtctt ggaaacaaat
     1141 cgagcttgat tcttgaacct atttcaatta ttgtatattt atttcttctt ttccaaatac
     1201 aaataagatt atactgtgaa ttaactattg tggcaatatg tgaagaaagt taaactgtat
     1261 aatttgttaa aggacaagct ggatttcttg gactagtgca tctccctgta tatcttgaag
     1321 ctttttaaaa ggaaaaatta ttgtagaacc acgtgtaatt ttttttaaaa taaaagaatc
     1381 ttctactacc tacctctaa
//
