LOCUS       NM_001347261            2787 bp    mRNA    linear   ROD 11-FEB-2025
DEFINITION  Mus musculus leucine rich repeat transmembrane neuronal 4 (Lrrtm4),
            transcript variant 4, mRNA.
ACCESSION   NM_001347261
VERSION     NM_001347261.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 2787)
  AUTHORS   Bedogni,F. and Hevner,R.F.
  TITLE     Cell-Type-Specific Gene Expression in Developing Mouse Neocortex:
            Intermediate Progenitors Implicated in Axon Development
  JOURNAL   Front Mol Neurosci 14, 686034 (2021)
   PUBMED   34321999
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2787)
  AUTHORS   Agosto,M.A. and Wensel,T.G.
  TITLE     LRRTM4 is a member of the transsynaptic complex between rod
            photoreceptors and bipolar cells
  JOURNAL   J Comp Neurol 529 (1), 221-233 (2021)
   PUBMED   32390181
  REMARK    GeneRIF: LRRTM4 is a member of the transsynaptic complex between
            rod photoreceptors and bipolar cells.
REFERENCE   3  (bases 1 to 2787)
  AUTHORS   Roppongi,R.T., Dhume,S.H., Padmanabhan,N., Silwal,P., Zahra,N.,
            Karimi,B., Bomkamp,C., Patil,C.S., Champagne-Jorgensen,K.,
            Twilley,R.E., Zhang,P., Jackson,M.F. and Siddiqui,T.J.
  TITLE     LRRTMs Organize Synapses through Differential Engagement of
            Neurexin and PTPsigma
  JOURNAL   Neuron 106 (1), 108-125 (2020)
   PUBMED   31995730
  REMARK    GeneRIF: LRRTMs engage the protein domains of Nrx but require its
            heparan sulfate (HS) modification to induce presynaptic
            differentiation. Binding to HS of Nrx is sufficient for LRRTM3 and
            LRRTM4 to induce synaptogenesis. Nrx1gamma is a potent synapse
            organizer and LRRTM4 is its postsynaptic ligand. Mice expressing a
            mutant form of LRRTM4 that can't bind HS show structural and
            functional deficits at dentate gyrus excitatory syn...
            Erratum:[Neuron. 2020 May 20;106(4):701. doi:
            10.1016/j.neuron.2020.05.003.. PMID: 32437657]
REFERENCE   4  (bases 1 to 2787)
  AUTHORS   Sinha,R., Siddiqui,T.J., Padmanabhan,N., Wallin,J., Zhang,C.,
            Karimi,B., Rieke,F., Craig,A.M., Wong,R.O. and Hoon,M.
  TITLE     LRRTM4: A Novel Regulator of Presynaptic Inhibition and Ribbon
            Synapse Arrangements of Retinal Bipolar Cells
  JOURNAL   Neuron 105 (6), 1007-1017 (2020)
   PUBMED   31974009
  REMARK    GeneRIF: LRRTM4 is a key synapse organizing molecule at rod bipolar
            cell (RBC) terminals, where it regulates function of GABAergic
            synapse and assembly of RBC synaptic dyads.
REFERENCE   5  (bases 1 to 2787)
  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   6  (bases 1 to 2787)
  AUTHORS   Siddiqui,T.J., Tari,P.K., Connor,S.A., Zhang,P., Dobie,F.A.,
            She,K., Kawabe,H., Wang,Y.T., Brose,N. and Craig,A.M.
  TITLE     An LRRTM4-HSPG complex mediates excitatory synapse development on
            dentate gyrus granule cells
  JOURNAL   Neuron 79 (4), 680-695 (2013)
   PUBMED   23911104
  REMARK    GeneRIF: This study demonistrated that LRRTM4-HSPG complex mediates
            excitatory synapse development on dentate gyrus granule cells.
REFERENCE   7  (bases 1 to 2787)
  AUTHORS   de Wit,J., O'Sullivan,M.L., Savas,J.N., Condomitti,G.,
            Caccese,M.C., Vennekens,K.M., Yates,J.R. 3rd and Ghosh,A.
  TITLE     Unbiased discovery of glypican as a receptor for LRRTM4 in
            regulating excitatory synapse development
  JOURNAL   Neuron 79 (4), 696-711 (2013)
   PUBMED   23911103
REFERENCE   8  (bases 1 to 2787)
  AUTHORS   Schwenk,J., Harmel,N., Brechet,A., Zolles,G., Berkefeld,H.,
            Muller,C.S., Bildl,W., Baehrens,D., Huber,B., Kulik,A., Klocker,N.,
            Schulte,U. and Fakler,B.
  TITLE     High-resolution proteomics unravel architecture and molecular
            diversity of native AMPA receptor complexes
  JOURNAL   Neuron 74 (4), 621-633 (2012)
   PUBMED   22632720
REFERENCE   9  (bases 1 to 2787)
  AUTHORS   Haines,B.P. and Rigby,P.W.
  TITLE     Developmentally regulated expression of the LRRTM gene family
            during mid-gestation mouse embryogenesis
  JOURNAL   Gene Expr Patterns 7 (1-2), 23-29 (2007)
   PUBMED   16860615
REFERENCE   10 (bases 1 to 2787)
  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
            AC156282.6 and AC153827.5.
            
            Transcript Variant: This variant (4) differs in the 3' UTR and has
            multiple differences in the coding region, compared to variant 1.
            The encoded isoform (4) has distinct N- and C-termini and is longer
            than isoform 1.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            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 :: SRR7345562.1118609.1,
                                           SRR7345562.1003463.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164131, SAMN01164132
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-64                AC156282.6         99776-99839         c
            65-1611             AC156282.6         96322-97868         c
            1612-2787           AC153827.5         109612-110787       c
FEATURES             Location/Qualifiers
     source          1..2787
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="6"
                     /map="6 35.05 cM"
     gene            1..2787
                     /gene="Lrrtm4"
                     /gene_synonym="7530419J18Rik; A230052N11"
                     /note="leucine rich repeat transmembrane neuronal 4"
                     /db_xref="GeneID:243499"
                     /db_xref="MGI:MGI:2389180"
     exon            1..64
                     /gene="Lrrtm4"
                     /gene_synonym="7530419J18Rik; A230052N11"
                     /inference="alignment:Splign:2.1.0"
     CDS             61..1833
                     /gene="Lrrtm4"
                     /gene_synonym="7530419J18Rik; A230052N11"
                     /note="isoform 4 precursor is encoded by transcript
                     variant 4; leucine-rich repeat transmembrane neuronal
                     protein 4"
                     /codon_start=1
                     /product="leucine-rich repeat transmembrane neuronal
                     protein 4 isoform 4 precursor"
                     /protein_id="NP_001334190.1"
                     /db_xref="CCDS:CCDS90065.1"
                     /db_xref="GeneID:243499"
                     /db_xref="MGI:MGI:2389180"
                     /translation="MGFRLITQLKGMSVFLVLFPTLLLVMLTGAQRACPKNCRCDGKI
                     VYCESHAFADIPENISGGSQGLSLRFNSIQKLKSNQFAGLNQLIWLYLDHNYISSVDE
                     DAFQGIRRLKELILSSNKITYLHNKTFHPVPNLRNLDLSYNKLQTLQSEQFKGLRKLI
                     ILHLRSNSLKTVPIRVFQDCRNLDFLDLGYNRLRSLSRNAFAGLLKLKELHLEHNQFS
                     KINFAHFPRLFNLRSIYLQWNRIRSVSQGLTWTWSSLHTLDLSGNDIQAIEPGTFKCL
                     PNLQKLNLDSNKLTNVSQETVNAWISLISITLSGNMWECSRSICPLFYWLKNFKGNKE
                     STMICAGPKHIQGEKVSDAVETYNICSDVQVVNTERSHLAPQTPQKPPFIPKPTIFKP
                     DAVPATLEAVSPSPGFQIPGTDHEYEHVSFHKIIAGSVALFLSVAMILLVIYVSWKRY
                     PASMKQLQQHSLMKRRRKKARESERQMNSPLQEYYVDYKPTNSETMDISVNGSGPCTY
                     TISGSRECEIPHHVKPLPYYSYDQPVIGYCQAHQPLHINKAYEAVSIEQDDSPSLELG
                     RDHSFIATIARSAAPAIYLERITN"
     exon            65..1611
                     /gene="Lrrtm4"
                     /gene_synonym="7530419J18Rik; A230052N11"
                     /inference="alignment:Splign:2.1.0"
     exon            1612..2787
                     /gene="Lrrtm4"
                     /gene_synonym="7530419J18Rik; A230052N11"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2763..2768
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Lrrtm4"
                     /gene_synonym="7530419J18Rik; A230052N11"
                     /note="hexamer: AAGAAA"
     polyA_site      2785
                     /gene="Lrrtm4"
                     /gene_synonym="7530419J18Rik; A230052N11"
                     /note="major polyA site"
ORIGIN      
        1 gagagaccaa ataagaagaa agctgagaga ggggggcaga cggtttttgg atgacaaagg
       61 atgggtttcc gtctaatcac gcagctgaaa ggcatgagtg tgtttctggt gctatttccc
      121 accctgctgc tggttatgct gacgggggct cagagagctt gcccaaagaa ctgcagatgc
      181 gatggcaaga ttgtatactg tgagtctcac gccttcgcag acatccctga gaacatttct
      241 ggagggtcac aaggtttatc cttaaggttc aacagcattc agaaactcaa atccaatcag
      301 tttgccggcc ttaaccagct tatatggctt tatcttgacc ataattacat tagctcagtg
      361 gacgaagatg cctttcaagg gatccgcaga ctgaaagaat taattctaag ctccaacaaa
      421 attacctatc tgcacaataa aacatttcac ccagtcccca acctccgcaa cctggatctc
      481 tcctacaaca aacttcagac cttacagtct gagcagttta aaggcctccg gaaactcatc
      541 attttgcact tgcgatctaa ttctctcaag accgtgccca tacgggtttt tcaagactgc
      601 cggaaccttg actttctgga tttgggttat aatcggctcc gaagcttatc ccgaaacgcg
      661 tttgccggtc ttctgaagtt aaaagagctc cacctggagc ataatcagtt ttcaaagatc
      721 aactttgctc attttcctcg tctcttcaac ctgcgatcca tctacctgca atggaacagg
      781 atccgctctg tcagtcaagg cctaacatgg acctggagtt ccttgcacac cttggattta
      841 tcagggaatg acatccaagc aatcgagcct ggcacattta aatgcctccc caatttgcaa
      901 aaattgaatt tggattccaa caagctcacc aatgtctccc aggagactgt caatgcatgg
      961 atatccttaa tatccatcac cttgtctgga aacatgtggg aatgtagtcg gagcatctgt
     1021 cctctattct actggctgaa gaatttcaaa gggaataaag aaagtaccat gatatgtgca
     1081 gggcctaagc acatacaggg tgagaaggtt agcgatgccg tggagactta caacatctgc
     1141 tctgatgtcc aggtggtcaa cacagaacga tcacatctgg cgcctcaaac tccccagaag
     1201 cccccgttca tccccaaacc taccatcttc aaaccggatg cagtcccagc caccctagag
     1261 gcagtgagcc catccccggg ctttcaaatt ccaggtacgg atcatgagta cgagcacgtg
     1321 tcgtttcaca aaatcatcgc agggagcgtg gctctgttcc tctccgtggc catgattctc
     1381 ctggtgatct atgtgtcttg gaaacggtac ccagccagca tgaaacaact ccaacagcac
     1441 tcacttatga agaggagacg gaaaaaggcg agggagtcgg agagacagat gaattcccct
     1501 ttacaggaat actacgtgga ctacaaaccg acgaactctg agaccatgga tatatcggtt
     1561 aatggatctg gtccctgcac atataccatc tctggctcca gggagtgtga gataccccac
     1621 catgtgaagc ccctgccgta ttacagctat gaccaaccag tgattgggta ctgccaggcc
     1681 caccagcctc tccacatcaa caaggcttat gaagctgtgt ctatagaaca ggatgacagc
     1741 cccagtttgg agcttgggag agaccacagc ttcattgcca ccatagccag gtcggctgca
     1801 cctgccattt atctggagag aataacaaac taacagcgaa actaacttct agatgaagag
     1861 ctcacaggaa aagggcagcc ttcatcacat aggagttgag gtgtccagca tcctccagcc
     1921 tcaagagttc attgctcctg tacagaagtt tagggaatag tgagaagcaa accccaaact
     1981 gcttatgaag ttgggcagct gataaacctg ccaccaaccc gggaggaccc agaacttcct
     2041 ttgctttaaa acataaaaca aacacaagca ctcccggatg taaatagtca agagtgttac
     2101 gttcttataa aaatagattt caccctagct atctataggt tggtttgtat atttgatttt
     2161 tctacaatgc atggttcctg ggctggagaa ccacagtggg agggtgggaa tttgggggaa
     2221 acaacacatt ttttttcttg taagatgtgc atagcactca cagacctttt ttcctaagtt
     2281 tttatgttat ttttccttta aaatctggtt ttatcctttt attaatttta tttttcttaa
     2341 tttcccggtt gagtgacttc tttctacttc taaatatgag tacttccatg gaaccaaaaa
     2401 ggtttggttt ttgcattgac ctaaagtaaa gaaagttgac tacaaagttc aataaactac
     2461 tggaatgaat caaatacatc gaagtgtata ttcacacagt acacattata gacaatagaa
     2521 ggagctctgg tttatttccc catctgtatc tgtcatggaa agaaacctga tgaccagacc
     2581 tgtgaacacg tggatgggga agagtctgaa tactaccctc aaatagagat gggctctgtg
     2641 aacaatggcc aggggtcctt tgaatgtcac tgtaatggga tgactttcta aactcaagat
     2701 gatgtgtaat attgctttta aatttaatta tcacttagct tttgtgtaat ttttatcaat
     2761 aaaagaaaaa tgttgaaaaa taaaata
//
