LOCUS       NM_011929               5198 bp    mRNA    linear   ROD 05-JUN-2024
DEFINITION  Mus musculus chloride channel, voltage-sensitive 6 (Clcn6), mRNA.
ACCESSION   NM_011929
VERSION     NM_011929.3
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 5198)
  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   2  (bases 1 to 5198)
  AUTHORS   Polovitskaya,M.M., Barbini,C., Martinelli,D., Harms,F.L.,
            Cole,F.S., Calligari,P., Bocchinfuso,G., Stella,L., Ciolfi,A.,
            Niceta,M., Rizza,T., Shinawi,M., Sisco,K., Johannsen,J.,
            Denecke,J., Carrozzo,R., Wegner,D.J., Kutsche,K., Tartaglia,M. and
            Jentsch,T.J.
  TITLE     A Recurrent Gain-of-Function Mutation in CLCN6, Encoding the ClC-6
            Cl-/H+-Exchanger, Causes Early-Onset Neurodegeneration
  JOURNAL   Am J Hum Genet 107 (6), 1062-1077 (2020)
   PUBMED   33217309
  REMARK    GeneRIF: A Recurrent Gain-of-Function Mutation in CLCN6, Encoding
            the ClC-6 Cl(-)/H(+)-Exchanger, Causes Early-Onset
            Neurodegeneration.
REFERENCE   3  (bases 1 to 5198)
  AUTHORS   Hirst,C.S., Foong,J.P., Stamp,L.A., Fegan,E., Dent,S., Cooper,E.C.,
            Lomax,A.E., Anderson,C.R., Bornstein,J.C., Young,H.M. and
            McKeown,S.J.
  TITLE     Ion channel expression in the developing enteric nervous system
  JOURNAL   PLoS One 10 (3), e0123436 (2015)
   PUBMED   25798587
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 5198)
  AUTHORS   Arnaiz,I., Johnson,M.H., Cook,D.I. and Day,M.L.
  TITLE     Changing expression of chloride channels during preimplantation
            mouse development
  JOURNAL   Reproduction 145 (1), 73-84 (2013)
   PUBMED   23115349
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 5198)
  AUTHORS   Templin,J.S., Bang,S.J., Soiza-Reilly,M., Berde,C.B. and
            Commons,K.G.
  TITLE     Patterned expression of ion channel genes in mouse dorsal raphe
            nucleus determined with the Allen Mouse Brain Atlas
  JOURNAL   Brain Res 1457, 1-12 (2012)
   PUBMED   22534482
  REMARK    GeneRIF: This study demonistrated that clcn6 gene expression in
            mouse dorsal raphe nucleus
REFERENCE   6  (bases 1 to 5198)
  AUTHORS   Lau,N.C., Seto,A.G., Kim,J., Kuramochi-Miyagawa,S., Nakano,T.,
            Bartel,D.P. and Kingston,R.E.
  TITLE     Characterization of the piRNA complex from rat testes
  JOURNAL   Science 313 (5785), 363-367 (2006)
   PUBMED   16778019
REFERENCE   7  (bases 1 to 5198)
  AUTHORS   Pickell,L., Tran,P., Leclerc,D., Hiscott,J. and Rozen,R.
  TITLE     Regulatory studies of murine methylenetetrahydrofolate reductase
            reveal two major promoters and NF-kappaB sensitivity
  JOURNAL   Biochim Biophys Acta 1731 (2), 104-114 (2005)
   PUBMED   16274753
REFERENCE   8  (bases 1 to 5198)
  AUTHORS   Kida,Y., Uchida,S., Miyazaki,H., Sasaki,S. and Marumo,F.
  TITLE     Localization of mouse CLC-6 and CLC-7 mRNA and their functional
            complementation of yeast CLC gene mutant
  JOURNAL   Histochem Cell Biol 115 (3), 189-194 (2001)
   PUBMED   11326746
REFERENCE   9  (bases 1 to 5198)
  AUTHORS   Kornak,U., Bosl,M.R. and Kubisch,C.
  TITLE     Complete genomic structure of the CLCN6 and CLCN7 putative chloride
            channel genes(1)
  JOURNAL   Biochim Biophys Acta 1447 (1), 100-106 (1999)
   PUBMED   10500249
REFERENCE   10 (bases 1 to 5198)
  AUTHORS   Eggermont,J., Buyse,G., Voets,T., Tytgat,J., De Smedt,H.,
            Droogmans,G. and Nilius,B.
  TITLE     Alternative splicing of ClC-6 (a member of the CIC chloride-channel
            family) transcripts generates three truncated isoforms one of
            which, ClC-6c, is kidney-specific
  JOURNAL   Biochem J 325 (Pt 1) (Pt 1), 269-276 (1997)
   PUBMED   9224655
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK165362.1, CX564347.1,
            CB521277.1, AL606929.13, CX205353.1, BQ178271.1, BM949055.1 and
            BQ174789.1.
            
            On Aug 22, 2015 this sequence version replaced NM_011929.2.
            
            Summary: This gene encodes a member of the ClC chloride channel and
            transporter family of proteins. The encoded protein may function as
            a vesicular Cl-/H+ antiporter. Homozygous knockout mice exhibit
            decreased pain sensitivity, behavioral abnormalities and features
            of lysosomal storage disease. [provided by RefSeq, Aug 2015].
            
            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 :: AK165362.1, SRR9219379.32965.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMN00849374,
                                           SAMN00849375 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-680               AK165362.1         1-680
            681-1088            CX564347.1         413-820
            1089-1650           CB521277.1         74-635
            1651-2627           AK165362.1         1655-2631
            2628-3306           AK165362.1         2633-3311
            3307-3462           AL606929.13        5899-6054           c
            3463-3901           CX205353.1         1-439
            3902-3932           AL606929.13        5429-5459           c
            3933-4518           BQ178271.1         1-586
            4519-4924           BM949055.1         328-733
            4925-5198           BQ174789.1         1-274               c
FEATURES             Location/Qualifiers
     source          1..5198
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="4"
                     /map="4 78.67 cM"
     gene            1..5198
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /note="chloride channel, voltage-sensitive 6"
                     /db_xref="GeneID:26372"
                     /db_xref="MGI:MGI:1347049"
     exon            1..133
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     CDS             47..2659
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /note="chloride transport protein 6; clC-6; chloride
                     channel protein 6; chloride channel 6"
                     /codon_start=1
                     /product="H(+)/Cl(-) exchange transporter 6"
                     /protein_id="NP_036059.1"
                     /db_xref="CCDS:CCDS18928.1"
                     /db_xref="GeneID:26372"
                     /db_xref="MGI:MGI:1347049"
                     /translation="MAGCRGSVCCCCRWCCCCGERESRTPEELTILGETQEEEDEILP
                     RKDYESLDYDRCINDPYLEVLETMDNKKGRRYEAVKWMVVFAIGVCTGLVGLFVDFSV
                     RLFTQLKFGVVQTSVEECSQKGCLALSLLELLGFNLTFVFLASLLVLIEPVAAGSGIP
                     EIKCYLNGVKVPGIVRLRTLLCKVFGVLFSVSGGLFVGKEGPMIHSGAVVGAGLPQFQ
                     SISLRKIQFNFPYFRSDRDKRDFVSAGAAAGVAAAFGAPIGGTLFSLEEGSSFWNQGL
                     TWKVLFCSMSATFTLNFFRSGIQFGSWGSFQLPGLLNFGEFKCSDSDKKCHLWTAMDL
                     GFFVVMGVIGGLLGATFNCLNKRLAKYRMRNVHPKPKLVRVLESLLVSLVTTVVVFVA
                     SMVLGECRQMSSTSQTGNGSFQLQVTSEDVNSTIKAFFCPNDTYNDMATLFFNSQESA
                     ILQLFHQDGTFSPVTLALFFILYFLLACWTFGTSVPSGLFVPSLLCGAAFGRLVANVL
                     KSYIGLGHLYSGTFALIGAAAFLGGVVRMTISLTVILIESTNEITYGLPIMVTLMVAK
                     WTGDLFNKGIYDVHIGLRGVPLLEWETDVEMDKLRASDIMEPNLTYVYPHTRIQSLVS
                     ILRTTVHHAFPVVTENRGNEKEFMKGNQLISNNIKFKKSSILTRAGEQRKRGQSMKSY
                     PSSELRNVCDEHVASEEPAEKEDLLQQMLERRYTPYPNLYPDQSPSEDWTMEERFRPL
                     TFHGLVLRSQLVTLLVRGVCYSESQSSASQPRLSYAEMAEDYPRYPDIHDLDLTLLNP
                     RMIVDVTPYMNPSPFTVSPNTHVSQVFNLFRTMGLRHLPVVNAVGEIVGIITRHNLTN
                     EFLQARLRQHYQTL"
     exon            134..193
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            194..259
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            260..325
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            326..392
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            393..499
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            500..626
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            627..694
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            695..753
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            754..886
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            887..1000
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            1001..1167
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            1168..1294
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            1295..1421
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            1422..1575
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            1576..1735
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            1736..1842
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            1843..2029
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            2030..2187
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            2188..2344
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            2345..2452
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            2453..2578
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     exon            2579..5181
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /inference="alignment:Splign:2.1.0"
     regulatory      5155..5160
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /note="hexamer: AATAAA"
     polyA_site      5181
                     /gene="Clcn6"
                     /gene_synonym="Clc6"
                     /note="major polyA site"
ORIGIN      
        1 gaggggggtt ggcctaggtg gtccggagcg gcagcaaagg aggaagatgg cggggtgcag
       61 ggggtccgtg tgctgctgct gccggtggtg ttgctgctgc ggtgaacggg agagccgcac
      121 ccccgaggag ctgaccatcc ttggggagac acaggaagaa gaggatgaga ttcttccaag
      181 gaaagactat gagagtctgg actatgaccg ctgcatcaat gacccttacc tggaggtgtt
      241 ggagaccatg gataataaga aagggcgaag atacgaggcg gtgaagtgga tggtggtgtt
      301 cgccattggc gtctgtacgg ggctggtggg tctctttgtg gacttttccg tgcgactctt
      361 cacccaactg aagttcggag tggttcaaac gtcggtggag gaatgcagtc agaagggctg
      421 ccttgccctg tccctcctgg agctcctggg ctttaacttg acctttgtct tcctggcaag
      481 ccttcttgtc ttgatagagc cagtggcagc aggttctgga atccccgaga tcaagtgcta
      541 cctgaatggt gtgaaagtgc caggaattgt ccggctccgg accctgctct gcaaagtctt
      601 tggggtgctg ttcagtgtgt ctggagggct ctttgtgggg aaagaaggcc ccatgatcca
      661 cagtggtgct gtggtaggag ctggcctccc tcagttccag agcatctcct tacggaagat
      721 ccagtttaac ttcccctact tccgcagcga cagagacaag cgtgactttg tgtcagcggg
      781 ggcagctgct ggcgttgctg cagcttttgg ggcccctata gggggcacct tgttcagtct
      841 ggaggagggt tcatccttct ggaaccaggg gctcacgtgg aaagtgctct tctgttccat
      901 gtccgccacc ttcaccctca acttcttccg ctctgggatt cagtttggaa gttggggttc
      961 cttccagctg cctggattgc tgaactttgg tgaatttaag tgctctgact ctgataaaaa
     1021 atgtcatctc tggacagcta tggatttggg tttcttcgtc gtgatggggg tcattggggg
     1081 cctcctggga gccacattca actgtctgaa caagaggctt gcaaagtacc gtatgcgcaa
     1141 cgtgcacccg aaacctaagc tcgtcagagt cttagagagc ctcttggtgt ccctggtgac
     1201 cactgtggtg gtgtttgtgg cctccatggt gttaggagaa tgccgacaga tgtcttccac
     1261 gagtcaaacc ggtaatggct cattccagct ccaggtcaca tcagaagatg tgaattcaac
     1321 tatcaaggct tttttctgtc ccaatgacac ttacaatgac atggccacac tcttcttcaa
     1381 ctcccaggag tctgccatcc tgcagctctt ccatcaggat gggactttca gccccgtcac
     1441 cctggcctta ttcttcatcc tctatttcct gctcgcatgc tggacttttg gcacatctgt
     1501 ccccagtggc ctcttcgtgc cttccctgct gtgtggagca gcttttggac gtttagttgc
     1561 caatgtcctg aaaagctaca ttggactggg ccacctctat tctgggacct ttgccctgat
     1621 tggtgcggca gctttcttgg gtggggttgt aaggatgacc atcagcctca cagtcatcct
     1681 gatcgagtct acaaatgaga tcacctatgg gcttccgatc atggtcactc tgatggtggc
     1741 caagtggact ggagacttgt tcaacaaggg catttatgac gtccatattg ggctgagagg
     1801 tgtgcctctt ctggagtggg agacagacgt ggaaatggac aagctgagag ccagtgacat
     1861 catggagccc aacctgacgt acgtctaccc gcacactcgc atccagtctc tggtgagcat
     1921 cctgcgcact acggtccacc atgccttccc agtggtcacg gagaaccggg gcaacgagaa
     1981 ggagttcatg aagggcaacc agctcataag caacaacatc aagttcaaga aatccagtat
     2041 cctgacccgt gctggtgagc agcgcaagcg gggccagtcc atgaagtcgt acccttccag
     2101 cgagctgcgc aacgtgtgtg atgagcatgt ggcttctgag gagccggcag agaaggagga
     2161 cctgctacag cagatgctgg agaggagata cactccctac cccaacctat accctgacca
     2221 gtccccgagt gaagactgga ccatggagga gcgtttccgt ccgctgacct ttcacggcct
     2281 tgtcctgcgc tctcagcttg tcaccctgct tgtccgagga gtgtgctatt cggaaagtca
     2341 gtccagtgcc agccaaccac gtctttctta cgctgagatg gctgaggact acccgcgata
     2401 cccggacata catgacctgg acctcacact gctgaatccc cgaatgattg tggatgtcac
     2461 cccatatatg aatccttcac catttaccgt ctcccccaac acccatgttt ctcaagtgtt
     2521 caacctgttc agaaccatgg gcctgcgcca cttgcctgtg gtgaatgcag taggagagat
     2581 cgtggggatc attacacggc acaacctgac aaatgaattc ctgcaggccc ggctgcggca
     2641 gcattaccag accctctgac agttgcaccc ggctgaagcc agcccactct cccagaggtg
     2701 cctctgcagg tggcccgctc acttactggc ccccacagcc ggcatgaagg ctcccactca
     2761 cccgtttgct cagatgcctg gagtcctgga agatgggggt cagaagtttt tggggatgtg
     2821 ttgagtagga agttggggtt ttactaactt cctctgtaag aatcttccat tccccagctc
     2881 ccctaaggag acgtcagggt gccgtcgggc tggatcctag gtggacactt ggtacctctc
     2941 tgttgctgtt tcttggagag cccagctctt gcccagaccc tcccgggaag gtgttggact
     3001 gaggcaaaca ttgaggatgt tatttgcata tcatgttcat tactaggttc aagaattggg
     3061 cactaagaac tgttccccat gtttggggag gcctgggatc agaaccaaga cttcagatac
     3121 attctgcctc ttcattggcc caactttctt ctccttctgt ttcctaggag cgggttcatg
     3181 ctctgacccc gtggcttgaa tgtctttaga ctcattcctg accagatcct tgatgcacta
     3241 aaattccagc taacagcctt tgaagcatta aatcccacca cagggggaca gcttctccct
     3301 tctgtgaaca ttcagtagtc cccactcact gattacacct gttctcccag tgacacacgc
     3361 tctcctccca ttgtcattcc tttcctctct acaactactc gactttctaa gccttcatct
     3421 gtcttcctgg tgggacagcc acaactttat cttggattca ttcccaaagt caaccaaaat
     3481 tgaggaaccc ctagacagaa ccactaccag agtcctggtg aatttgagat cactctacaa
     3541 gctggcaagc aagctgtcct gagccaggac cgaccaaagg tccaacctta ggagaaagcc
     3601 aatggcccct gttgtggtcg ctactcgagc ccagcttccc agtgcactcc cgactcggcc
     3661 tcttcccgag gacttgtagg ggaacctgtg tggctgctgg tctcggggcc caggtaggag
     3721 tgggatgctc ttgcccttgt gcttcattac ttcatggctt ctttctctcc tggctgctgg
     3781 tcctctcgga accaacatct gagtagggac atttgcattc atcttcctgc aacccaaggc
     3841 ccttgtggca gctgttcttt ggatacatgt ggcattcatt tgttttagat tctttttaaa
     3901 tcatggaact tggtggtagg catctgtgat acgcttggct tctagtagtg tggccaccag
     3961 gcctggcaga gtcctctgac cagcactcgg gaaattgttc cacggccatg gtcaggggct
     4021 accttggatc tttagggctg acagtgaccc tggccctctg ttttccccat ttgcttacct
     4081 ttttaccaga aagagcttga cttactctgt tttcaacttc tgactggggg ttgggagtgg
     4141 ggtgggggtt gaaactcttc ccaagtagtt gggaaaatag ctaagcatgg ttgtgtttgg
     4201 ccgctgccag cttcatttta tggctgattt caattcctgc cctgctgtgt gctctatcaa
     4261 gaagaaaacc agttgctccc actaagagaa aagtgtgaca caccacagaa ctgtcttccc
     4321 agcctggtgg gtttgcagaa ttgtagcctg tggaggacct cagtccacag cttccctgcc
     4381 tccaagccag tcctgttgtg atttgtccat cgagtgtgtg tgtgtgtgtg tgtgaccatc
     4441 agtttagccc agagtggaca gggtccaggc atacccaccc tggcccatgc tcctctagga
     4501 cactcagttt tctgggtccc tgctgaacct gcctttccag aaaagcccaa agacaacagc
     4561 tttttcacct gtgaactata actaagccgt ggacccctcc acccatggca gtcccttcga
     4621 actagtggct cagtctctta cttgtcgaag cttggtcccc caccccatcc cccaatgcac
     4681 cacagcacct tgtcagacac agttccatgg ggggtcactg aggttggctt gaggcagttt
     4741 cctggctggc ttctgcgcct gggcatttgt gtggctccgg tactgctgtg ggagttgggt
     4801 attttatgag atgtctgcat gtgaccttgt taagcagttc cagctgggac ggacattagc
     4861 ttgactcagc tagccatgtg acagtttgat gcagaccttg gtgacaagaa agcttccgga
     4921 gaggccagcc cagccttcct ggcccagcca tgttgacaag gagagttgcc cttggctcct
     4981 gtggacctca gagactgtcc agttgcagct tccgcctttc ggtcatactg tgtttatacg
     5041 gtaacattag ctgattccac tgtgtagata aatggtatct tttttaattt gtaaaagtct
     5101 atttttattt ggccctttgg aaggtggacg ttcttgtggt cactcttaag tcagaataaa
     5161 aatgtctgca ccttctctgt aaaaaaaaaa aaaaaaaa
//
