LOCUS       NM_001289081            3928 bp    mRNA    linear   PRI 23-MAR-2024
DEFINITION  Homo sapiens contactin 6 (CNTN6), transcript variant 3, mRNA.
ACCESSION   NM_001289081
VERSION     NM_001289081.2
KEYWORDS    RefSeq.
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 3928)
  AUTHORS   Zhang,H.Y., Wu,F.Y., Zhang,C.X., Wu,C.Y., Cui,R.J., Liu,X.Y.,
            Yang,L., Zhang,Y., Sun,F., Cheng,F., Yang,R.M., Song,H.D. and
            Zhao,S.X.
  TITLE     Contactin 6, A Novel Causative Gene for Congenital Hypothyroidism,
            Mediates Thyroid Hormone Biosynthesis Through Notch Signaling
  JOURNAL   Thyroid 34 (3), 324-335 (2024)
   PUBMED   38183624
  REMARK    GeneRIF: Contactin 6, A Novel Causative Gene for Congenital
            Hypothyroidism, Mediates Thyroid Hormone Biosynthesis Through Notch
            Signaling.
REFERENCE   2  (bases 1 to 3928)
  AUTHORS   Repnikova,E.A., Lyalin,D.A., McDonald,K., Astbury,C.,
            Hansen-Kiss,E., Cooley,L.D., Pfau,R., Herman,G.E., Pyatt,R.E. and
            Hickey,S.E.
  TITLE     CNTN6 copy number variations: Uncertain clinical significance in
            individuals with neurodevelopmental disorders
  JOURNAL   Eur J Med Genet 63 (1), 103636 (2020)
   PUBMED   30836150
  REMARK    GeneRIF: CNTN6 copy number variations: Uncertain clinical
            significance in individuals with neurodevelopmental disorders.
REFERENCE   3  (bases 1 to 3928)
  AUTHORS   Tassano,E., Uccella,S., Giacomini,T., Severino,M., Fiorio,P.,
            Gimelli,G. and Ronchetto,P.
  TITLE     Clinical and Molecular Characterization of Two Patients with CNTN6
            Copy Number Variations
  JOURNAL   Cytogenet Genome Res 156 (3), 144-149 (2018)
   PUBMED   30508811
  REMARK    GeneRIF: this study describes of 2 boys with intellectual
            disability, attention-deficit hyperactivity disorder harboring a
            3p26.3 microdeletion and a 3p26.3 microduplication, which are both
            paternally inherited and include only the CNTN6 gene.
REFERENCE   4  (bases 1 to 3928)
  AUTHORS   Huang,A.Y., Yu,D., Davis,L.K., Sul,J.H., Tsetsos,F., Ramensky,V.,
            Zelaya,I., Ramos,E.M., Osiecki,L., Chen,J.A., McGrath,L.M.,
            Illmann,C., Sandor,P., Barr,C.L., Grados,M., Singer,H.S.,
            Nothen,M.M., Hebebrand,J., King,R.A., Dion,Y., Rouleau,G.,
            Budman,C.L., Depienne,C., Worbe,Y., Hartmann,A., Muller-Vahl,K.R.,
            Stuhrmann,M., Aschauer,H., Stamenkovic,M., Schloegelhofer,M.,
            Konstantinidis,A., Lyon,G.J., McMahon,W.M., Barta,C., Tarnok,Z.,
            Nagy,P., Batterson,J.R., Rizzo,R., Cath,D.C., Wolanczyk,T.,
            Berlin,C., Malaty,I.A., Okun,M.S., Woods,D.W., Rees,E., Pato,C.N.,
            Pato,M.T., Knowles,J.A., Posthuma,D., Pauls,D.L., Cox,N.J.,
            Neale,B.M., Freimer,N.B., Paschou,P., Mathews,C.A., Scharf,J.M. and
            Coppola,G.
  CONSRTM   Tourette Syndrome Association International Consortium for Genetics
            (TSAICG); Gilles de la Tourette Syndrome GWAS Replication
            Initiative (GGRI)
  TITLE     Rare Copy Number Variants in NRXN1 and CNTN6 Increase Risk for
            Tourette Syndrome
  JOURNAL   Neuron 94 (6), 1101-1111 (2017)
   PUBMED   28641109
  REMARK    GeneRIF: CNTN6 copy number variants (duplications) were associated
            with increased risk of Tourette syndrome.
REFERENCE   5  (bases 1 to 3928)
  AUTHORS   Mercati,O., Huguet,G., Danckaert,A., Andre-Leroux,G., Maruani,A.,
            Bellinzoni,M., Rolland,T., Gouder,L., Mathieu,A., Buratti,J.,
            Amsellem,F., Benabou,M., Van-Gils,J., Beggiato,A., Konyukh,M.,
            Bourgeois,J.P., Gazzellone,M.J., Yuen,R.K., Walker,S., Delepine,M.,
            Boland,A., Regnault,B., Francois,M., Van Den Abbeele,T.,
            Mosca-Boidron,A.L., Faivre,L., Shimoda,Y., Watanabe,K., Bonneau,D.,
            Rastam,M., Leboyer,M., Scherer,S.W., Gillberg,C., Delorme,R.,
            Cloez-Tayarani,I. and Bourgeron,T.
  TITLE     CNTN6 mutations are risk factors for abnormal auditory sensory
            perception in autism spectrum disorders
  JOURNAL   Mol Psychiatry 22 (4), 625-633 (2017)
   PUBMED   27166760
  REMARK    GeneRIF: Clinical investigations of the patients carrying CNTN5 or
            CNTN6 variants showed that they were hypersensitive to sounds (a
            condition called hyperacusis) and displayed changes in wave latency
            within the auditory pathway.
REFERENCE   6  (bases 1 to 3928)
  AUTHORS   Barber,M.J., Mangravite,L.M., Hyde,C.L., Chasman,D.I., Smith,J.D.,
            McCarty,C.A., Li,X., Wilke,R.A., Rieder,M.J., Williams,P.T.,
            Ridker,P.M., Chatterjee,A., Rotter,J.I., Nickerson,D.A.,
            Stephens,M. and Krauss,R.M.
  TITLE     Genome-wide association of lipid-lowering response to statins in
            combined study populations
  JOURNAL   PLoS One 5 (3), e9763 (2010)
   PUBMED   20339536
  REMARK    Publication Status: Online-Only
REFERENCE   7  (bases 1 to 3928)
  AUTHORS   Gratacos,M., Costas,J., de Cid,R., Bayes,M., Gonzalez,J.R.,
            Baca-Garcia,E., de Diego,Y., Fernandez-Aranda,F.,
            Fernandez-Piqueras,J., Guitart,M., Martin-Santos,R., Martorell,L.,
            Menchon,J.M., Roca,M., Saiz-Ruiz,J., Sanjuan,J., Torrens,M.,
            Urretavizcaya,M., Valero,J., Vilella,E., Estivill,X. and
            Carracedo,A.
  CONSRTM   Psychiatric Genetics Network Group
  TITLE     Identification of new putative susceptibility genes for several
            psychiatric disorders by association analysis of regulatory and
            non-synonymous SNPs of 306 genes involved in neurotransmission and
            neurodevelopment
  JOURNAL   Am J Med Genet B Neuropsychiatr Genet 150B (6), 808-816 (2009)
   PUBMED   19086053
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   8  (bases 1 to 3928)
  AUTHORS   Manderson,E.N., Birch,A.H., Shen,Z., Mes-Masson,A.M., Provencher,D.
            and Tonin,P.N.
  TITLE     Molecular genetic analysis of a cell adhesion molecule with
            homology to L1CAM, contactin 6, and contactin 4 candidate
            chromosome 3p26pter tumor suppressor genes in ovarian cancer
  JOURNAL   Int J Gynecol Cancer 19 (4), 513-525 (2009)
   PUBMED   19509545
  REMARK    GeneRIF: results do not support the candidacy of CHL1, CNTN6, and
            CNTN4 as tumor suppressor genes in the 3p26-pter region in ovarian
            cancer
REFERENCE   9  (bases 1 to 3928)
  AUTHORS   Kamei,Y., Tsutsumi,O., Taketani,Y. and Watanabe,K.
  TITLE     cDNA cloning and chromosomal localization of neural adhesion
            molecule NB-3 in human
  JOURNAL   J Neurosci Res 51 (3), 275-283 (1998)
   PUBMED   9486763
REFERENCE   10 (bases 1 to 3928)
  AUTHORS   Walsh,F.S. and Doherty,P.
  TITLE     Glycosylphosphatidylinositol anchored recognition molecules that
            function in axonal fasciculation, growth and guidance in the
            nervous system
  JOURNAL   Cell Biol Int Rep 15 (11), 1151-1166 (1991)
   PUBMED   1838307
  REMARK    Review article
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA094373.1, AK294786.1,
            BC113118.1, CN364480.1, AC034192.5 and AC026214.4.
            
            On May 31, 2019 this sequence version replaced NM_001289081.1.
            
            Summary: The protein encoded by this gene is a member of the
            immunoglobulin superfamily. It is a glycosylphosphatidylinositol
            (GPI)-anchored neuronal membrane protein that functions as a cell
            adhesion molecule. It may play a role in the formation of axon
            connections in the developing nervous system. Alternative splicing
            results in multiple transcript variants. [provided by RefSeq, Jan
            2014].
            
            Transcript Variant: This variant (3) differs in the 5' UTR, lacks a
            portion of the 5' coding region and initiates translation at a
            downstream start codon, compared to variant 1. It encodes isoform
            2, which has a shorter N-terminus, compared to 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 :: SRR1803613.79495.1, AK294786.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2145240, SAMN03465404
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-97                DA094373.1         115-211
            98-201              DA094373.1         349-452
            202-2300            AK294786.1         568-2666
            2301-2389           BC113118.1         2439-2527
            2390-3153           AK294786.1         2756-3519
            3154-3321           CN364480.1         180-347
            3322-3344           AC034192.5         1-23                c
            3345-3928           AC026214.4         32148-32731
FEATURES             Location/Qualifiers
     source          1..3928
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3p26.3"
     gene            1..3928
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /note="contactin 6"
                     /db_xref="GeneID:27255"
                     /db_xref="HGNC:HGNC:2176"
                     /db_xref="MIM:607220"
     exon            1..97
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            98..224
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            225..400
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     CDS             259..3129
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /note="isoform 2 is encoded by transcript variant 3;
                     neural adhesion molecule; neural recognition molecule
                     NB-3"
                     /codon_start=1
                     /product="contactin-6 isoform 2"
                     /protein_id="NP_001276010.1"
                     /db_xref="GeneID:27255"
                     /db_xref="HGNC:HGNC:2176"
                     /db_xref="MIM:607220"
                     /translation="MSYHYRLDGGSLAINSPHTDQDIGMYQCLATNLLGTILSRKAKL
                     QFAYIEDFETKTRSTVSVREGQGVVLLCGPPPHFGDLSYAWTFNDNPLYVQEDNRRFV
                     SQETGNLYIAKVEPSDVGNYTCFITNKEAQRSVQGPPTPLVQRTDGVMGEYEPKIEVR
                     FPETIQAAKDSSVKLECFALGNPVPDISWRRLDGSPLPGKVKYSKSQAILEIPNFQQE
                     DEGFYECIASNLRGRNLAKGQLIFYAPPEWEQKIQNTHLSIYDNLLWECKASGKPNPW
                     YTWLKNGERLNPEERIQIENGTLIITMLNVSDSGVYQCAAENKYQIIYANAELRVLAS
                     APDFSKSPVKKKSFVQVGGDIVIGCKPNAFPRAAISWKRGTETLRQSKRIFLLEDGSL
                     KIYNITRSDAGSYTCIATNQFGTAKNTGSLIVKERTVITVPPSKMDVTVGESIVLPCQ
                     VSHDPSIEVVFVWFFNGDVIDLKKGVAHFERIGGESVGDLMIRNIQLHHSGKYLCTVQ
                     TTLESLSAVADIIVRGPPGPPEDVQVEDISSTTSQLSWRAGPDNNSPIQIFTIQTRTP
                     FSVGWQAVATVPEILNGKTYNATVVGLSPWVEYEFRVVAGNSIGIGEPSEPSELLRTK
                     ASVPVVAPVNIHGGGGSRSELVITWESIPEELQNGEGFGYIIMFRPVGSTTWSKEKVS
                     SVESSRFVYRNESIIPLSPFEVKVGVYNNEGEGSLSTVTIVYSGEDEPQLAPRGTSLQ
                     SFSASEMEVSWNAIAWNRNTGRVLGYEVLYWTDDSKESMIGKIRVSGNVTTKNITGLK
                     ANTIYFASVRAYNTAGTGPSSPPVNVTTKKSPPSQPPANIAWKLTNSKLCLNWEHVKT
                     MENESEVLGYKILYRQNRQSKTHILETNNTSAELLVPFEEDYLIEIRTVSDGGDGSSS
                     EEIRIPKMSSLSSRGIQFLEPSTHFLSIVIVIFHCFAIQPLI"
     exon            401..496
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            497..700
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            701..803
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            804..988
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            989..1125
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            1126..1255
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            1256..1406
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            1407..1534
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            1535..1710
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            1711..1828
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            1829..1987
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            1988..2137
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            2138..2208
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            2209..2443
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            2444..2559
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            2560..2746
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            2747..2859
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            2860..3028
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     exon            3029..3928
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3906..3911
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /note="hexamer: AATAAA"
     polyA_site      3928
                     /gene="CNTN6"
                     /gene_synonym="NB3"
                     /note="major polyA site"
ORIGIN      
        1 atacggcttg gttctgcctg gacgcacagc atgcctggct gagagcttga aacagagttc
       61 tgcagaaaaa ctgtaaagat cccgagacat ttccctggtg atggtctttt aagccgtcct
      121 atttttactc aggagccaca tgatgtcatt tttcctttgg atttatcaaa atctgaggtc
      181 atcctgaatt gtgctgctaa tggttaccct tcgcctcatt ataggtggaa gcaaaatggc
      241 acagacattg attttactat gagttatcac tacaggttgg atggaggcag tcttgcaatc
      301 aatagccccc acacagatca agatattggc atgtaccagt gcctggccac caatcttctg
      361 gggacaattc tgagtcggaa ggcaaagctc caatttgcat atattgaaga ctttgaaact
      421 aaaacaagaa gcacagtatc tgtccgagaa ggtcaaggtg tggtgcttct ctgtggccca
      481 ccgccacatt ttggagattt atcttatgca tggaccttca atgataaccc cttatacgtc
      541 caagaggaca ataggcgatt tgtatctcaa gagacgggaa acttgtacat tgccaaagtg
      601 gaaccatcag atgtgggcaa ctacacttgc tttataacta acaaagaggc ccagagaagt
      661 gttcaaggtc cacccactcc attagtgcag cgcactgatg gtgtgatggg ggaatatgaa
      721 ccaaagattg aagtgcgttt tcctgaaact atacaagctg caaaggattc atctgtaaaa
      781 ctggaatgtt ttgcccttgg aaatccagtc cccgatatta gttggagaag gttggacggg
      841 agcccgttgc cagggaaagt caagtacagc aaatcccaag ctatccttga aatcccgaac
      901 ttccaacaag aagatgaagg cttttatgag tgcattgcaa gcaaccttcg aggaagaaac
      961 cttgcaaagg gtcaactcat tttttatgct cctccagaat gggaacagaa aatccaaaat
     1021 acacacctct ctatctatga caacttgctc tgggaatgta aagctagtgg aaagccaaac
     1081 ccttggtata catggttaaa aaatggtgaa cgactcaacc cagaggagag aattcaaata
     1141 gaaaatggga cactcatcat aacgatgctg aatgtgtcag attctggtgt gtaccaatgt
     1201 gctgcagaaa acaaatatca gataatttat gcaaatgctg aattgagagt tttagcctca
     1261 gctccagatt tctccaaaag tccagttaaa aaaaagtctt ttgttcaagt tggtggggat
     1321 attgttatcg gatgcaaacc aaatgctttt cccagggcag ctatctcttg gaaaagagga
     1381 acggagaccc ttagacaaag caaaagaata tttctcttgg aggatggcag cctcaagata
     1441 tataatatta ccaggtcaga tgctggatca tatacatgca tagccacaaa tcagtttggc
     1501 actgcaaaga acactggcag cctcattgta aaagagagaa ctgtcattac cgtcccacct
     1561 tccaaaatgg atgttacagt tggcgagagt atagtgctac catgccaggt gtcccatgac
     1621 ccctccattg aagtggtatt tgtatggttt ttcaatggag atgtcataga cttaaaaaaa
     1681 ggagtggctc attttgaaag gattggagga gaatctgttg gggatttgat gataaggaat
     1741 attcagttac atcattcagg aaaatatctc tgcacagtac aaacaaccct agaaagttta
     1801 tctgcagtag ccgatatcat tgttagaggt ccaccaggtc ctcctgagga tgtgcaagtg
     1861 gaagacattt ccagtactac ttctcaacta agttggagag caggcccaga taataacagt
     1921 cccattcaaa tatttactat tcagactcgg acaccatttt ctgtgggttg gcaggctgtt
     1981 gctacagttc cagaaattct caatggtaag acatacaatg caacagtggt tggtttgagt
     2041 ccttgggtgg aatatgaatt tcgtgttgtt gccggcaaca gcattgggat tggagaacca
     2101 agtgaaccat cagaattgtt aagaactaaa gcatcagtcc ctgttgtggc accagtaaac
     2161 atccatggag gtggaggaag tcggtctgaa ctcgtcatta cgtgggagtc aattccagaa
     2221 gaactgcaga atggggaggg atttggatat atcatcatgt tccggccagt gggctcgaca
     2281 acctggtcca aggagaaagt gtcatctgtg gaatcatcaa ggtttgtcta cagaaatgaa
     2341 agcatcatcc cactgtctcc ctttgaagtc aaagtgggtg tgtataataa tgaaggagaa
     2401 ggatccctga gtactgtgac cattgtctac tctggggaag atgaacctca actggcccca
     2461 aggggaactt ctctccagag tttttctgct tctgaaatgg aggtttcatg gaatgctatt
     2521 gcctggaata gaaacactgg aagagtgctg ggctatgagg tcttatactg gacagatgac
     2581 tccaaagaat ccatgatagg taaaattaga gtcagtggaa atgtcacaac caaaaacatc
     2641 acggggctga aagctaatac catctacttt gcttccgtaa gagcttacaa cactgctggg
     2701 acagggccct caagcccccc agtcaatgtt accaccaaaa agtctcctcc aagccaacca
     2761 ccagcaaaca ttgcctggaa gctgacaaac tctaaattat gcttgaactg ggagcatgta
     2821 aaaaccatgg aaaatgagtc tgaagttttg gggtacaaga ttctgtaccg gcaaaacaga
     2881 cagagtaaaa ctcatatttt ggaaacaaac aatacatcag ctgagcttct ggttccattt
     2941 gaagaagact acttaattga aataagaaca gtcagtgatg gtggagatgg aagcagcagt
     3001 gaggaaatta ggattccaaa aatgtcaagt ttgagttcca gaggaattca attcttagaa
     3061 cctagcaccc attttctttc cattgtcatt gtgatttttc actgttttgc tattcagcca
     3121 cttatctgat gaataaaacc ataaatcttt gagagttttt tgaaagcaaa tcattctgta
     3181 tatatgctct ccagcctctg acacaagatg cgttcttaat acagacttgt ttgcaaagaa
     3241 aaaaaaaagt atattattaa aatcctgtaa atatctatgg tatattaata aaacaatttt
     3301 aaacactttt gaattttaaa atccgcacat gattacatga attcctaggt gccacattaa
     3361 cctggggagt tgtaactgct gtgtctttta agttacttat atggagaaaa taaataactc
     3421 ccctcaatga tgctgatgat gaatacaaac ttggctccta gttaccataa ctcacatgta
     3481 catttttatg tattccagac aatcacttca gtatttaaaa tttccaccct acttcaaaat
     3541 aaaatacaat tatttgttta tagttgggat tctttaaaaa tacaaactat tccaaagcat
     3601 ggggtgcttt tatctctgaa tcaagttgga ataagaaatc tttttactca agaatatttc
     3661 aatatacatg atgttcttct cagcccactt ttcagaagat tcagtcacaa taaaggcaga
     3721 aaaagtattt tatggcaaag aaaaataaat gatgggaaat gagcacccac ctaaaataat
     3781 cttctaacaa ctctggtata tattaagcaa ttgctcatgg caaagttgaa catttgaact
     3841 gctgcatgaa caaatctcag gtaattatga caagttgatt gcaatgtatg tggccttatt
     3901 tttataataa aacaatgtgg aaacagaa
//
