LOCUS       NM_017806               1157 bp    mRNA    linear   PRI 20-SEP-2024
DEFINITION  Homo sapiens Lck interacting transmembrane adaptor 1 (LIME1),
            transcript variant 1, mRNA.
ACCESSION   NM_017806
VERSION     NM_017806.4
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 1157)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   2  (bases 1 to 1157)
  AUTHORS   Ban,M., Liao,W., Baker,A., Compston,A., Thorpe,J., Molyneux,P.,
            Fraser,M., Khadake,J., Jones,J., Coles,A. and Sawcer,S.
  TITLE     Transcript specific regulation of expression influences
            susceptibility to multiple sclerosis
  JOURNAL   Eur J Hum Genet 28 (6), 826-834 (2020)
   PUBMED   31932686
REFERENCE   3  (bases 1 to 1157)
  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 1157)
  AUTHORS   Mohandas,N., Bass-Stringer,S., Maksimovic,J., Crompton,K.,
            Loke,Y.J., Walstab,J., Reid,S.M., Amor,D.J., Reddihough,D. and
            Craig,J.M.
  TITLE     Epigenome-wide analysis in newborn blood spots from monozygotic
            twins discordant for cerebral palsy reveals consistent regional
            differences in DNA methylation
  JOURNAL   Clin Epigenetics 10, 25 (2018)
   PUBMED   29484035
  REMARK    GeneRIF: Results identified one differentially methylated region
            associated with cerebral palsy within the transcription start site
            of the LIME1 gene, which plays a key role in inflammatory pathways.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1157)
  AUTHORS   Kim,M.S., Pinto,S.M., Getnet,D., Nirujogi,R.S., Manda,S.S.,
            Chaerkady,R., Madugundu,A.K., Kelkar,D.S., Isserlin,R., Jain,S.,
            Thomas,J.K., Muthusamy,B., Leal-Rojas,P., Kumar,P.,
            Sahasrabuddhe,N.A., Balakrishnan,L., Advani,J., George,B.,
            Renuse,S., Selvan,L.D., Patil,A.H., Nanjappa,V., Radhakrishnan,A.,
            Prasad,S., Subbannayya,T., Raju,R., Kumar,M.,
            Sreenivasamurthy,S.K., Marimuthu,A., Sathe,G.J., Chavan,S.,
            Datta,K.K., Subbannayya,Y., Sahu,A., Yelamanchi,S.D., Jayaram,S.,
            Rajagopalan,P., Sharma,J., Murthy,K.R., Syed,N., Goel,R.,
            Khan,A.A., Ahmad,S., Dey,G., Mudgal,K., Chatterjee,A., Huang,T.C.,
            Zhong,J., Wu,X., Shaw,P.G., Freed,D., Zahari,M.S., Mukherjee,K.K.,
            Shankar,S., Mahadevan,A., Lam,H., Mitchell,C.J., Shankar,S.K.,
            Satishchandra,P., Schroeder,J.T., Sirdeshmukh,R., Maitra,A.,
            Leach,S.D., Drake,C.G., Halushka,M.K., Prasad,T.S., Hruban,R.H.,
            Kerr,C.L., Bader,G.D., Iacobuzio-Donahue,C.A., Gowda,H. and
            Pandey,A.
  TITLE     A draft map of the human proteome
  JOURNAL   Nature 509 (7502), 575-581 (2014)
   PUBMED   24870542
REFERENCE   6  (bases 1 to 1157)
  AUTHORS   Edwards,N.J.
  TITLE     Novel peptide identification from tandem mass spectra using ESTs
            and sequence database compression
  JOURNAL   Mol Syst Biol 3, 102 (2007)
   PUBMED   17437027
REFERENCE   7  (bases 1 to 1157)
  AUTHORS   Ahn,E., Lee,H. and Yun,Y.
  TITLE     LIME acts as a transmembrane adapter mediating BCR-dependent B-cell
            activation
  JOURNAL   Blood 107 (4), 1521-1527 (2006)
   PUBMED   16249387
REFERENCE   8  (bases 1 to 1157)
  AUTHORS   Tedoldi,S., Paterson,J.C., Hansmann,M.L., Natkunam,Y., Rudiger,T.,
            Angelisova,P., Du,M.Q., Roberton,H., Roncador,G., Sanchez,L.,
            Pozzobon,M., Masir,N., Barry,R., Pileri,S., Mason,D.Y.,
            Marafioti,T. and Horejsi,V.
  TITLE     Transmembrane adaptor molecules: a new category of lymphoid-cell
            markers
  JOURNAL   Blood 107 (1), 213-221 (2006)
   PUBMED   16160011
REFERENCE   9  (bases 1 to 1157)
  AUTHORS   Brdickova,N., Brdicka,T., Angelisova,P., Horvath,O., Spicka,J.,
            Hilgert,I., Paces,J., Simeoni,L., Kliche,S., Merten,C., Schraven,B.
            and Horejsi,V.
  TITLE     LIME: a new membrane Raft-associated adaptor protein involved in
            CD4 and CD8 coreceptor signaling
  JOURNAL   J Exp Med 198 (10), 1453-1462 (2003)
   PUBMED   14610046
REFERENCE   10 (bases 1 to 1157)
  AUTHORS   Hur,E.M., Son,M., Lee,O.H., Choi,Y.B., Park,C., Lee,H. and Yun,Y.
  TITLE     LIME, a novel transmembrane adaptor protein, associates with p56lck
            and mediates T cell activation
  JOURNAL   J Exp Med 198 (10), 1463-1473 (2003)
   PUBMED   14610044
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK000413.1 and AL121845.20.
            
            On Nov 22, 2018 this sequence version replaced NM_017806.3.
            
            Summary: This gene encodes a transmembrane adaptor protein that
            links the T and B-cell receptor stimulation to downstream signaling
            pathways via its association with the Src family kinases Lck and
            Lyn, respectively. Alternative splicing of this gene results in
            multiple transcript variants. [provided by RefSeq, Mar 2015].
            
            Transcript Variant: This variant (1) 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 :: AK000413.1, BC017016.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000309546.8/ ENSP00000309521.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-802               AK000413.1         22-823
            803-803             AL121845.20        42346-42346
            804-1157            AK000413.1         825-1178
FEATURES             Location/Qualifiers
     source          1..1157
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="20"
                     /map="20q13.33"
     gene            1..1157
                     /gene="LIME1"
                     /gene_synonym="dJ583P15.4; LIME"
                     /note="Lck interacting transmembrane adaptor 1"
                     /db_xref="GeneID:54923"
                     /db_xref="HGNC:HGNC:26016"
                     /db_xref="MIM:609809"
     exon            1..49
                     /gene="LIME1"
                     /gene_synonym="dJ583P15.4; LIME"
                     /inference="alignment:Splign:2.1.0"
     exon            50..164
                     /gene="LIME1"
                     /gene_synonym="dJ583P15.4; LIME"
                     /inference="alignment:Splign:2.1.0"
     CDS             67..954
                     /gene="LIME1"
                     /gene_synonym="dJ583P15.4; LIME"
                     /note="isoform 1 is encoded by transcript variant 1;
                     lck-interacting transmembrane adapter 1; lck-interacting
                     molecule; lck-interacting membrane protein"
                     /codon_start=1
                     /product="lck-interacting transmembrane adapter 1 isoform
                     1"
                     /protein_id="NP_060276.2"
                     /db_xref="CCDS:CCDS13536.1"
                     /db_xref="GeneID:54923"
                     /db_xref="HGNC:HGNC:26016"
                     /db_xref="MIM:609809"
                     /translation="MGLPVSWAPPALWVLGCCALLLSLWALCTACRRPEDAVAPRKRA
                     RRQRARLQGSATAAEASLLRRTHLCSLSKSDTRLHELHRGPRSSRALRPASMDLLRPH
                     WLEVSRDITGPQAAPSAFPHQELPRALPAAAATAGCAGLEATYSNVGLAALPGVSLAA
                     SPVVAEYARVQKRKGTHRSPQEPQQGKTEVTPAAQVDVLYSRVCKPKRRDPGPTTDPL
                     DPKGQGAILALAGDLAYQTLPLRALDVDSGPLENVYESIRELGDPAGRSSTCGAGTPP
                     ASSCPSLGRGWRPLPASLP"
     exon            165..246
                     /gene="LIME1"
                     /gene_synonym="dJ583P15.4; LIME"
                     /inference="alignment:Splign:2.1.0"
     exon            247..334
                     /gene="LIME1"
                     /gene_synonym="dJ583P15.4; LIME"
                     /inference="alignment:Splign:2.1.0"
     exon            335..651
                     /gene="LIME1"
                     /gene_synonym="dJ583P15.4; LIME"
                     /inference="alignment:Splign:2.1.0"
     exon            652..1157
                     /gene="LIME1"
                     /gene_synonym="dJ583P15.4; LIME"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1130..1135
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LIME1"
                     /gene_synonym="dJ583P15.4; LIME"
                     /note="hexamer: AATAAA"
     polyA_site      1157
                     /gene="LIME1"
                     /gene_synonym="dJ583P15.4; LIME"
                     /note="major polyA site"
ORIGIN      
        1 cttcctggcc tgccccagac agagctgagg acccctggcc gtgggcttgg gcctcggctt
       61 cacaggatgg ggctgccagt gtcctgggcc cctcctgccc tctgggttct agggtgctgc
      121 gccctgctcc tctcgctgtg ggcgctgtgc acagcctgcc gcaggcccga ggacgctgta
      181 gcccccagga agagggcgcg gaggcagcgg gcgaggctgc agggcagtgc gacggcggcg
      241 gaagcgtccc tactgaggcg gacccacctc tgctccctca gcaagtcgga caccagactg
      301 cacgagctgc accggggccc gcgcagcagc agggccctgc ggcctgccag catggatctc
      361 ctgcgcccac actggctgga ggtgtccagg gacatcaccg gaccgcaggc agccccctct
      421 gccttcccac accaggagct gccccgggct ctgccggcag ctgcagccac cgcagggtgc
      481 gctggcctcg aggccaccta ttccaacgtg gggctggcgg cccttcccgg ggtcagcctg
      541 gcggccagcc ctgtggtggc cgagtatgcc cgcgtccaga agcgcaaagg gacccatcgc
      601 agtccccaag agccacagca ggggaagact gaggtgaccc cggccgctca ggtggacgtc
      661 ctgtactcca gggtctgcaa gcctaaaagg agggacccag gacccaccac agacccgctg
      721 gaccccaagg gccagggagc gattctggcc ctggcgggtg acctggccta ccagaccctc
      781 ccgctcaggg ccctggatgt ggacagcggc cccctggaaa acgtgtatga gagcatccgg
      841 gagctggggg accctgctgg caggagcagc acgtgcgggg ctgggacgcc ccctgcttcc
      901 agctgcccca gcctagggag gggctggaga cccctccctg cctccctgcc ctgaacactc
      961 aaggacctgt gctccttcct ccagagtgag gcccgtcccc cgccccgccc cgcctcacag
     1021 ctgacagcgc cagtcccagg tccccgggct gccagcccgt gaggtccgtg aggtcctggc
     1081 cgctctgaca gccgcggcct ccccgggctc cagagaaggc ccgcgtctaa ataaagcgcc
     1141 agcgcaggat gaaagcg
//
