LOCUS       NM_178011               6049 bp    mRNA    linear   PRI 01-AUG-2024
DEFINITION  Homo sapiens leucine rich repeat transmembrane neuronal 3 (LRRTM3),
            transcript variant 1, mRNA.
ACCESSION   NM_178011
VERSION     NM_178011.5
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 6049)
  AUTHORS   Um,J.W., Choi,T.Y., Kang,H., Cho,Y.S., Choii,G., Uvarov,P.,
            Park,D., Jeong,D., Jeon,S., Lee,D., Kim,H., Lee,S.H., Bae,Y.C.,
            Choi,S.Y., Airaksinen,M.S. and Ko,J.
  TITLE     LRRTM3 Regulates Excitatory Synapse Development through Alternative
            Splicing and Neurexin Binding
  JOURNAL   Cell Rep 14 (4), 808-822 (2016)
   PUBMED   26776509
REFERENCE   2  (bases 1 to 6049)
  AUTHORS   Wang,J., Yu,J.T., Jiang,T., Tan,M.S., Wang,H.F., Tan,L., Hu,N.,
            Sun,L., Zhang,W. and Tan,L.
  TITLE     Association of LRRTM3 polymorphisms with late-onset Alzheimer's
            disease in Han Chinese
  JOURNAL   Exp Gerontol 52, 18-22 (2014)
   PUBMED   24463050
  REMARK    GeneRIF: LRRTM3 polymorphisms may play a role in the pathogenesis
            of late-onset Alzheimer's disease (LOAD) in a Northern Han Chinese
            population.
REFERENCE   3  (bases 1 to 6049)
  AUTHORS   Lincoln,S., Allen,M., Cox,C.L., Walker,L.P., Malphrus,K., Qiu,Y.,
            Nguyen,T., Rowley,C., Kouri,N., Crook,J., Pankratz,V.S.,
            Younkin,S., Younkin,L., Carrasquillo,M., Zou,F., Abdul-Hay,S.O.,
            Springer,W., Sando,S.B., Aasly,J.O., Barcikowska,M., Wszolek,Z.K.,
            Lewis,J.M., Dickson,D., Graff-Radford,N.R., Petersen,R.C.,
            Eckman,E., Younkin,S.G. and Ertekin-Taner,N.
  TITLE     LRRTM3 interacts with APP and BACE1 and has variants associating
            with late-onset Alzheimer's disease (LOAD)
  JOURNAL   PLoS One 8 (6), e64164 (2013)
   PUBMED   23750206
  REMARK    GeneRIF: protein interactions between LRRTM3, APP and BACE1, as
            well as complex associations between mRNA levels of LRRTM3, CTNNA3,
            APP and BACE1 in humans might influence APP metabolism and
            ultimately risk of AD
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 6049)
  AUTHORS   Reitz,C., Conrad,C., Roszkowski,K., Rogers,R.S. and Mayeux,R.
  TITLE     Effect of genetic variation in LRRTM3 on risk of Alzheimer disease
  JOURNAL   Arch Neurol 69 (7), 894-900 (2012)
   PUBMED   22393166
  REMARK    GeneRIF: One single-nucleotide polymorphism in the promoter region
            and a block of 4 single-nucleotide polymorphisms in intron 2 were
            associated with AD in the National Institute on Aging Late-Onset
            Alzheimer's Disease data set or the Caribbean Hispanic data set.
REFERENCE   5  (bases 1 to 6049)
  AUTHORS   Laakso,T., Muggalla,P., Kysenius,K., Lauren,J., Paatero,A.,
            Huttunen,H.J. and Airaksinen,M.S.
  TITLE     LRRTM3 is dispensable for amyloid-beta production in mice
  JOURNAL   J Alzheimers Dis 31 (4), 759-764 (2012)
   PUBMED   22710909
  REMARK    GeneRIF: LRRTM3 is not an essential regulator of amyloid-beta
            production in adult mice; there are no differences in genotype
            between levels of Abeta or Abeta protein precursor C-terminal
            fragments in vivo.
REFERENCE   6  (bases 1 to 6049)
  AUTHORS   Smith,J.D., Meehan,M.H., Crean,J. and McCann,A.
  TITLE     Alpha T-catenin (CTNNA3): a gene in the hand is worth two in the
            nest
  JOURNAL   Cell Mol Life Sci 68 (15), 2493-2498 (2011)
   PUBMED   21598020
  REMARK    GeneRIF: Apart from the complexity of its regulation, alterations
            in both CTNNA3 and LRTMM3 are implicated in human disease.
            Review article
REFERENCE   7  (bases 1 to 6049)
  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   8  (bases 1 to 6049)
  AUTHORS   Edwards,T.L., Pericak-Vance,M., Gilbert,J.R., Haines,J.L.,
            Martin,E.R. and Ritchie,M.D.
  TITLE     An association analysis of Alzheimer disease candidate genes
            detects an ancestral risk haplotype clade in ACE and putative
            multilocus association between ACE, A2M, and LRRTM3
  JOURNAL   Am J Med Genet B Neuropsychiatr Genet 150B (5), 721-735 (2009)
   PUBMED   19105203
  REMARK    GeneRIF: An ancestral risk haplotype clade in ACE and putative
            multilocus association between ACE, A2M, and LRRTM3 in Alzheimer
            disease.
            GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   9  (bases 1 to 6049)
  AUTHORS   Majercak,J., Ray,W.J., Espeseth,A., Simon,A., Shi,X.P., Wolffe,C.,
            Getty,K., Marine,S., Stec,E., Ferrer,M., Strulovici,B., Bartz,S.,
            Gates,A., Xu,M., Huang,Q., Ma,L., Shughrue,P., Burchard,J.,
            Colussi,D., Pietrak,B., Kahana,J., Beher,D., Rosahl,T.,
            Shearman,M., Hazuda,D., Sachs,A.B., Koblan,K.S., Seabrook,G.R. and
            Stone,D.J.
  TITLE     LRRTM3 promotes processing of amyloid-precursor protein by BACE1
            and is a positional candidate gene for late-onset Alzheimer's
            disease
  JOURNAL   Proc Natl Acad Sci U S A 103 (47), 17967-17972 (2006)
   PUBMED   17098871
  REMARK    GeneRIF: Data suggest that LRRTM3 is a functional and positional
            candidate gene for Alzheimer disease, and, given its receptor-like
            structure and restricted expression, a potential therapeutic
            target.
REFERENCE   10 (bases 1 to 6049)
  AUTHORS   Lauren,J., Airaksinen,M.S., Saarma,M. and Timmusk,T.
  TITLE     A novel gene family encoding leucine-rich repeat transmembrane
            proteins differentially expressed in the nervous system
  JOURNAL   Genomics 81 (4), 411-421 (2003)
   PUBMED   12676565
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC069536.4, BC111492.1 and AC022401.4.
            
            On Nov 22, 2018 this sequence version replaced NM_178011.4.
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the protein.
            
            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.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1803617.24566.1,
                                           SRR1660805.223309.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2145544, SAMEA2145743
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000361320.5/ ENSP00000355187.3
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-136               AC069536.4         65008-65143
            137-4278            BC111492.1         91-4232
            4279-6049           AC022401.4         43493-45263
FEATURES             Location/Qualifiers
     source          1..6049
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="10"
                     /map="10q21.3"
     gene            1..6049
                     /gene="LRRTM3"
                     /note="leucine rich repeat transmembrane neuronal 3"
                     /db_xref="GeneID:347731"
                     /db_xref="HGNC:HGNC:19410"
                     /db_xref="MIM:610869"
     exon            1..552
                     /gene="LRRTM3"
                     /inference="alignment:Splign:2.1.0"
     CDS             549..2294
                     /gene="LRRTM3"
                     /note="leucine-rich repeat transmembrane neuronal protein
                     3"
                     /codon_start=1
                     /product="leucine-rich repeat transmembrane neuronal
                     protein 3 precursor"
                     /protein_id="NP_821079.3"
                     /db_xref="CCDS:CCDS7270.1"
                     /db_xref="GeneID:347731"
                     /db_xref="HGNC:HGNC:19410"
                     /db_xref="MIM:610869"
                     /translation="MGFNVIRLLSGSAVALVIAPTVLLTMLSSAERGCPKGCRCEGKM
                     VYCESQKLQEIPSSISAGCLGLSLRYNSLQKLKYNQFKGLNQLTWLYLDHNHISNIDE
                     NAFNGIRRLKELILSSNRISYFLNNTFRPVTNLRNLDLSYNQLHSLGSEQFRGLRKLL
                     SLHLRSNSLRTIPVRIFQDCRNLELLDLGYNRIRSLARNVFAGMIRLKELHLEHNQFS
                     KLNLALFPRLVSLQNLYLQWNKISVIGQTMSWTWSSLQRLDLSGNEIEAFSGPSVFQC
                     VPNLQRLNLDSNKLTFIGQEILDSWISLNDISLAGNIWECSRNICSLVNWLKSFKGLR
                     ENTIICASPKELQGVNVIDAVKNYSICGKSTTERFDLARALPKPTFKPKLPRPKHESK
                     PPLPPTVGATEPGPETDADAEHISFHKIIAGSVALFLSVLVILLVIYVSWKRYPASMK
                     QLQQRSLMRRHRKKKRQSLKQMTPSTQEFYVDYKPTNTETSEMLLNGTGPCTYNKSGS
                     RECEIPLSMNVSTFLAYDQPTISYCGVHHELLSHKSFETNAQEDTMETHLETELDLST
                     ITTAGRISDHKQQLA"
     exon            553..2084
                     /gene="LRRTM3"
                     /inference="alignment:Splign:2.1.0"
     exon            2085..6049
                     /gene="LRRTM3"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3050..3055
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LRRTM3"
                     /note="hexamer: GATAAA"
     polyA_site      3073
                     /gene="LRRTM3"
                     /note="major polyA site"
     regulatory      4410..4415
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LRRTM3"
                     /note="hexamer: TATAAA"
     polyA_site      4437
                     /gene="LRRTM3"
                     /note="major polyA site"
     regulatory      5572..5577
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LRRTM3"
                     /note="hexamer: ATTAAA"
     polyA_site      5597
                     /gene="LRRTM3"
                     /note="major polyA site"
     regulatory      6027..6032
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LRRTM3"
                     /note="hexamer: AATATA"
     polyA_site      6049
                     /gene="LRRTM3"
ORIGIN      
        1 aacagtccga gcagctttca gaatgacagt ctgcagaagt gagctgagcg tgtgcgcggt
       61 acggggctct cctgccttct gggctccaac gcagctctgt ggctgaactg ggtgctcatc
      121 acgggaactg ctggggtatg gaatacagat gtggcagctc aggtagcccc aaattgcctg
      181 gaagaataca tcatgttttt cgataagaag aaattgtagg atccagtttt ttttttaacc
      241 gccccctccc caccccccaa aaaactgtaa agatgcaaaa acgtaatatc catgaagatc
      301 ctattaccta ggaagatttt gatgttttgc tgcgaatgcg gtgttgggat ttatttgttc
      361 ttggagtgtt ctgcgtggct ggcaaagaat aatgttccaa aatcggtcca tctcccaagg
      421 ggtccaattt ttcttcctgg gtgtcagcga gccctgactc actacagtgc agctgacagg
      481 ggctgtcatg caactggccc ctaagccaaa gcaaaagacc taaggacgac ctttgaacaa
      541 tacaaaggat gggtttcaat gtaattaggc tactgagcgg atcagctgta gcactggtta
      601 tagcccccac tgtcttactg acaatgcttt cttctgccga acgaggatgc cctaagggct
      661 gtaggtgtga aggcaaaatg gtatattgtg aatctcagaa attacaggag ataccctcaa
      721 gtatatctgc tggttgctta ggtttgtccc ttcgctataa cagccttcaa aaacttaagt
      781 ataatcaatt taaagggctc aaccagctca cctggctata ccttgaccat aaccatatca
      841 gcaatattga cgaaaatgct tttaatggaa tacgcagact caaagagctg attcttagtt
      901 ccaatagaat ctcctatttt cttaacaata ccttcagacc tgtgacaaat ttacggaact
      961 tggatctgtc ctataatcag ctgcattctc tgggatctga acagtttcgg ggcttgcgga
     1021 agctgctgag tttacattta cggtctaact ccctgagaac catccctgtg cgaatattcc
     1081 aagactgccg caacctggaa cttttggacc tgggatataa ccggatccga agtttagcca
     1141 ggaatgtctt tgctggcatg atcagactca aagaacttca cctggagcac aatcaatttt
     1201 ccaagctcaa cctggccctt tttccaaggt tggtcagcct tcagaacctt tacttgcagt
     1261 ggaataaaat cagtgtcata ggacagacca tgtcctggac ctggagctcc ttacaaaggc
     1321 ttgatttatc aggcaatgag atcgaagctt tcagtggacc cagtgttttc cagtgtgtcc
     1381 cgaatctgca gcgcctcaac ctggattcca acaagctcac atttattggt caagagattt
     1441 tggattcttg gatatccctc aatgacatca gtcttgctgg gaatatatgg gaatgcagca
     1501 gaaatatttg ctcccttgta aactggctga aaagttttaa aggtctaagg gagaatacaa
     1561 ttatctgtgc cagtcccaaa gagctgcaag gagtaaatgt gatcgatgca gtgaagaact
     1621 acagcatctg tggcaaaagt actacagaga ggtttgatct ggccagggct ctcccaaagc
     1681 cgacgtttaa gcccaagctc cccaggccga agcatgagag caaaccccct ttgcccccga
     1741 cggtgggagc cacagagccc ggcccagaga ccgatgctga cgccgagcac atctctttcc
     1801 ataaaatcat cgcgggcagc gtggcgcttt tcctgtccgt gctcgtcatc ctgctggtta
     1861 tctacgtgtc atggaagcgg taccctgcga gcatgaagca gctgcagcag cgctccctca
     1921 tgcgaaggca caggaaaaag aaaagacagt ccctaaagca aatgactccc agcacccagg
     1981 aattttatgt agattataaa cccaccaaca cggagaccag cgagatgctg ctgaatggga
     2041 cgggaccctg cacctataac aaatcgggct ccagggagtg tgagatacct ttatcaatga
     2101 atgtgtcaac ctttctggca tacgaccagc ccacaataag ttactgtggg gtgcatcatg
     2161 aacttctctc ccataagtcc tttgaaacga atgcacagga agatacgatg gaaacacacc
     2221 tagagactga gctggacctg agcacaatca caacagctgg ccgaatcagt gaccataaac
     2281 agcagctagc ttaactgaga tcattggtag ccaggggttg ctaccaaact ttgtaacctc
     2341 aaggacaaaa tgaggaagat gtgttcattg tggactctaa aaacaaaaca aaacacaaaa
     2401 tcccctgttc aaataaacaa aaaatccaag attgattcat gaaataaaga agacatgaat
     2461 tgttttaagt ctacactttg taattagcta agttgtgcag tattttttga cttaaacaga
     2521 gtatgaccct gaaaaataaa agaatctttt tttttcaaaa ctcatcctac ctacctgtaa
     2581 aaactgtaca aagctaatgt atttttcata ttgtaaagtt tcaattgtag aaacaactgg
     2641 tatgtacagt accataattt aattacattt tactttaaaa actttacaca tttcagtttc
     2701 taaaatttta aattaacaaa aattatttct tgtgttattc agagttactc agttttgtaa
     2761 ggactgtttt gttactgctt ttgtgcccag aaaccttgac tctaaaattc tgtgctgtgc
     2821 gaaacatgca cgatttttat tatgcttact gcgtagaatt ttatctactt gttccagaaa
     2881 taatacatta accaaaaagg atttaattgt tcagacttgt aagaggttct tcaattacat
     2941 aggcaggttt ttcttaaaaa tgaaaaaaaa atcaaagatt tttttaacag ttctcagact
     3001 taactgttgc cttgaattac agcctagttt ctaagcagtg aaatgtaatg ataaagaggg
     3061 atattttaac atatttccga atgaatgact cattatttca ttcttttgag taaccattgt
     3121 taagggttgg gggaaagcat ggacaaaaca tcactggaaa caaaggctgt aaccacagca
     3181 acagactttg tgatacagtt aaaaggtgca gctgccagtg acaaataaaa acttttgtta
     3241 catctcatta ttttcaggcc aaggtgggag tatagtgcat aataattgta cagtagcaat
     3301 ttttatccta attaacccat agcggtttac ctaaaagtaa ccatcagtca gtgcaaaatg
     3361 tgcctggttc ttaagacaac tttttattta gaactgtgag accggtattt tggaaacatt
     3421 tcaaaggaaa catatgaatt tgttttgcgt tgtgcactac atcatttctc tcctgaggaa
     3481 gaattttaaa catgtacagc tcattcaata tagatatgag ccatggtgga gaactttatc
     3541 actcaagtag acggtaaaca tccttaatat gttctaaatt gtttatattg ctatccataa
     3601 tgggattcac ctccaaatta tcaaagaaat aactcagagt aatttgacac cagcccagat
     3661 catatattga ttatacaatt gtattataaa gttcattcaa atcaaattaa gaaaacctga
     3721 gtctttagaa gctgaaataa tcaacttgtt tgtgctgttt gcttgacata ggttattgtt
     3781 tgaaaatatt gttactttat caatagtaat catgcattct tgtgtttttt tttaatggaa
     3841 aactgcaagt ttcaattact gttgcactag aagtgctttt tatgttgtca ttttatattc
     3901 atgccatcaa aagtagattg acaatacatc aatctaacag gggccaatca aaacaatgaa
     3961 gaaaagaata actgaaaaca atgtcaaact tttaaatttt tatctcttcc aaagaagtta
     4021 tatctataaa atctagtttt atgcaggttt gtcacagcaa atgtaaaagc ggattcaaga
     4081 agaatgaact taaaaactgt ggagcaaatt tttgttgaaa atatataaag tcagaaagaa
     4141 aaaagatgta aatgttggaa gaagcaaatt ctattactaa ttcaaatgaa actaaatgtc
     4201 aaacacagta cttgtgtcaa ctatttagca tcccagattt tgtaacatat tttgcataaa
     4261 ttatttgctc ttcaaaaatt tttgtcattt taaatctaat tttaatcttt atgttttcca
     4321 ttttctaatt tccttgcaat gtattattct tattcttaat tctctacatt gaaatttggc
     4381 tttacgtcgt tagcaaattt ataaagggtt ataaagctat gattcgtgag tctaaaatca
     4441 aatgcaaaat tttatttatt atgtaaacca aaatgtcatt tgcaagtttt ctcattagaa
     4501 gttatccttg caaagataga aaaagaagaa ttaatttgtg taaacaagca caaattaaca
     4561 tatttgttaa taaataggtt tatctactaa taaacctatt tctagacaca ttcaaattga
     4621 taatgatttt tagaaatgtt aaggttccaa ggagtcttac aagtgtatgc ccttgatttc
     4681 ctgaaggaaa ccactttctt tcttaaatat tttaaattca tctaaagtga acgactataa
     4741 atagaagcaa tcaccttgga accacagctc tgtgcaacca aggccctaag ctacaccaaa
     4801 tacgccagga attttgagac ttctcatctt taaattcaac caaaagggtc tttagcaaga
     4861 aaaaaaatgc tggatgatga ttattattat ttttgcttaa tttttatttt gccatgtcca
     4921 ggttaagggt gagggtggtg acaatctgaa agactgtgtc tggaatcttt atcacatatt
     4981 tccaatttat ttcagttttt gtctaaaact tgcatttcta acctatcttt tccagcattt
     5041 gataatctcc catttcctcc ttctaacccc cattcctatg tctcccttcc tgtctattcc
     5101 tcaccgattt aaacaactga aatgtttact tatgtttgga gctgaaaaat ggaaagtttc
     5161 acccagcatg gttacaataa cagccagcag ctgcagcaaa ccataaagtt atgcagtgtt
     5221 ttgaagttca caaaccacat tttacataaa ttatctcatt ttgtcttcat aacaacccta
     5281 tgaagacaca ttaatctcaa agaaattgag ctcttacccc aaaacacagg gccaataatt
     5341 ggtgcagttg aattattctc aaaatttaca ggctgttagt ctttccactg tactaaaaga
     5401 tttctttctc tgatcagagc aagagaactt ccagagataa tggatagaat gaaagaatat
     5461 atatctatat atatttgaca tgttgtttag taatccctat tttaattcaa ttctccatct
     5521 gtaaaatatt agctaactga attatttctg tgttctactc tgggctctca cattaaaact
     5581 ctgttcaaaa agtttaacaa gtcacatatt tcttaacata caagttcgtt tgtgaatgtg
     5641 cagaacagat gctcccaaga tgtggatgca tgtaggcccc gaggtacaga cataaaatca
     5701 aggaagcaca aggaaagaaa ccccaaggaa aaaaccaaag accttctaaa ttgagactgc
     5761 ataattataa aagagatcca tagtacaggg ttgaacacat gttcaacact ttgtcaactg
     5821 aacacatgtt caattcggag ctaattggga agacttacat aaaattcttt ttcttttttt
     5881 cttttggcaa gatttcttct taaaccatga aatttttttt acttgtaata atagagaaca
     5941 attttctcca ttttcttata agaaaaataa aatataattt atccaaattg atgtatagaa
     6001 cctaaaacat atgctaactt gcaaataata tattttactg atcaactca
//
