LOCUS       NM_001163489            3046 bp    mRNA    linear   ROD 11-NOV-2023
DEFINITION  Mus musculus sema domain, immunoglobulin domain (Ig), transmembrane
            domain (TM) and short cytoplasmic domain, (semaphorin) 4A (Sema4a),
            transcript variant 2, mRNA.
ACCESSION   NM_001163489
VERSION     NM_001163489.1
KEYWORDS    RefSeq.
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 3046)
  AUTHORS   Naito Y, Koyama S, Masuhiro K, Hirai T, Uenami T, Inoue T, Osa A,
            Machiyama H, Watanabe G, Sax N, Villa J, Kinugasa-Katayama Y,
            Nojima S, Yaga M, Hosono Y, Okuzaki D, Satoh S, Tsuda T, Nakanishi
            Y, Suga Y, Morita T, Fukushima K, Nishide M, Shiroyama T, Miyake K,
            Iwahori K, Hirata H, Nagatomo I, Yano Y, Tamiya M, Kumagai T,
            Takemoto N, Inohara H, Yamasaki S, Yamashita K, Aoshi T, Akbay EA,
            Hosen N, Shintani Y, Takamatsu H, Mori M, Takeda Y and Kumanogoh A.
  TITLE     Tumor-derived semaphorin 4A improves PD-1-blocking antibody
            efficacy by enhancing CD8+ T cell cytotoxicity and proliferation
  JOURNAL   Sci Adv 9 (20), eade0718 (2023)
   PUBMED   37205755
REFERENCE   2  (bases 1 to 3046)
  AUTHORS   Martins LF, Brambilla I, Motta A, de Pretis S, Bhat GP, Badaloni A,
            Malpighi C, Amin ND, Imai F, Almeida RD, Yoshida Y, Pfaff SL and
            Bonanomi D.
  TITLE     Motor neurons use push-pull signals to direct vascular remodeling
            critical for their connectivity
  JOURNAL   Neuron 110 (24), 4090-4107 (2022)
   PUBMED   36240771
REFERENCE   3  (bases 1 to 3046)
  AUTHORS   Xu R, Hoss C, Swiercz JM, Brandt DT, Lutz V, Petersen N, Li R, Zhao
            D, Oleksy A, Creigh-Pulatmen T, Trokter M, Fedorova M, Atzberger A,
            Strandby RB, Olsen AA, Achiam MP, Matthews D, Huber M, Grone HJ,
            Offermanns S and Worzfeld T.
  TITLE     A semaphorin-plexin-Rasal1 signaling pathway inhibits gastrin
            expression and protects against peptic ulcers
  JOURNAL   Sci Transl Med 14 (654), eabf1922 (2022)
   PUBMED   35857828
REFERENCE   4  (bases 1 to 3046)
  AUTHORS   Suga Y, Nagatomo I, Kinehara Y, Koyama S, Okuzaki D, Osa A, Naito
            Y, Takamatsu H, Nishide M, Nojima S, Ito D, Tsuda T, Nakatani T,
            Nakanishi Y, Futami Y, Koba T, Satoh S, Hosono Y, Miyake K,
            Fukushima K, Shiroyama T, Iwahori K, Hirata H, Takeda Y and
            Kumanogoh A.
  TITLE     IL-33 Induces Sema4A Expression in Dendritic Cells and Exerts
            Antitumor Immunity
  JOURNAL   J Immunol 207 (5), 1456-1467 (2021)
   PUBMED   34380650
REFERENCE   5  (bases 1 to 3046)
  AUTHORS   Limoni G, Murthy S, Jabaudon D, Dayer A and Niquille M.
  TITLE     PlexinA4-Semaphorin3A-mediated crosstalk between main cortical
            interneuron classes is required for superficial interneuron
            lamination
  JOURNAL   Cell Rep 34 (4), 108644 (2021)
   PUBMED   33503438
REFERENCE   6  (bases 1 to 3046)
  AUTHORS   Oster SF, Bodeker MO, He F and Sretavan DW.
  TITLE     Invariant Sema5A inhibition serves an ensheathing function during
            optic nerve development
  JOURNAL   Development 130 (4), 775-784 (2003)
   PUBMED   12506007
REFERENCE   7  (bases 1 to 3046)
  AUTHORS   Dionne MS, Brunet LJ, Eimon PM and Harland RM.
  TITLE     Noggin is required for correct guidance of dorsal root ganglion
            axons
  JOURNAL   Dev Biol 251 (2), 283-293 (2002)
   PUBMED   12435358
REFERENCE   8  (bases 1 to 3046)
  AUTHORS   Kumanogoh A, Marukawa S, Suzuki K, Takegahara N, Watanabe C, Ch'ng
            E, Ishida I, Fujimura H, Sakoda S, Yoshida K and Kikutani H.
  TITLE     Class IV semaphorin Sema4A enhances T-cell activation and interacts
            with Tim-2
  JOURNAL   Nature 419 (6907), 629-633 (2002)
   PUBMED   12374982
REFERENCE   9  (bases 1 to 3046)
  AUTHORS   Puschel AW, Adams RH and Betz H.
  TITLE     The sensory innervation of the mouse spinal cord may be patterned
            by differential expression of and differential responsiveness to
            semaphorins
  JOURNAL   Mol Cell Neurosci 7 (5), 419-431 (1996)
   PUBMED   8812066
REFERENCE   10 (bases 1 to 3046)
  AUTHORS   Puschel AW, Adams RH and Betz H.
  TITLE     Murine semaphorin D/collapsin is a member of a diverse gene family
            and creates domains inhibitory for axonal extension
  JOURNAL   Neuron 14 (5), 941-948 (1995)
   PUBMED   7748561
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC102388.7, AK153164.1 and AK077976.1.
            
            Transcript Variant: This variant (2) differs in the 5' UTR compared
            to variant 1. All four variants encode the same 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.
            
            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 :: X85991.1, SRR7345562.3841632.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMN00849374,
                                           SAMN00849375 [ECO:0006172]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-36                AC102388.7         29740-29775
            37-1630             AK153164.1         207-1800
            1631-1918           AK077976.1         1790-2077
            1919-2798           AK153164.1         2089-2968
            2799-3046           AK077976.1         2958-3205
FEATURES             Location/Qualifiers
     source          1..3046
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="3"
                     /map="3 38.83 cM"
     gene            1..3046
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="sema domain, immunoglobulin domain (Ig),
                     transmembrane domain (TM) and short cytoplasmic domain,
                     (semaphorin) 4A"
                     /db_xref="GeneID:20351"
                     /db_xref="MGI:MGI:107560"
     exon            1..36
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
     exon            37..204
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
     CDS             66..2348
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="semaphorin-4A; sema B; semaphorin-B"
                     /codon_start=1
                     /product="semaphorin-4A precursor"
                     /protein_id="NP_001156961.1"
                     /db_xref="CCDS:CCDS17475.1"
                     /db_xref="GeneID:20351"
                     /db_xref="MGI:MGI:107560"
                     /translation="

MALPSLGQDSWSLLRVFFFQLFLLPSLPPASGTGGQGPMPRVKYHAGDGHRALSFFQQKGLRDFDTLLLSDDGNTLYVGAREAVLALNIQNPGIPRLKNMIPWPASERKKTECAFKKKSNETQCFNFIRVLVSYNATHLYACGTFAFSPACTFIELQDSLLLPILIDKVMDGKGQSPFDPVHKHTAVLVDGMLYSGTMNNFLGSEPILMRTLGSQPVLKTDIFLRWLHADASFVAAIPSTQVVYFFFEETASEFDFFEELYISRVAQVCKNDVGGEKLLQKKWTTFLKAQLLCAQPGQLPFNIIRHAVLLPADSPSVSRIYAVFTSQWQVGGTRSSAVCAFSLTDIERVFKGKYKELNKETSRWTTYRGSEVSPRPGSCSMGPSSDKALTFMKDHFLMDEHVVGTPLLVKSGVEYTRLAVESARGLDGSSHVVMYLGTSTGSLHKAVVPQDSSAYLVEEIQLSPDSEPVRNLQLAPAQGAVFAGFSGGIWRVPRANCSVYESCVDCVLARDPHCAWDPESRLCSLLSGSTKPWKQDMERGNPEWVCTRGPMARSPRRQSPPQLIKEVLTVPNSILELPCPHLSALASYHWSHGRAKISEASATVYNGSLLLLPQDGVGGLYQCVATENGYSYPVVSYWVDSQDQPLALDPELAGVPRERVQVPLTRVGGGASMAAQRSYWPHFLIVTVLLAIVLLGVLTLLLASPLGALRARGKVQGCGMLPPREKAPLSRDQHLQPSKDHRTSASDVDADNNHLGAEVA"

     sig_peptide     66..161
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="COORDINATES: ab initio prediction:SignalP:4.0"
     mat_peptide     162..2345
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /product="Semaphorin-4A. /id=PRO_0000032323"
                     /note="propagated from UniProtKB/Swiss-Prot (Q62178.2)"
     misc_feature    228..1550
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="The Sema domain, a protein interacting module, of
                     semaphorins and plexins; Region: Sema; cl15693"
                     /db_xref="CDD:449580"
     misc_feature    423..425
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="N-linked (GlcNAc...) asparagine.
                     /evidence=ECO:0000255; propagated from
                     UniProtKB/Swiss-Prot (Q62178.2); glycosylation site"
     misc_feature    468..470
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="N-linked (GlcNAc...) asparagine.
                     /evidence=ECO:0000255; propagated from
                     UniProtKB/Swiss-Prot (Q62178.2); glycosylation site"
     misc_feature    1551..1685
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="domain found in Plexins, Semaphorins and Integrins;
                     Region: PSI; smart00423"
                     /db_xref="CDD:214655"
     misc_feature    1551..1553
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="N-linked (GlcNAc...) asparagine.
                     /evidence=ECO:0000255; propagated from
                     UniProtKB/Swiss-Prot (Q62178.2); glycosylation site"
     misc_feature    1773..1976
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="Immunoglobulin domain; Region: Ig; cl11960"
                     /db_xref="CDD:448366"
     misc_feature    1788..1802
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="Ig strand B [structural motif]; Region: Ig strand
                     B"
                     /db_xref="CDD:409353"
     misc_feature    1824..1838
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="Ig strand C [structural motif]; Region: Ig strand
                     C"
                     /db_xref="CDD:409353"
     misc_feature    1881..1895
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="Ig strand E [structural motif]; Region: Ig strand
                     E"
                     /db_xref="CDD:409353"
     misc_feature    1881..1883
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="N-linked (GlcNAc...) asparagine.
                     /evidence=ECO:0000255; propagated from
                     UniProtKB/Swiss-Prot (Q62178.2); glycosylation site"
     misc_feature    1923..1940
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="Ig strand F [structural motif]; Region: Ig strand
                     F"
                     /db_xref="CDD:409353"
     misc_feature    2112..2174
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="propagated from UniProtKB/Swiss-Prot (Q62178.2);
                     transmembrane region"
     misc_feature    2223..2345
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /note="propagated from UniProtKB/Swiss-Prot (Q62178.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            205..365
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
     exon            366..428
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
     exon            429..527
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
     exon            528..633
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
     exon            634..750
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
     exon            751..875
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
     exon            876..1048
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
     exon            1049..1199
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
     exon            1200..1380
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
     exon            1381..1499
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
     exon            1500..1657
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
     exon            1658..1755
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
     exon            1756..3046
                     /gene="Sema4a"
                     /gene_synonym="Semab; SemB"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

ctcggacgcctgggttaggggtctgtactgctggggaaccatctggtgaccatctcaggctgaccatggccctaccatccctgggccaggactcatggagtctcctgcgtgtttttttcttccaactcttcctgctgccatcactgccacctgcttctgggactggtggtcaggggcccatgcccagagtcaaataccatgctggagacgggcacagggccctcagcttcttccaacaaaaaggcctccgagactttgacacgctgctcctgagtgacgatggcaacactctctatgtgggggctcgagaggccgtcctggccttgaatatccagaacccaggaatcccaaggctaaagaacatgataccctggccagccagtgagagaaaaaagaccgaatgtgcctttaagaagaagagcaatgagacacagtgtttcaacttcattcgagtcctggtctcttacaatgctactcacctctatgcctgtgggacctttgccttcagccctgcctgtaccttcattgaactccaagattccctcctgttgcccatcttgatagacaaggtcatggacgggaagggccaaagcccctttgaccctgttcacaagcacacagctgtcttggtcgatgggatgctttattccggcaccatgaacaacttcctgggcagcgagcccatcctgatgcggacactgggatcccagcctgttctcaagactgacatcttcttacgctggctgcacgcggatgcctccttcgtggcagccattccatccacccaggtcgtctatttcttctttgaggagacagccagcgagtttgacttctttgaagagctgtatatatccagggtggctcaagtctgcaagaacgacgtgggcggtgaaaagctgctgcagaagaagtggaccaccttcctcaaagcccagttgctctgcgctcagccagggcagctgccattcaacatcatccgccacgcggtcctgctgcccgccgattctccctctgtttcccgcatctacgcagtctttacctcccagtggcaggttggcgggaccaggagctcagcagtctgtgccttctctctcacggacattgagcgagtctttaaagggaagtacaaggagctgaacaaggagacctcccgctggaccacttaccggggctcagaggtcagcccgaggccaggcagttgctccatgggcccctcctctgacaaagccttgaccttcatgaaggaccattttctgatggatgagcacgtggtaggaacacccctgctggtgaagtctggtgtggagtacacacggcttgctgtggagtcagctcggggccttgatgggagcagccatgtggtcatgtatctgggtacctccacggggtccctgcacaaggctgtggtgcctcaggacagcagtgcttatctcgtggaggagattcagctgagccctgactctgagcctgttcgaaacctgcagctggcccccgcccagggtgcagtgtttgcaggcttctctggaggcatctggagagttcccagggccaattgcagtgtctacgagagctgtgtggactgtgtgcttgccagggaccctcactgtgcctgggaccctgaatcaagactctgcagccttctgtctggctctaccaagccttggaagcaggacatggaacgcggcaacccggagtgggtatgcacccgtggccccatggccaggagcccccggcgtcagagcccccctcaactaattaaagaagtcctgacagtccccaactccatcctggagctgccctgcccccacctgtcagcactggcctcttaccactggagtcatggccgagccaaaatctcagaagcctctgctaccgtctacaatggctccctcttgctgctgccgcaggatggtgtcgggggcctctaccagtgtgtggcgactgagaacggctactcataccctgtggtctcctattgggtagacagccaggaccagcccctggcgctggaccctgagctggcgggcgttccccgtgagcgtgtgcaggtcccgctgaccagggtcggaggcggagcttccatggctgcccagcggtcctactggccccattttctcatcgttaccgtcctcctggccatcgtgctcctgggagtgctcactctcctcctcgcttccccactgggggcgctgcgggctcggggtaaggttcagggctgtgggatgctgccccccagggaaaaggctccactgagcagggaccagcacctccagccctccaaggaccacaggacctctgccagtgacgtagatgccgacaacaaccatctgggcgccgaagtggcttaaacagggacacagatccgcagctgagcagagcaagccactggccttgttggctatgccaggcacagtgccactctgaccagggtaggaggctctcctgctaacgtgtgtcacctacagcacccagtaggtcctcccctgtgggactctcttctgcaagcacattgggctgtctccatacctgtacttgtgctgtgacaggaagagccagacaggtttctttgattttgattgacccaagagccctcctgtaacaaacgtgctccaggagaccatgaaaggtgtggctgtctgggattctgtggtgacaaacctaagcatccgagcaagctggggctattcctgcaaactccatcctgaacgctgtcactctagaagcagctgctgctttgaacaccagcccaccctccttcccaagagtctctatggagttggccccttgtgtttcctttaccagtcatgccatactgtttgggaagtcatctctgaagtctaaccaccttccttcttgcttcagtttggacagattgttattattgtctctgccctggctagaatggggggcataatctgagccttgttcccttgtccagtgtggctgacccttgacctcttccttcctcctccctttgttttgggattcagaaaactgcttgtcacagacaatttattttttattaaaaaagatataagctttaaag

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