LOCUS       NM_030913               3873 bp    mRNA    linear   PRI 15-FEB-2024
DEFINITION  Homo sapiens semaphorin 6C (SEMA6C), transcript variant 2, mRNA.
ACCESSION   NM_030913
VERSION     NM_030913.6
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 3873)
  AUTHORS   Gregorio,S.P., Sallet,P.C., Do,K.A., Lin,E., Gattaz,W.F. and
            Dias-Neto,E.
  TITLE     Polymorphisms in genes involved in neurodevelopment may be
            associated with altered brain morphology in schizophrenia:
            preliminary evidence
  JOURNAL   Psychiatry Res 165 (1-2), 1-9 (2009)
   PUBMED   19054571
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   2  (bases 1 to 3873)
  AUTHORS   Qu,X., Wei,H., Zhai,Y., Que,H., Chen,Q., Tang,F., Wu,Y., Xing,G.,
            Zhu,Y., Liu,S., Fan,M. and He,F.
  TITLE     Identification, characterization, and functional study of the two
            novel human members of the semaphorin gene family
  JOURNAL   J Biol Chem 277 (38), 35574-35585 (2002)
   PUBMED   12110693
  REMARK    GeneRIF: identification, characterization, and functional study of
            the two novel human members of the semaphorin gene family
REFERENCE   3  (bases 1 to 3873)
  AUTHORS   Pasterkamp,R.J. and Verhaagen,J.
  TITLE     Emerging roles for semaphorins in neural regeneration
  JOURNAL   Brain Res Brain Res Rev 35 (1), 36-54 (2001)
   PUBMED   11245885
  REMARK    Review article
REFERENCE   4  (bases 1 to 3873)
  AUTHORS   Kikuchi,K., Chedotal,A., Hanafusa,H., Ujimasa,Y., de Castro,F.,
            Goodman,C.S. and Kimura,T.
  TITLE     Cloning and characterization of a novel class VI semaphorin,
            semaphorin Y
  JOURNAL   Mol Cell Neurosci 13 (1), 9-23 (1999)
   PUBMED   10049528
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA787858.1, AF339152.1,
            AB022434.1 and AL592424.13.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Feb 27, 2020 this sequence version replaced NM_030913.5.
            
            Summary: This gene encodes a member of the semaphorin family.
            Semaphorins represent important molecular signals controlling
            multiple aspects of the cellular response that follows CNS injury,
            and thus may play an important role in neural regeneration.
            [provided by RefSeq, May 2010].
            
            Transcript Variant: This variant (2) lacks an exon in the 3' coding
            region compared to variant 1. The resulting protein (isoform 2) is
            shorter but has the same N- and C-termini compared to isoform 1.
            
            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 :: AF339152.1, AB022434.1 [ECO:0000332]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000368914.8/ ENSP00000357910.3
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-174               DA787858.1         34-207
            175-1665            AF339152.1         1-1491
            1666-2231           AB022434.1         1550-2115
            2232-3873           AL592424.13        25810-27451         c
FEATURES             Location/Qualifiers
     source          1..3873
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1q21.3"
     gene            1..3873
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /note="semaphorin 6C"
                     /db_xref="GeneID:10500"
                     /db_xref="HGNC:HGNC:10740"
                     /db_xref="MIM:609294"
     exon            1..199
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            200..249
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            250..421
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     CDS             304..3096
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; sema Y; semaphorin-Y; sema domain,
                     transmembrane domain (TM), and cytoplasmic domain,
                     (semaphorin) 6C"
                     /codon_start=1
                     /product="semaphorin-6C isoform 2 precursor"
                     /protein_id="NP_112175.2"
                     /db_xref="CCDS:CCDS984.1"
                     /db_xref="GeneID:10500"
                     /db_xref="HGNC:HGNC:10740"
                     /db_xref="MIM:609294"
                     /translation="MPRAPHFMPLLLLLLLLSLPHTQAAFPQDPLPLLISDLQGTSPL
                     SWFRGLEDDAVAAELGLDFQRFLTLNRTLLVAARDHVFSFDLQAEEEGEGLVPNKYLT
                     WRSQDVENCAVRGKLTDECYNYIRVLVPWDSQTLLACGTNSFSPVCRSYGITSLQQEG
                     EELSGQARCPFDATQSNVAIFAEGSLYSATAADFQASDAVVYRSLGPQPPLRSAKYDS
                     KWLREPHFVQALEHGDHVYFFFREVSVEDARLGRVQFSRVARVCKRDMGGSPRALDRH
                     WTSFLKLRLNCSVPGDSTFYFDVLQALTGPVNLHGRSALFGVFTTQTNSIPGSAVCAF
                     YLDEIERGFEGKFKEQRSLDGAWTPVSEDRVPSPRPGSCAGVGGAALFSSSRDLPDDV
                     LTFIKAHPLLDPAVPPVTHQPLLTLTSRALLTQVAVDGMAGPHSNITVMFLGSNDGTV
                     LKVLTPGGRSGGPEPILLEEIDAYSPARCSGKRTAQTARRIIGLELDTEGHRLFVAFS
                     GCIVYLPLSRCARHGACQRSCLASQDPYCGWHSSRGCVDIRGSGGTDVDQAGNQESME
                     HGDCQDGATGSQSGPGDSAYGVRRDLPPASASRSVPIPLLLASVAAAFALGASVSGLL
                     VSCACRRAHRRRGKDIETPGLPRPLSLRSLARLHGGGPEPPPPSKDGDAVQTPQLYTT
                     FLPPPEGVPPPELACLPTPESTPELPVKHLRAAGDPWEWNQNRNNAKEGPGRSRGGHA
                     AGGPAPRVLVRPPPPGCPGQAVEVTTLEELLRYLHGPQPPRKGAEPPAPLTSRALPPE
                     PAPALLGGPSPRPHECASPLRLDVPPEGRCASAPARPALSAPAPRLGVGGGRRLPFSG
                     HRAPPALLTRVPSGGPSRYSGGPGKHLLYLGRPEGYRGRALKRVDVEKPQLSLKPPLV
                     GPSSRQAVPNGGRFNF"
     exon            422..536
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            537..600
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            601..657
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            658..759
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            760..850
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            851..970
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            971..1059
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            1060..1277
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            1278..1409
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            1410..1562
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            1563..1736
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            1737..1883
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            1884..1961
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            1962..2017
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            2018..2062
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     exon            2063..3873
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3507..3512
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /note="hexamer: AATACA"
     polyA_site      3524
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /note="major polyA site"
     regulatory      3847..3852
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /note="hexamer: AATAAA"
     polyA_site      3873
                     /gene="SEMA6C"
                     /gene_synonym="m-SemaY; m-SemaY2; Sema-Y; SEMAY"
                     /note="major polyA site"
ORIGIN      
        1 attgttttcc tccgcggatc cgcggctgga cttggaccca gggctctccc gacagcgccc
       61 tggaacccaa attcaagcac catccaattc ggacgctcat cgcatctcgc ctgagcacaa
      121 ccacggattg cgaactcagc gcagcgcgtg gccgctggcc gcccgcggcg atctcgatcc
      181 cgctgacccg aatcctggag tcagaggttt cctatccccc tcaagccccc acaggagtca
      241 ccaacccagg gccggcttat gggtgagggg gcaccccctg gggcctgagc tgccccgcac
      301 aggatgcccc gtgcccccca cttcatgccc ttgctgctac tgctgctgct gctctcactt
      361 ccccatactc aggccgcctt tccccaggac cccctccctc tgttgatctc tgaccttcaa
      421 ggtacttccc cattatcctg gtttcggggc ctggaggatg atgctgtggc tgcagaactt
      481 gggctggact ttcagagatt cctgaccttg aaccggacct tgctagtggc tgcccgggat
      541 cacgttttct ccttcgatct tcaagccgaa gaagaagggg aggggctggt gcccaacaag
      601 tatctaacat ggagaagcca agatgtggag aactgtgctg tacggggaaa gctgacggat
      661 gagtgctaca actatattcg tgttcttgtt ccctgggact cccagacgct ccttgcctgt
      721 ggaacgaact cattcagccc tgtgtgccgc agctatggga taacttcgct gcagcaggag
      781 ggtgaggaac tgagtgggca ggctcgatgc ccctttgatg ccacccagtc caacgtggcc
      841 atctttgcag agggcagcct gtactcagcc acagctgcgg atttccaggc cagtgatgct
      901 gtagtttaca gaagccttgg gccccagccc ccactccgct ccgccaagta tgactccaag
      961 tggctccgag agccacactt tgtccaggcc ttggagcatg gagaccatgt ctacttcttc
     1021 ttccgcgagg tctctgtgga ggatgctcgg ctggggaggg tgcagttctc ccgcgtagcc
     1081 cgagtatgta aacgtgacat gggcggctcg cctcgggcct tggaccgcca ctggacatcc
     1141 ttcctgaagc ttcggctcaa ctgctctgtc cctggggact ctactttcta ttttgatgtt
     1201 ttacaggcct tgactgggcc tgtgaacctg catggccgct ctgctctctt tggggtcttc
     1261 accacccaga ccaatagcat ccctggctct gccgtctgcg ccttctacct ggatgagatt
     1321 gagcgtgggt ttgagggcaa gttcaaggag cagaggagtc tggatggggc ctggactcct
     1381 gtgtctgagg acagagttcc ctcacccagg ccaggatcct gtgcaggagt agggggagct
     1441 gccttgttct cctcttcccg agacctccct gatgatgtcc tgaccttcat caaggctcac
     1501 ccgctgctgg accccgctgt accacctgtc acccatcagc ctctactcac tctcactagc
     1561 agggccctac tgacccaagt agctgtggat ggcatggctg gtccccacag taacatcaca
     1621 gtcatgttcc ttggctccaa tgatgggaca gtgctgaagg tgctgacccc aggtgggcga
     1681 tccgggggac ctgagcccat cctcctggaa gagattgatg cctacagccc tgcccggtgc
     1741 agtgggaagc ggacagccca aacagcacga cggatcatag ggctggagct ggacactgag
     1801 ggtcacaggc tttttgtggc tttttctggc tgtattgtct acctccctct cagccggtgt
     1861 gcccggcatg gggcctgtca gaggagctgt ttggcttctc aggacccata ctgtggatgg
     1921 catagctcca ggggctgtgt ggatatcagg ggatctggtg ggactgatgt ggatcaggct
     1981 gggaaccagg aatccatgga gcatggtgac tgccaagatg gagctactgg gagtcagtct
     2041 ggccctgggg attctgctta tggcgtgcgc cgggacctgc ccccagcctc ggcctcccgc
     2101 tccgtcccca tcccactcct cctggccagt gtggccgcag cttttgccct gggcgcctca
     2161 gtctctggcc tcctggtctc ctgtgcttgt cgccgcgccc accgacgtcg gggcaaggac
     2221 atcgagactc cggggctccc gcgccctctc tccctccgca gtttggcccg gctccacggt
     2281 gggggcccag agcccccgcc gccctccaag gacggggacg cggtgcagac gccgcagctc
     2341 tacaccacct tcctgccgcc tccggagggc gtgcccccgc cggagctggc ctgcctgccc
     2401 acccccgagt ccacgccgga gctgccggtc aagcacctcc gcgccgccgg ggacccctgg
     2461 gagtggaacc agaacaggaa caacgccaag gagggtccgg gccgctcacg gggcgggcac
     2521 gcggcgggcg ggcccgcgcc ccgcgtgctg gtgaggccac cgccgcccgg ctgtcccggg
     2581 caggccgtgg aagtcaccac cctggaggaa ctgctgcgct acctgcacgg cccgcagccg
     2641 cccagaaagg gggccgagcc ccccgcccct ttaacctcgc gggcgctccc gccggagccc
     2701 gcccccgccc tcttgggcgg ccccagcccc aggccccacg agtgcgcctc gccgctgagg
     2761 ctggacgtgc cccccgaggg caggtgcgcc tctgcccccg cccggcccgc gctctccgcc
     2821 cccgctcccc ggctgggcgt cggcggaggc cggaggttgc ctttctccgg ccaccgggcc
     2881 ccccctgccc tgctcactcg agtcccctcg ggaggtccct ccaggtactc cgggggtccc
     2941 gggaagcacc tcctgtacct gggccggccc gagggctacc ggggccgcgc cctgaaaagg
     3001 gtggacgtcg agaagcccca gttgtccctg aagcctcccc tcgtcgggcc ctcctcccgc
     3061 caggccgtcc cgaacggcgg ccgtttcaac ttttaaaggg agcggcccac ggcctccagc
     3121 gtggggagcg cccgagtcct ctcggccacg agctggacgc tcttcaggac gtttcaccgc
     3181 cccctcgccc cgcacctcca gccttcccga ctcgcagagt ctcccgaggc cccttttcgc
     3241 ctcgggttta tttattgact gtctttcccc ctgtcctcga cagaagagtg ggaggtgaga
     3301 agcccgtctc ctcagtgagc cagcatttca gggggagctg gcggactccc actccccgct
     3361 cccttccagc caagctgcct taactcgccc ctcggggctc ccccagagac tgtgccccgg
     3421 gcgggccgcg cgcgctgtgt ccagagtcct cgggccttct gggtctggga cgtgcctctc
     3481 ctactgtgta ggagcctccg cttcccaata cagccgtgtc tgcagccact gcctgacttc
     3541 actcgggcgg gggagggcgg cagtcggtcg gctcgctctg ggcgccctcg ctctctgcct
     3601 tcatctgggc cctgggctct cccgggtaat gggatggctg cggtcccgcc ggggggcagt
     3661 ctggaaaggt ttcctaaagg agacgagcga attaacggtg tcgaggtgag ccagggccag
     3721 ggggaccccg gtaaagttta gttgaggctg gggaaggccc tcggagctcg tttccagatc
     3781 gaggtaagag ggactttctt aaaggcctag tctatgggat ggggcggcgg agggaatttt
     3841 ttgagaaata aaatgaagct gcagtgtacg tta
//
