LOCUS       NM_001310586            4417 bp    mRNA    linear   ROD 05-JUN-2024
DEFINITION  Mus musculus leucine rich repeat and fibronectin type III domain
            containing 5 (Lrfn5), transcript variant 2, mRNA.
ACCESSION   NM_001310586 XM_006515832
VERSION     NM_001310586.1
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 4417)
  AUTHORS   Noack,F., Vangelisti,S., Raffl,G., Carido,M., Diwakar,J., Chong,F.
            and Bonev,B.
  TITLE     Multimodal profiling of the transcriptional regulatory landscape of
            the developing mouse cortex identifies Neurog2 as a key epigenome
            remodeler
  JOURNAL   Nat Neurosci 25 (2), 154-167 (2022)
   PUBMED   35132236
REFERENCE   2  (bases 1 to 4417)
  AUTHORS   Markenscoff-Papadimitriou,E., Binyameen,F., Whalen,S., Price,J.,
            Lim,K., Ypsilanti,A.R., Catta-Preta,R., Pai,E.L., Mu,X., Xu,D.,
            Pollard,K.S., Nord,A.S., State,M.W. and Rubenstein,J.L.
  TITLE     Autism risk gene POGZ promotes chromatin accessibility and
            expression of clustered synaptic genes
  JOURNAL   Cell Rep 37 (10), 110089 (2021)
   PUBMED   34879283
REFERENCE   3  (bases 1 to 4417)
  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   4  (bases 1 to 4417)
  AUTHORS   Lie,E., Ko,J.S., Choi,S.Y., Roh,J.D., Cho,Y.S., Noh,R., Kim,D.,
            Li,Y., Kang,H., Choi,T.Y., Nam,J., Mah,W., Lee,D., Lee,S.G.,
            Kim,H.M., Kim,H., Choi,S.Y., Um,J.W., Kang,M.G., Bae,Y.C., Ko,J.
            and Kim,E.
  TITLE     SALM4 suppresses excitatory synapse development by cis-inhibiting
            trans-synaptic SALM3-LAR adhesion
  JOURNAL   Nat Commun 7, 12328 (2016)
   PUBMED   27480238
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 4417)
  AUTHORS   Choi,Y., Nam,J., Whitcomb,D.J., Song,Y.S., Kim,D., Jeon,S.,
            Um,J.W., Lee,S.G., Woo,J., Kwon,S.K., Li,Y., Mah,W., Kim,H.M.,
            Ko,J., Cho,K. and Kim,E.
  TITLE     SALM5 trans-synaptically interacts with LAR-RPTPs in a
            splicing-dependent manner to regulate synapse development
  JOURNAL   Sci Rep 6, 26676 (2016)
   PUBMED   27225731
  REMARK    GeneRIF: These results suggest that postsynaptic SALM5 promotes
            synapse development by trans-synaptically interacting with
            presynaptic LAR-RPTPs and is important for the regulation of
            excitatory synaptic strength.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 4417)
  AUTHORS   Nam,J., Mah,W. and Kim,E.
  TITLE     The SALM/Lrfn family of leucine-rich repeat-containing cell
            adhesion molecules
  JOURNAL   Semin Cell Dev Biol 22 (5), 492-498 (2011)
   PUBMED   21736948
  REMARK    Review article
REFERENCE   7  (bases 1 to 4417)
  AUTHORS   Mah,W., Ko,J., Nam,J., Han,K., Chung,W.S. and Kim,E.
  TITLE     Selected SALM (synaptic adhesion-like molecule) family proteins
            regulate synapse formation
  JOURNAL   J Neurosci 30 (16), 5559-5568 (2010)
   PUBMED   20410109
REFERENCE   8  (bases 1 to 4417)
  AUTHORS   Homma,S., Shimada,T., Hikake,T. and Yaginuma,H.
  TITLE     Expression pattern of LRR and Ig domain-containing protein (LRRIG
            protein) in the early mouse embryo
  JOURNAL   Gene Expr Patterns 9 (1), 1-26 (2009)
   PUBMED   18848646
REFERENCE   9  (bases 1 to 4417)
  AUTHORS   Yoshida,Y., Han,B., Mendelsohn,M. and Jessell,T.M.
  TITLE     PlexinA1 signaling directs the segregation of proprioceptive
            sensory axons in the developing spinal cord
  JOURNAL   Neuron 52 (5), 775-788 (2006)
   PUBMED   17145500
REFERENCE   10 (bases 1 to 4417)
  AUTHORS   Morimura,N., Inoue,T., Katayama,K. and Aruga,J.
  TITLE     Comparative analysis of structure, expression and PSD95-binding
            capacity of Lrfn, a novel family of neuronal transmembrane proteins
  JOURNAL   Gene 380 (2), 72-83 (2006)
   PUBMED   16828986
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AK162923.1 and BC052038.1.
            
            On Jul 16, 2015 this sequence version replaced XM_006515832.2.
            
            Transcript Variant: This variant (2) differs in the 3' structure,
            resulting in a novel 3' coding region, compared to variant 1. The
            encoded isoform (2) has a distinct C-terminus, and is shorter than
            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 :: BC052038.1, SRR1660817.123824.1
                                           [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##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1635              AK162923.1         2-1636
            1636-4417           BC052038.1         1-2782
FEATURES             Location/Qualifiers
     source          1..4417
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="12"
                     /map="12 26.43 cM"
     gene            1..4417
                     /gene="Lrfn5"
                     /gene_synonym="C130061B21; mKIAA4208; Salm5"
                     /note="leucine rich repeat and fibronectin type III domain
                     containing 5"
                     /db_xref="GeneID:238205"
                     /db_xref="MGI:MGI:2144814"
     exon            1..1664
                     /gene="Lrfn5"
                     /gene_synonym="C130061B21; mKIAA4208; Salm5"
                     /inference="alignment:Splign:2.1.0"
     exon            1665..1839
                     /gene="Lrfn5"
                     /gene_synonym="C130061B21; mKIAA4208; Salm5"
                     /inference="alignment:Splign:2.1.0"
     exon            1840..3244
                     /gene="Lrfn5"
                     /gene_synonym="C130061B21; mKIAA4208; Salm5"
                     /inference="alignment:Splign:2.1.0"
     exon            3245..3957
                     /gene="Lrfn5"
                     /gene_synonym="C130061B21; mKIAA4208; Salm5"
                     /inference="alignment:Splign:2.1.0"
     exon            3958..4001
                     /gene="Lrfn5"
                     /gene_synonym="C130061B21; mKIAA4208; Salm5"
                     /inference="alignment:Splign:2.1.0"
     exon            4002..4396
                     /gene="Lrfn5"
                     /gene_synonym="C130061B21; mKIAA4208; Salm5"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4373..4378
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Lrfn5"
                     /gene_synonym="C130061B21; mKIAA4208; Salm5"
                     /note="hexamer: AATAAA"
     polyA_site      4391
                     /gene="Lrfn5"
                     /gene_synonym="C130061B21; mKIAA4208; Salm5"
                     /note="major polyA site"
ORIGIN      
        1 ctctgggccg gcgttgcctg ctcgcaccac gctggggagc ggctctccca ggcctgccgg
       61 ggcggcggct gcctgcccgg actgcagctt cccgccttga gcctgagctg aggactcgtc
      121 ccagggcctc agccagcggg aggggcgccc accgcgctgt gtgcagcggc gcagggaggt
      181 ggtgagcccg tgcagagcag ccggagctgt gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt
      241 gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt tcgcctgcga gcttttcttc ttcccttgaa
      301 gatgtgagat gtgaatggct tcttagctag ctggtcctta ggattctgga ctttgtggag
      361 ctgtgggcac aacgcaccca tgtaattcat gttgtgtggt cggttatctt aggggaaaaa
      421 aaaaaggcgc aactcgacgg gggtggggca gatccaggaa acattctgga aaggagaaat
      481 agaaagagag aggcgtagaa atgtgaatat tgaaagacct gagaagactt ttggaatctc
      541 ccggctggcc cttcagtttt cccggcacta atctggaggt tttccacctt ttcaagtcat
      601 cttggtgttc ctctagtgtt ttgtaagcct cttttcagct agctgcgtgt gtgtatgcgt
      661 gtgtttgtgc gcctgtgtat gtgcgcgcgc ctatcagatg catttgacag tcttttttcc
      721 aactgcccag aagcaaacgt gttaactcag agatgcccct ccgtgcccag gttctcgcag
      781 agcatggagg acacccagac cggttttcca ggctggattc tgggaggctg atgggctgtg
      841 aacccaggtg taaggatcac ttaatccaga ggcttggaaa gtggctgtat taacgagctt
      901 ccaggtacat cgcaaggtca agagagggac ttgcagctgt attaattccc tgcatcttga
      961 ctttcctgtt ttggtccgaa gaatatgaat gtgtctgtcc acaacatttg aagcccaaac
     1021 ttcagcactc cgagctggtt tactgtacaa acaaggtaat gaggattgct tttcaaactg
     1081 cttaacgaat ccccgacgct tccacagccc ttccaggact ccctttctgc ccagcgaaat
     1141 gtcaccagct tttgaattcc aaggatttgg ctgcaggaga acttgaagga aacgtgatca
     1201 aagggctatg tgagaacgcg actgctcttt ttgccggtag gctggtgggc ttccggaccg
     1261 gatcttgaga aggaccagaa ctgtttctcc ctcccggtgc ggttctggga gtgcttgtgc
     1321 aagtgtgagt gcgcgcgcgc ccggctgaga atgtgtgagt gtgtgtgagc gtgtctctgt
     1381 gtgtgcgcgg ccgccctgct tctgcccgct ccccgggcgc ggagccaccg gtttgggcga
     1441 tttgcgctga ttccccaccc agcgcgacct gcgagcagcg aaggcagggg caggagccac
     1501 ctctctgact ccctaggatg cgggtgctga gctatggcaa agggcagcga agtgatgagc
     1561 tagaccccag tacgactgtg aaagccacct ggagccacct tgcctggatc ttacctgccg
     1621 gcagaaagtc ttcctatgac cgtctttccc cctagaggca ccagagctcc tgtatccatt
     1681 cagccgggta ttgagaagat atgtagtagc tgacaacctt ctgtctgaca gcactctcag
     1741 aaccagcatt ggaaatgcgt tcaccctgcc ggtcttctgc agcagccagg ccacgtgctg
     1801 actccttcac ggtagtaagg aactctccag gcttcagaag ctcttaatcc tgatctacaa
     1861 tggaaaaatt ccttttttac ctgtttctca ttggcatagc tgtgcgagct cagatctgtc
     1921 caaagcgttg tgtctgtcag attttgtctc caaatcttgc aaccctttgt gccaagaaag
     1981 ggcttctatt tgttccacca aacattgaca gaagaactgt ggagctacgg ctggcagaca
     2041 attttgttac aaatatcaaa aggaaagatt ttgccaatat gaccagcttg gtggacctga
     2101 ctctatccag gaatacaata agttttatta caccccatgc ttttgctgat ctacgaaatt
     2161 tgagagcact gcatttgaat agcaacagat tgactaaaat tacaaatgat atgttcagtg
     2221 ggctttccaa tctccaccat ttgatattga acaacaatca gctgacttta atttcttcca
     2281 cagccttcga tgatgttttt gcccttgagg agctggacct gtcctataat aatctagaaa
     2341 cgattccctg ggatgctgta gagaagatgg tgagcttgca cacccttagt ttggatcaca
     2401 atatgattga caacattcct aagggtactt tctcccactt gcacaagatg actcggctag
     2461 atgtaacatc aaataaactg caaaagctgc ctcctgaccc tctgtttcag cgagcacagg
     2521 tgctggccac ctcaggaatc ataagcccat cgacttttgc attgagtttt ggtggaaacc
     2581 ccttgcattg caattgtgag ttgctgtggc tgaggcgatt gtctcgagaa gatgaccttg
     2641 agacgtgtgc ttctcctgca cttttaactg gtcgttattt ttggtcaatt cctgaggaag
     2701 agtttttgtg tgagcctccg ctcatcactc gtcatacaca tgagatgaga gtcttggagg
     2761 gtcaaagggc aacactgagg tgcaaagctc gaggagaccc tgaacctgcg attcattgga
     2821 tttcccctga agggaagctg atttcaaatg caacacgatc tctggtgtat gataacggga
     2881 cacttgacat ccttataaca actgtaaaag atacaggagc ttttacctgt attgcttcca
     2941 atccggcagg ggaagcaaca caaaccgtgg atcttcacat aattaaactc cctcacctac
     3001 taaacagcac caatcatatc catgagcctg atcctggttc ttctgatatc tccacatcca
     3061 ctaagtcagg ctcgaatgct agcagtagta atggtgatac aaaaatgagt caagataaaa
     3121 tcgtggtggc agaagcaact tcgtcaacag cattactaaa atttaatttt caaagaaata
     3181 ttcccggaat ccgtatgttt caaatccagt acaatggtac ttatgatgac acccttgttt
     3241 acagaatgat acctcctacg agcaaaacat ttctggtcaa taatctggca tctggaacta
     3301 tgtatgactt gtgtgtcttg gccatctatg acgatggcat cacttccctc actgccacaa
     3361 gagtcgtggg ttgcatccag tttactacgg aacaggatta tgtccgttgc cactttatgc
     3421 agtcccagtt cttgggtggc accatgatta ttatcattgg tggaatcatt gttgcatccg
     3481 tgttggtttt catcatcata ctaatgatcc ggtataaggt ttgtaacaat aatgggcaac
     3541 acaaggtcac gaaggttagc aacgtttatt ctcagactaa tggggctcag atgcaaggct
     3601 gcagtgtcac gctgccccag tccatgtcca aacaagccat gggccatgaa gagaatgccc
     3661 agtgctgtaa agttgccagt gacaatgcaa ttcagtcttc agaaacatgt tcgagtcagg
     3721 actcttctac cactacctct gctttgcctc ctacctggac ttcaagtgcg cctgtgtctc
     3781 aaaagcagaa aagaaagact ggcacgaagc caagtgctga gccgcagagt gaagctgtca
     3841 caaatgttga gtcccaaaac actaacagga acaactcaac tgccttgcag ttagctagct
     3901 gccctcctga ttctgttaca gaggggccca catctcaaag agcacatacc aagccaaatg
     3961 ctttgctgac taatgttgat cagaatgtcc aggaaacaca gaggctggag tccatatgaa
     4021 gagcaacact tctctctctc tcctgagaac agttgcccct aatattttta ctggataaaa
     4081 tttgaaaatg tttcagttca cagctgtgga ttgttgaact gcttgtccca gaacgaattg
     4141 ctcatgggag ccaaagctac aaggtctctg atgtggtgaa actggctccc tcccaacatg
     4201 gttcatcccc ttttaaaacc aaattttttt cttctgatct acaaatattt tttttaataa
     4261 aggaaaaaga acaagccttc attggcatca agttctgtat caaatccatc ctacattgcc
     4321 atccatgatt taacagactg tagaatcttg aataatctat atcactttaa caaataaatg
     4381 ttttactatg acacaaaaaa aaaaaaaaaa aaaaaaa
//
