LOCUS       NM_001099658            3500 bp    mRNA    linear   PRI 20-SEP-2024
DEFINITION  Homo sapiens leucine rich repeat neuronal 3 (LRRN3), transcript
            variant 2, mRNA.
ACCESSION   NM_001099658
VERSION     NM_001099658.2
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 3500)
  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 3500)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Paulo,J.A., Cannon,J.R., Ting,L.,
            Baltier,K., Colby,G., Gebreab,F., Gygi,M.P., Parzen,H., Szpyt,J.,
            Tam,S., Zarraga,G., Pontano-Vaites,L., Swarup,S., White,A.E.,
            Schweppe,D.K., Rad,R., Erickson,B.K., Obar,R.A., Guruharsha,K.G.,
            Li,K., Artavanis-Tsakonas,S., Gygi,S.P. and Harper,J.W.
  TITLE     Architecture of the human interactome defines protein communities
            and disease networks
  JOURNAL   Nature 545 (7655), 505-509 (2017)
   PUBMED   28514442
REFERENCE   3  (bases 1 to 3500)
  AUTHORS   Akter,J., Takatori,A., Islam,M.S., Nakazawa,A., Ozaki,T., Nagase,H.
            and Nakagawara,A.
  TITLE     Intracellular fragment of NLRR3 (NLRR3-ICD) stimulates
            ATRA-dependent neuroblastoma differentiation
  JOURNAL   Biochem Biophys Res Commun 453 (1), 86-93 (2014)
   PUBMED   25256744
  REMARK    GeneRIF: NLRR3 is proteolytically processed by secretases and its
            intracellular domain is then released to translocate into the cell
            nucleus during ATRA-mediated neuroblastoma differentiation.
REFERENCE   4  (bases 1 to 3500)
  AUTHORS   Akter,J., Takatori,A., Hossain,M.S., Ozaki,T., Nakazawa,A.,
            Ohira,M., Suenaga,Y. and Nakagawara,A.
  TITLE     Expression of NLRR3 orphan receptor gene is negatively regulated by
            MYCN and Miz-1, and its downregulation is associated with
            unfavorable outcome in neuroblastoma
  JOURNAL   Clin Cancer Res 17 (21), 6681-6692 (2011)
   PUBMED   21908575
  REMARK    GeneRIF: NLRR3 is a direct target of MYCN, which associates with
            Miz-1 and negatively regulates NLRR3 expression. NLRR3 may play a
            role in NBL differentiation and the survival of NBL patients by
            inversely correlating with MYCN amplification.
REFERENCE   5  (bases 1 to 3500)
  AUTHORS   Sousa,I., Clark,T.G., Holt,R., Pagnamenta,A.T., Mulder,E.J.,
            Minderaa,R.B., Bailey,A.J., Battaglia,A., Klauck,S.M., Poustka,F.
            and Monaco,A.P.
  CONSRTM   International Molecular Genetic Study of Autism Consortium (IMGSAC)
  TITLE     Polymorphisms in leucine-rich repeat genes are associated with
            autism spectrum disorder susceptibility in populations of European
            ancestry
  JOURNAL   Mol Autism 1 (1), 7 (2010)
   PUBMED   20678249
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3500)
  AUTHORS   Clark,H.F., Gurney,A.L., Abaya,E., Baker,K., Baldwin,D., Brush,J.,
            Chen,J., Chow,B., Chui,C., Crowley,C., Currell,B., Deuel,B.,
            Dowd,P., Eaton,D., Foster,J., Grimaldi,C., Gu,Q., Hass,P.E.,
            Heldens,S., Huang,A., Kim,H.S., Klimowski,L., Jin,Y., Johnson,S.,
            Lee,J., Lewis,L., Liao,D., Mark,M., Robbie,E., Sanchez,C.,
            Schoenfeld,J., Seshagiri,S., Simmons,L., Singh,J., Smith,V.,
            Stinson,J., Vagts,A., Vandlen,R., Watanabe,C., Wieand,D., Woods,K.,
            Xie,M.H., Yansura,D., Yi,S., Yu,G., Yuan,J., Zhang,M., Zhang,Z.,
            Goddard,A., Wood,W.I., Godowski,P. and Gray,A.
  TITLE     The secreted protein discovery initiative (SPDI), a large-scale
            effort to identify novel human secreted and transmembrane proteins:
            a bioinformatics assessment
  JOURNAL   Genome Res 13 (10), 2265-2270 (2003)
   PUBMED   12975309
  REMARK    Erratum:[Genome Res. 2003 Dec;13(12):2759]
REFERENCE   7  (bases 1 to 3500)
  AUTHORS   Fukamachi,K., Matsuoka,Y., Kitanaka,C., Kuchino,Y. and Tsuda,H.
  TITLE     Rat neuronal leucine-rich repeat protein-3: cloning and regulation
            of the gene expression
  JOURNAL   Biochem Biophys Res Commun 287 (1), 257-263 (2001)
   PUBMED   11549284
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DA494543.1, AY358280.1, BC035133.2 and AL442092.1.
            
            On Nov 24, 2018 this sequence version replaced NM_001099658.1.
            
            Transcript Variant: This variant (2) differs in the 5' UTR compared
            to variant 1. Variants 1, 2 and 3 encode the same protein.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1660809.103722.1,
                                           SRR1803613.155770.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1968540
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000308478.10/ ENSP00000312001.5
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-339               DA494543.1         125-463
            340-2978            AY358280.1         1-2639
            2979-3452           BC035133.2         2897-3370
            3453-3500           AL442092.1         2898-2945
FEATURES             Location/Qualifiers
     source          1..3500
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="7"
                     /map="7q31.1"
     gene            1..3500
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; NLRR-3; NLRR3"
                     /note="leucine rich repeat neuronal 3"
                     /db_xref="GeneID:54674"
                     /db_xref="HGNC:HGNC:17200"
                     /db_xref="MIM:619748"
     exon            1..378
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; NLRR-3; NLRR3"
                     /inference="alignment:Splign:2.1.0"
     exon            379..460
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; NLRR-3; NLRR3"
                     /inference="alignment:Splign:2.1.0"
     exon            461..3500
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; NLRR-3; NLRR3"
                     /inference="alignment:Splign:2.1.0"
     CDS             819..2945
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; NLRR-3; NLRR3"
                     /note="leucine-rich repeat protein, neuronal 3;
                     fibronectin type III, immunoglobulin and leucine rich
                     repeat domains 5; leucine-rich repeat neuronal protein 3;
                     neuronal leucine-rich repeat protein 3"
                     /codon_start=1
                     /product="leucine-rich repeat neuronal protein 3
                     precursor"
                     /protein_id="NP_001093128.1"
                     /db_xref="CCDS:CCDS5754.1"
                     /db_xref="GeneID:54674"
                     /db_xref="HGNC:HGNC:17200"
                     /db_xref="MIM:619748"
                     /translation="MKDMPLRIHVLLGLAITTLVQAVDKKVDCPRLCTCEIRPWFTPR
                     SIYMEASTVDCNDLGLLTFPARLPANTQILLLQTNNIAKIEYSTDFPVNLTGLDLSQN
                     NLSSVTNINVKKMPQLLSVYLEENKLTELPEKCLSELSNLQELYINHNLLSTISPGAF
                     IGLHNLLRLHLNSNRLQMINSKWFDALPNLEILMIGENPIIRIKDMNFKPLINLRSLV
                     IAGINLTEIPDNALVGLENLESISFYDNRLIKVPHVALQKVVNLKFLDLNKNPINRIR
                     RGDFSNMLHLKELGINNMPELISIDSLAVDNLPDLRKIEATNNPRLSYIHPNAFFRLP
                     KLESLMLNSNALSALYHGTIESLPNLKEISIHSNPIRCDCVIRWMNMNKTNIRFMEPD
                     SLFCVDPPEFQGQNVRQVHFRDMMEICLPLIAPESFPSNLNVEAGSYVSFHCRATAEP
                     QPEIYWITPSGQKLLPNTLTDKFYVHSEGTLDINGVTPKEGGLYTCIATNLVGADLKS
                     VMIKVDGSFPQDNNGSLNIKIRDIQANSVLVSWKASSKILKSSVKWTAFVKTENSHAA
                     QSARIPSDVKVYNLTHLNPSTEYKICIDIPTIYQKNRKKCVNVTTKGLHPDQKEYEKN
                     NTTTLMACLGGLLGIIGVICLISCLSPEMNCDGGHSYVRNYLQKPTFALGELYPPLIN
                     LWEAGKEKSTSLKVKATVIGLPTNMS"
     regulatory      3430..3435
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; NLRR-3; NLRR3"
                     /note="hexamer: AATACA"
     polyA_site      3452
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; NLRR-3; NLRR3"
     regulatory      3478..3483
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; NLRR-3; NLRR3"
                     /note="hexamer: AATAAA"
     polyA_site      3500
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; NLRR-3; NLRR3"
                     /note="major polyA site"
ORIGIN      
        1 gtcagtgtga caactgatcg ggtgaacgat gcaccactaa ccaccatgga aacaaggaaa
       61 aataaagcca gctcacagga tctctcttca ctggattgag agcctcagcc tgccgactga
      121 gaaaaagagt tccaggaaaa agaaggaatc ccggctgcag cctcctgcct tcctttatat
      181 tttaaaatag agagataaga ttgcgtgcat gtgtgcatat ctatagtata tattttgtac
      241 actttgttac acagacacac aaatgcacct atttataccg ggcaagaaca caaccatgtg
      301 attatctcaa ccaaggaact gaggaatcca gcacgcaagg acatcggagg tgggctagca
      361 ctgaaactgc ttttcaagac gaggaagagg aggagaaaga gaaagaagag gaagatgttg
      421 ggcaacattt atttaacatg ctccacagcc cggaccctgg catcatgctg ctattcctgc
      481 aaatactgaa gaagcatggg atttaaatat tttacttcta aataaatgaa ttactcaatc
      541 tcctatgacc atctatacat actccacctt caaaaagtac atcaatatta tatcattaag
      601 gaaatagtaa ccttctcttc tccaatatgc atgacatttt tggacaatgc aattgtggca
      661 ctggcactta tttcagtgaa gaaaaacttt gtggttctat ggcattcatc atttgacaaa
      721 tgcaagcatc ttccttatca atcagctcct attgaactta ctagcactga ctgtggaatc
      781 cttaagggcc cattacattt ctgaagaaga aagctaagat gaaggacatg ccactccgaa
      841 ttcatgtgct acttggccta gctatcacta cactagtaca agctgtagat aaaaaagtgg
      901 attgtccacg gttatgtacg tgtgaaatca ggccttggtt tacacccaga tccatttata
      961 tggaagcatc tacagtggat tgtaatgatt taggtctttt aactttccca gccagattgc
     1021 cagctaacac acagattctt ctcctacaga ctaacaatat tgcaaaaatt gaatactcca
     1081 cagactttcc agtaaacctt actggcctgg atttatctca aaacaattta tcttcagtca
     1141 ccaatattaa tgtaaaaaag atgcctcagc tcctttctgt gtacctagag gaaaacaaac
     1201 ttactgaact gcctgaaaaa tgtctgtccg aactgagcaa cttacaagaa ctctatatta
     1261 atcacaactt gctttctaca atttcacctg gagcctttat tggcctacat aatcttcttc
     1321 gacttcatct caattcaaat agattgcaga tgatcaacag taagtggttt gatgctcttc
     1381 caaatctaga gattctgatg attggggaaa atccaattat cagaatcaaa gacatgaact
     1441 ttaagcctct tatcaatctt cgcagcctgg ttatagctgg tataaacctc acagaaatac
     1501 cagataacgc cttggttgga ctggaaaact tagaaagcat ctctttttac gataacaggc
     1561 ttattaaagt accccatgtt gctcttcaaa aagttgtaaa tctcaaattt ttggatctaa
     1621 ataaaaatcc tattaataga atacgaaggg gtgattttag caatatgcta cacttaaaag
     1681 agttggggat aaataatatg cctgagctga tttccatcga tagtcttgct gtggataacc
     1741 tgccagattt aagaaaaata gaagctacta acaaccctag attgtcttac attcacccca
     1801 atgcattttt cagactcccc aagctggaat cactcatgct gaacagcaat gctctcagtg
     1861 ccctgtacca tggtaccatt gagtctctgc caaacctcaa ggaaatcagc atacacagta
     1921 accccatcag gtgtgactgt gtcatccgtt ggatgaacat gaacaaaacc aacattcgat
     1981 tcatggagcc agattcactg ttttgcgtgg acccacctga attccaaggt cagaatgttc
     2041 ggcaagtgca tttcagggac atgatggaaa tttgtctccc tcttatagct cctgagagct
     2101 ttccttctaa tctaaatgta gaagctggga gctatgtttc ctttcactgt agagctactg
     2161 cagaaccaca gcctgaaatc tactggataa caccttctgg tcaaaaactc ttgcctaata
     2221 ccctgacaga caagttctat gtccattctg agggaacact agatataaat ggcgtaactc
     2281 ccaaagaagg gggtttatat acttgtatag caactaacct agttggcgct gacttgaagt
     2341 ctgttatgat caaagtggat ggatcttttc cacaagataa caatggctct ttgaatatta
     2401 aaataagaga tattcaggcc aattcagttt tggtgtcctg gaaagcaagt tctaaaattc
     2461 tcaaatctag tgttaaatgg acagcctttg tcaagactga aaattctcat gctgcgcaaa
     2521 gtgctcgaat accatctgat gtcaaggtat ataatcttac tcatctgaat ccatcaactg
     2581 agtataaaat ttgtattgat attcccacca tctatcagaa aaacagaaaa aaatgtgtaa
     2641 atgtcaccac caaaggtttg caccctgatc aaaaagagta tgaaaagaat aataccacaa
     2701 cacttatggc ctgtcttgga ggccttctgg ggattattgg tgtgatatgt cttatcagct
     2761 gcctctctcc agaaatgaac tgtgatggtg gacacagcta tgtgaggaat tacttacaga
     2821 aaccaacctt tgcattaggt gagctttatc ctcctctgat aaatctctgg gaagcaggaa
     2881 aagaaaaaag tacatcactg aaagtaaaag caactgttat aggtttacca acaaatatgt
     2941 cctaaaaacc accaaggaaa cctactccaa aaatgaacaa aaaaaaaaaa agcgaaagac
     3001 tgcagttgtg ctaaaaacaa aacaaaacaa acaaacaaac aaaaaagtaa aaaaagatta
     3061 ctttcgagag agaagtttaa gcttcaccaa tgctgctcct gaccaatgga aatatgtaca
     3121 acttcagcat tttaagtaac tggcttcaag gggtactgtg gcaaccaaat aaaataactc
     3181 cattttctaa aactttcatg taacttttat gtctggacta cagttcaagt ggacaaaaac
     3241 atttctgtat tttttttaag taaataagag tagttgaact gagcaatacc tcctcctgtg
     3301 ttgtattaca catattagcc acgagttttt gcagtgacca gataaacttg aattgacacg
     3361 tggtgtaata aaatggacaa attctgtaga gtagacacag tgagtatgtg gacctctttt
     3421 ataaggaaaa atacattttg gattaaaatc aattgcttct gtcttgtttt gtttctaaat
     3481 aaagaataat ttctgggaaa
//
