LOCUS       NM_001104633            4922 bp    mRNA    linear   ROD 31-MAR-2024
DEFINITION  Rattus norvegicus semaphorin 3D (Sema3d), mRNA.
ACCESSION   NM_001104633 XM_001065379 XM_342625
VERSION     NM_001104633.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 4922)
  AUTHORS   Abonnenc,M., Nabeebaccus,A.A., Mayr,U., Barallobre-Barreiro,J.,
            Dong,X., Cuello,F., Sur,S., Drozdov,I., Langley,S.R., Lu,R.,
            Stathopoulou,K., Didangelos,A., Yin,X., Zimmermann,W.H., Shah,A.M.,
            Zampetaki,A. and Mayr,M.
  TITLE     Extracellular matrix secretion by cardiac fibroblasts: role of
            microRNA-29b and microRNA-30c
  JOURNAL   Circ Res 113 (10), 1138-1147 (2013)
   PUBMED   24006456
REFERENCE   2  (bases 1 to 4922)
  AUTHORS   Takahashi,K., Ishida,M. and Takahashi,H.
  TITLE     Expression of Sema3D in subsets of neurons in the developing dorsal
            root ganglia of the rat
  JOURNAL   Neurosci Lett 455 (1), 17-21 (2009)
   PUBMED   19429098
  REMARK    GeneRIF: Sema3D may regulate the axonal navigation of the large
            diameter DRG neurons.
REFERENCE   3  (bases 1 to 4922)
  AUTHORS   Takahashi,K., Tomizawa,K., Ishida,M., Hirokawa,K. and Takahashi,H.
  TITLE     Identification and tissue-specific expression of a novel isoform of
            Semaphorin 3D
  JOURNAL   Biochim Biophys Acta 1790 (5), 395-400 (2009)
   PUBMED   19345252
  REMARK    GeneRIF: Gene regulation, via an alternative splicing mechanism,
            affects not only the tissue-specificity of Sema 3D expression, but
            also the distance over which it can act.
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from
            JAXUCZ010000004.1.
            
            On or before Sep 16, 2007 this sequence version replaced
            XM_342625.3, XM_001065379.1.
            
            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.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26643285.15131.1,
                                           SRR26643298.21489.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA5760383,
                                           SAMEA5760386 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-508               JAXUCZ010000004.1  23460464-23460971   c
            509-696             JAXUCZ010000004.1  23397133-23397320   c
            697-857             JAXUCZ010000004.1  23377525-23377685   c
            858-920             JAXUCZ010000004.1  23357022-23357084   c
            921-1040            JAXUCZ010000004.1  23347677-23347796   c
            1041-1134           JAXUCZ010000004.1  23339617-23339710   c
            1135-1263           JAXUCZ010000004.1  23337107-23337235   c
            1264-1406           JAXUCZ010000004.1  23325056-23325198   c
            1407-1521           JAXUCZ010000004.1  23312646-23312760   c
            1522-1591           JAXUCZ010000004.1  23311532-23311601   c
            1592-1736           JAXUCZ010000004.1  23306499-23306643   c
            1737-1959           JAXUCZ010000004.1  23295738-23295960   c
            1960-2048           JAXUCZ010000004.1  23293189-23293277   c
            2049-2090           JAXUCZ010000004.1  23290596-23290637   c
            2091-2248           JAXUCZ010000004.1  23287584-23287741   c
            2249-2313           JAXUCZ010000004.1  23284158-23284222   c
            2314-2453           JAXUCZ010000004.1  23280100-23280239   c
            2454-4922           JAXUCZ010000004.1  23271815-23274283   c
FEATURES             Location/Qualifiers
     source          1..4922
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="4"
                     /map="4q12"
     gene            1..4922
                     /gene="Sema3d"
                     /note="semaphorin 3D"
                     /db_xref="GeneID:246262"
                     /db_xref="RGD:727939"
     exon            1..508
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            509..696
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     CDS             546..2879
                     /gene="Sema3d"
                     /note="semaphorin, homolog of the avian Sema3D; sema
                     domain, immunoglobulin domain (Ig), short basic domain,
                     secreted, (semaphorin) 3D"
                     /codon_start=1
                     /product="semaphorin-3D"
                     /protein_id="NP_001098103.1"
                     /db_xref="GeneID:246262"
                     /db_xref="RGD:727939"
                     /translation="MNANKDENPRPRSQDLHLFHAGMMLIVTVLYLPVTETSKQNIPR
                     LKLTYKDLLLSNTCIPFLGSSEGLDFQTLLLDEERGILLLGAKDHVFLLNLVDLNKNF
                     KKIYWPAAKERVELCKLAGKDANTECANFIRVLQPYNKTHVYVCGTGAFHPLCGYIDL
                     GANKEELIFKLDMQNLESGRLKCPFDPQQPFASVMTDEHLYSGTASDFLGKDTAFTRS
                     LGLMQDHHYIRTDISEHYWLNGAKFIGTFPIPDTYNPDDDKIYFFFRESSQEGSTSDR
                     SILSRVGRVCKNDVGGQRSLINKWTTFLKARLVCSIPGSDGADTHFDELQDIYLLPTR
                     DERNPVVYGVFTTTSSIFKGSAVCVYSMADIRAVFNGPYAHKESADHRWVQYDGRIPY
                     PRPGTCPSKTYDPLIKSTRDFPDDVISFIRRHPVMYKSVYPVAGAPTFKRINVDYRLT
                     QIVVDHVVAEDGQYDVMFLGTDIGTVLKVVSISKEKWNMEEVVLEELQVFKHPTAILN
                     MELSLKQQQLYVGSWDGLVQLSLHRCDTYGKACADCCLARDPYCAWDGNACSRYAPTS
                     KRRARRQDVKYGDPITQCWDIEDSISHEAADEKVIFGIEFNSTFLECIPKSQQASVEW
                     YIQRSGDEHREELKPDERIIKTDYGLLIRSLQKKDSGIYYCKAQEHTFIHTIVKLTLN
                     VIENEQMENNQRAEYQEGQVKDLLAESRLRYKDYIQILSSPNFSLDQYCEQMWYREKR
                     RQRNKGSAKWKHMQEMKKKRNRRHHRDLDELQRSVAT"
     exon            697..857
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            858..920
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            921..1040
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            1041..1134
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            1135..1263
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            1264..1406
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            1407..1521
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            1522..1591
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            1592..1736
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            1737..1959
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            1960..2048
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            2049..2090
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            2091..2248
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            2249..2313
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            2314..2453
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
     exon            2454..4922
                     /gene="Sema3d"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 aaaccaaccc tggacagcac ggcagggaag gggaaggttt gctcgctctg agggattgcc
       61 agcacatcag aaggggccgg gtgctggggg aggagattgg agggagaggt aatccctggt
      121 gttttgagca tccccttttt tagaaagacg gagtctctcc caggacagct gctgcggtca
      181 caccacaaac ttaaaagccg tcctcctgct tggagcgtgc ctttccgcac caggctcgct
      241 ggactgagcg ccaactggtt ggtcgctgtc cgtgaggaga ggcgctcagg ggacaggagc
      301 gccccctgcc ttcccgcctg gccccagcca ggacctcggt gctccgctag ggccgcccgc
      361 gctccgcggt tcagcccgag ctgccgctcc aaagaactcg cgcctgtgcc ccggtcgccg
      421 tcctctcggc ttccactggc tgtcccttcc tctctcctga gcctgcgttg taaggaaagg
      481 aaaagcaaca agagttgcca gcaggaaggg tgaagtaaca gtgtttggaa gacaaaattt
      541 tcatcatgaa tgctaataaa gatgagaacc caaggcccag aagtcaagat cttcaccttt
      601 ttcatgctgg gatgatgtta atcgtgactg tgctatatct tcctgtcact gaaacatcta
      661 aacaaaatat tccacggctc aagctaacct acaaagactt gctgctctca aacacctgca
      721 ttcccttttt gggttcatca gaaggactgg atttccagac tcttcttttg gatgaggaga
      781 ggggcatact gctcctagga gccaaagacc atgtcttcct gctcaatctg gtagacttga
      841 acaagaactt taagaagatt tattggcctg ctgcaaagga acgagtggaa ctatgtaaac
      901 tagctgggaa agatgccaat acagaatgtg caaatttcat ccgtgtgctt caaccctaca
      961 ataagactca tgtttacgtg tgtggaactg gagcatttca tccactgtgt ggatatattg
     1021 atcttggagc caacaaggag gaactcatat ttaaactaga catgcagaac ctggagtctg
     1081 gcagactgaa atgtcccttt gatcctcagc agccttttgc ttcggtaatg acagatgagc
     1141 acctctactc tggaacagct tctgattttc ttggcaaaga cactgcattc acaagatccc
     1201 ttgggctaat gcaggaccac cattacatca gaactgacat ttcggaacac tactggctca
     1261 atggagcaaa atttatcgga acgttcccca tcccagacac ctataatccg gacgatgaca
     1321 aaatatattt cttctttcgg gaatcatctc aggaaggcag tacttctgac agaagcattc
     1381 tttcaagagt tgggagagtt tgtaagaatg atgtgggtgg gcagcggagt ctgataaaca
     1441 aatggactac ttttcttaag gcaagactgg tttgctcaat tcctggaagt gatggggcag
     1501 atactcactt tgatgaactt caagatattt acttactccc tacgagagat gaaagaaatc
     1561 ctgttgtgta tggagtcttt accacaacca gttccatctt caaaggctct gctgtctgtg
     1621 tgtacagcat ggctgatatc agagcagttt ttaacggtcc ctatgctcat aaggaaagtg
     1681 cagaccatcg ttgggtgcaa tatgatggaa ggatacctta tccccgaccc ggaacgtgtc
     1741 ccagcaaaac ctatgatcca ctgattaagt ccacccgaga cttcccagat gatgttatca
     1801 gtttcataag gcggcacccg gtgatgtata agtcggtgta tccagtggcc ggagcaccca
     1861 ccttcaagag aattaacgtg gattacagac tgacgcagat agtggtggat cacgtggtcg
     1921 ctgaagacgg acagtatgat gtcatgtttc tcggaacaga cattggaacc gtcctgaaag
     1981 ttgtgagcat ttccaaggag aagtggaata tggaggaggt agtcctcgag gagcttcagg
     2041 tattcaagca cccaacagcc atcttgaaca tggagttgtc gctgaagcag caacagttgt
     2101 acgtcggttc ctgggatgga ttggttcagc tctccttgca cagatgcgat acttatggga
     2161 aagcctgtgc agactgctgt ctcgccagag acccttactg tgcttgggat ggaaatgctt
     2221 gctccagata tgcacccact tccaaaaggc gagctagacg ccaggatgta aaatatggag
     2281 acccaatcac tcagtgctgg gacatagaag acagcattag tcatgaagca gctgatgaaa
     2341 aggtgatttt cggaattgaa tttaattcaa cctttttgga atgtatacct aaatcccaac
     2401 aagcctctgt tgagtggtac atccagcggt caggagatga gcatcgagaa gagttgaaac
     2461 ccgatgaaag gatcatcaaa acggactatg ggctactgat tcgaagcctg cagaagaagg
     2521 actctgggat ttattactgc aaagcacagg agcacacttt catccacacc atagtgaagc
     2581 tgactttgaa tgtcattgag aatgaacaga tggaaaataa ccagagggca gaataccagg
     2641 aggggcaggt caaggatctg ttggctgagt cacggttgag atacaaagac tacatccaaa
     2701 tccttagcag cccaaacttc agcctggacc agtactgtga gcagatgtgg tacagggaga
     2761 agcggagaca gcgcaacaag ggcagcgcaa agtggaagca catgcaggaa atgaagaaga
     2821 aacggaatcg acggcatcac agagacctgg atgagcttca gagatcagtg gctacatagc
     2881 tttctattta atttaaagag agaattattt acctgcctgc agaagtaatg ttttttgttc
     2941 tgtacatccc ttaaactaac tcgtacatgc tttcccatgg agtctcacta aggcacagaa
     3001 cgctatgctg aataaagacg gtataggaca aaactgaact atctttctga gagcaaaacc
     3061 tatatcagca aagtcaagaa ctgtcctaaa aataggggca tcacgtttgt aaatgtttta
     3121 cagtctgaac tccatgtcac gtaaataagc aagctaagtg aacaccgggt ccactgagga
     3181 aggtccttta ttcccaagca tgtccattga gcgtagactt tcccatgctg gtggctgtgt
     3241 gcttagaagc agcttaatca tcccagtcta gaacaggtga tcttgtaggg actggagaaa
     3301 aggcacacat tagaacagct tatgttagca ataggaactt tctcaaggag ccatcagcct
     3361 acacttggag ccaggcatgg gaatttagga aggtgggttc tgtctttctg gcaacaggct
     3421 acatctagtg tactgcagta gtactttgtg agagggtatt aaggatccta accaggttcg
     3481 ttttgattgg tcaagagaag cagcgtcaca gtcggaacct gatactcaac gatgagctct
     3541 agaatgcata ctctagtaac ttagtacacg attcctgtgc actttgggag acatggtaaa
     3601 atatcttaat ataataataa gggtgacatg gtgtacactg tatcctaatc tgtagatggg
     3661 aattgttagg agacagacag aaggataact gtaaattctg gctctgagaa aaacttatat
     3721 tgccataaaa aaaggagaaa gccaaaaagt agatagaatg tgatggaatt ctttccactg
     3781 gagtataaat atctgccaac ttgtaatgtg tcagttaaaa ataatttaga ttatagcaca
     3841 ttgttagcaa aagctcaagt gaaagtaaaa tttgtaaaaa aaaatatggg atggcaatat
     3901 tttatttata accaatgtat ttctctgttc tctttttttc taagtattta tcattctgta
     3961 tattgtttgc atttatatcc tttattgatt atatttgagg aaataggaga aagcaatgcg
     4021 taatacatag agataattgg atagatgacc aaggtgggga gtggggttat atatttgtta
     4081 actggatgga taaaagcaaa attttgatga cgacgagaag ggttaaatta actcttcgac
     4141 atctctttac aaaaactttc aagcagcact gtttttagca gtcacaagtc acaagtaagt
     4201 cttccacatg taaagaaaaa agttcacagc attagcataa ataccatttt tattctgcta
     4261 gcatgtgtta aattcaactt tccctctgaa ctgtgttttc ctgccagtct cctgtagaaa
     4321 tcacctttct ttccttcctt tagcacaaag cccttagcct tcctctgttt tgccttttca
     4381 cgccctttat agtgtgaaat gaacaattag tcacttcctc gcaaagaatg cagcttttta
     4441 gtaaaccaac agaccttgct tgtttctcat gcattctaca tgttttgaaa gattctgtga
     4501 gaagcctgtg tgattaaagg ccagtgttac agagtcaaac aatctctctg ttcaaagtag
     4561 catcagtatt ttacattcat ttaatttgca ttggttatct atctcaaggg cataacattg
     4621 atctgcaaag gtctagtata atgatgaata tttgtagatg cttcactgta agaaaaagaa
     4681 aaattgaagg aacgatttta atatgtaaac cagaatgaat tgcatctcca gaagaaatgc
     4741 atacaaattt tttgtcatgg ttagaatact aatcatatat cacacagggt ttactggctt
     4801 actgagtgct acaaactcat agcaaactca agtcaatgag ggcgtgcttc atttaaaaaa
     4861 tattttcaga tagttgtgta tcaaagagta atattcaaat attaaaagta ttaaaaattg
     4921 ca
//
