LOCUS       NM_001412260            4502 bp    mRNA    linear   ROD 13-JUN-2024
DEFINITION  Mus musculus chloride channel, voltage-sensitive 4 (Clcn4),
            transcript variant 10, mRNA.
ACCESSION   NM_001412260 XM_006539502
VERSION     NM_001412260.1
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 4502)
  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 4502)
  AUTHORS   Weinert,S., Gimber,N., Deuschel,D., Stuhlmann,T., Puchkov,D.,
            Farsi,Z., Ludwig,C.F., Novarino,G., Lopez-Cayuqueo,K.I.,
            Planells-Cases,R. and Jentsch,T.J.
  TITLE     Uncoupling endosomal CLC chloride/proton exchange causes severe
            neurodegeneration
  JOURNAL   EMBO J 39 (9), e103358 (2020)
   PUBMED   32118314
  REMARK    GeneRIF: Uncoupling endosomal CLC chloride/proton exchange causes
            severe neurodegeneration.
REFERENCE   3  (bases 1 to 4502)
  AUTHORS   Slaats,G.G., Wheway,G., Foletto,V., Szymanska,K., van Balkom,B.W.,
            Logister,I., Den Ouden,K., Keijzer-Veen,M.G., Lilien,M.R.,
            Knoers,N.V., Johnson,C.A. and Giles,R.H.
  TITLE     Screen-based identification and validation of four new ion channels
            as regulators of renal ciliogenesis
  JOURNAL   J Cell Sci 128 (24), 4550-4559 (2015)
   PUBMED   26546361
REFERENCE   4  (bases 1 to 4502)
  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   5  (bases 1 to 4502)
  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   6  (bases 1 to 4502)
  AUTHORS   Carninci,P., Waki,K., Shiraki,T., Konno,H., Shibata,K., Itoh,M.,
            Aizawa,K., Arakawa,T., Ishii,Y., Sasaki,D., Bono,H., Kondo,S.,
            Sugahara,Y., Saito,R., Osato,N., Fukuda,S., Sato,K., Watahiki,A.,
            Hirozane-Kishikawa,T., Nakamura,M., Shibata,Y., Yasunishi,A.,
            Kikuchi,N., Yoshiki,A., Kusakabe,M., Gustincich,S., Beisel,K.,
            Pavan,W., Aidinis,V., Nakagawara,A., Held,W.A., Iwata,H., Kono,T.,
            Nakauchi,H., Lyons,P., Wells,C., Hume,D.A., Fagiolini,M.,
            Hensch,T.K., Brinkmeier,M., Camper,S., Hirota,J., Mombaerts,P.,
            Muramatsu,M., Okazaki,Y., Kawai,J. and Hayashizaki,Y.
  TITLE     Targeting a complex transcriptome: the construction of the mouse
            full-length cDNA encyclopedia
  JOURNAL   Genome Res 13 (6B), 1273-1289 (2003)
   PUBMED   12819125
REFERENCE   7  (bases 1 to 4502)
  AUTHORS   Adler,D.A., Rugarli,E.I., Lingenfelter,P.A., Tsuchiya,K.,
            Poslinski,D., Liggitt,H.D., Chapman,V.M., Elliott,R.W., Ballabio,A.
            and Disteche,C.M.
  TITLE     Evidence of evolutionary up-regulation of the single active X
            chromosome in mammals based on Clc4 expression levels in Mus
            spretus and Mus musculus
  JOURNAL   Proc Natl Acad Sci U S A 94 (17), 9244-9248 (1997)
   PUBMED   9256467
REFERENCE   8  (bases 1 to 4502)
  AUTHORS   Kubagawa,H., Burrows,P.D. and Cooper,M.D.
  TITLE     A novel pair of immunoglobulin-like receptors expressed by B cells
            and myeloid cells
  JOURNAL   Proc Natl Acad Sci U S A 94 (10), 5261-5266 (1997)
   PUBMED   9144225
REFERENCE   9  (bases 1 to 4502)
  AUTHORS   Palmer,S., Perry,J. and Ashworth,A.
  TITLE     A contravention of Ohno's law in mice
  JOURNAL   Nat Genet 10 (4), 472-476 (1995)
   PUBMED   7670497
REFERENCE   10 (bases 1 to 4502)
  AUTHORS   Rugarli,E.I., Adler,D.A., Borsani,G., Tsuchiya,K., Franco,B.,
            Hauge,X., Disteche,C., Chapman,V. and Ballabio,A.
  TITLE     Different chromosomal localization of the Clcn4 gene in Mus spretus
            and C57BL/6J mice
  JOURNAL   Nat Genet 10 (4), 466-471 (1995)
   PUBMED   7670496
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC149056.6.
            
            On Sep 27, 2022 this sequence version replaced XM_006539502.5.
            
            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 :: SRR10662774.1064381.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164139, SAMN01164141
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-188               AC149056.6         62196-62383         c
            189-333             AC149056.6         60237-60381         c
            334-488             AC149056.6         58269-58423         c
            489-588             AC149056.6         57515-57614         c
            589-776             AC149056.6         56541-56728         c
            777-899             AC149056.6         56278-56400         c
            900-1106            AC149056.6         55460-55666         c
            1107-1187           AC149056.6         54583-54663         c
            1188-1733           AC149056.6         52956-53501         c
            1734-1920           AC149056.6         51944-52130         c
            1921-2319           AC149056.6         50420-50818         c
            2320-2536           AC149056.6         49191-49407         c
            2537-4502           AC149056.6         43854-45819         c
FEATURES             Location/Qualifiers
     source          1..4502
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="7"
                     /map="7 4.23 cM"
     gene            1..4502
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /note="chloride channel, voltage-sensitive 4"
                     /db_xref="GeneID:12727"
                     /db_xref="MGI:MGI:104571"
     exon            1..188
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /inference="alignment:Splign:2.1.0"
     exon            189..333
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /inference="alignment:Splign:2.1.0"
     exon            334..488
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /inference="alignment:Splign:2.1.0"
     CDS             384..2627
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /note="isoform 1 is encoded by transcript variant 10;
                     h(+)/Cl(-) exchange transporter 4; voltage-gated chloride
                     channel ClC-4A; chloride channel 4-2; chloride channel
                     protein 4; chloride transporter ClC-4"
                     /codon_start=1
                     /product="H(+)/Cl(-) exchange transporter 4 isoform 1"
                     /protein_id="NP_001399189.1"
                     /db_xref="GeneID:12727"
                     /db_xref="MGI:MGI:104571"
                     /translation="MDFLEEPFPDVGTYEDFHTIDWLREKSRDTDRHRKITSKSKESI
                     WEFIKSLLDAWSGWVVMLLIGLLAGTLAGVIDLAVDWMTDLKEGVCLSAFWYSHEQCC
                     WTSNETTFEDRDKCPLWQKWSELLLSQSEGASAYILNYLMYILWALLFAFLAVSLVRV
                     FAPYACGSGIPEIKTILSGFIIRGYLGKWTLLIKTVTLVLVVSSGLSLGKEGPLVHVA
                     CCCGNFFSSLFSKYSKNEGKRREVLSAAAAAGVSVAFGAPIGGVLFSLEEVSYYFPLK
                     TLWRSFFAALVAAFTLRSINPFGNSRLVLFYVEYHTPWYMAELFPFILLGVFGGLWGT
                     LFTRCNIAWCRRRKTTRLGRYPVLEVIAVTAVTAIVAYPNPYTRQSTSELISELFNDC
                     GALESSQLCDYINDPNMTRPVDDIPDRPAGVGVYTAMWQLALALIFKIVITIFTFGMK
                     IPSGLFIPSMAVGAMAGRMVGIGVEQLAYHHHDWIIFRNWCRPGADCVTPGLYAMVGA
                     AACLGGVTRMTVSLVVIMFELTGGLEYIVPLMAAAVTSKWVADAFGKEGIYEAHIHLN
                     GYPFLDVKDEFTHRTLATDVMRPRRGEPPLSVLTQDSMTVEDVETLIKETDYNGFPVL
                     VSRDSERLIGFAQRRELILAIKNARQRQEGIVSNSIMYFTEEPPELPANSPHPLKLRR
                     ILNLSPFTVTDHTPMETVVDIFRKLGLRQCLVTRSGRLLGIITKKDVLRHMAQMANQD
                     PESIMFN"
     exon            489..588
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /inference="alignment:Splign:2.1.0"
     exon            589..776
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /inference="alignment:Splign:2.1.0"
     exon            777..899
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /inference="alignment:Splign:2.1.0"
     exon            900..1106
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1107..1187
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1188..1733
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1734..1920
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /inference="alignment:Splign:2.1.0"
     exon            1921..2319
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /inference="alignment:Splign:2.1.0"
     exon            2320..2536
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /inference="alignment:Splign:2.1.0"
     exon            2537..4502
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4477..4482
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /note="hexamer: ATTAAA"
     polyA_site      4502
                     /gene="Clcn4"
                     /gene_synonym="clC-4; Clc4-2; Clcn4-2"
                     /note="major polyA site"
ORIGIN      
        1 ctgagtctct cggcgcctgg gctgctgcag ctcacgcagc tgccggggtc tgacaggggt
       61 tgcgagaggc aggtcctgtt cagagcgagc tccgagcggc ggctcgtctc ggggtctgtg
      121 ggcgggaccc gctgtcaccc cagccgacgt cctcgggcct cgggtgtcac tatgagtgac
      181 tgctgtggac acttgccccg ccccgcctgc ctgcctgtca cccgcctcgc gatgacgtca
      241 cacgacctgc cgcagacagc cgcgctgaag agaggaggat gatctaggac gctgtccggg
      301 tggacggcca cgccgcaaga cgcggccctg caggagtgac tagcacggtc agggcgggag
      361 ccacgagcgc ctctgggaac ctcatggact tcctcgagga gcccttccct gacgtgggga
      421 cctacgagga cttccacacc atagactggc tgagggaaaa gtcccgggat accgacagac
      481 ataggaagat caccagcaaa agtaaggagt ctatttggga gttcatcaag agcctgctgg
      541 acgcgtggtc gggatgggtg gtgatgctac tcattgggct gctggcaggt accttggctg
      601 gagtcatcga tctcgctgtg gattggatga cggacctcaa ggagggggtc tgtctgtccg
      661 cattctggta cagccatgaa cagtgctgtt ggacctccaa cgagaccact tttgaggaca
      721 gggacaagtg tcccctgtgg cagaagtggt cagagcttct tctgagccag tcagagggcg
      781 ccagcgctta cattctgaat tacttaatgt acattctatg ggcgttgctg tttgcatttc
      841 tggctgtctc cctggtacgt gtgttcgcac cgtatgcctg tggctctggc atacccgaga
      901 taaagactat tttgagtggc tttatcatca ggggatactt ggggaaatgg actcttctaa
      961 tcaagactgt caccctcgtg ctcgtcgtat cctctggcct gagccttggc aaagagggcc
     1021 cactggtgca tgtggcatgt tgctgtggca acttcttcag cagccttttc tccaagtata
     1081 gcaagaatga aggcaagagg cgtgaggtgc tttcagctgc agctgctgct ggtgtctctg
     1141 tggcctttgg tgctccgata ggaggtgtgc tcttcagtct agaggaggtc agttactact
     1201 ttcccttgaa aaccttgtgg aggtcattct ttgcagccct ggtggctgcc ttcacactgc
     1261 gctccatcaa cccctttgga aatagccgcc tggttctctt ttatgtggag tatcatacac
     1321 cctggtacat ggctgaactc ttccctttca tcctgcttgg agtctttggg ggtttatggg
     1381 gaaccctctt cacacgctgc aacattgctt ggtgcaggag gcgtaagacc accaggctgg
     1441 gcaggtaccc agtgttggag gttattgcgg tgacagccgt caccgccatc gtggcctacc
     1501 ccaatcccta cactcgccag agcaccagtg agctcatctc tgagctcttc aacgattgtg
     1561 gggctctcga gtcttctcag ctctgtgact acatcaacga ccccaacatg actcggcctg
     1621 tggatgacat tccggaccgg ccggctgggg ttggagttta cacagccatg tggcagctgg
     1681 ccttggcact gatcttcaaa atagtcatta ctatatttac ctttggcatg aagattccct
     1741 caggtctctt catccccagt atggctgtcg gagccatggc aggccggatg gtgggaatcg
     1801 gtgtggagca gctggcctac catcaccatg actggatcat cttcaggaac tggtgcaggc
     1861 ctggagcgga ctgtgtcaca ccagggcttt atgcgatggt gggagctgca gcctgtctag
     1921 gtggggtgac taggatgaca gtgtctctag tggtcattat gtttgaactg actggaggtc
     1981 tggagtatat tgtacccctg atggcagctg ctgtcaccag caagtgggtg gctgatgcct
     2041 ttgggaaaga agggatttat gaagcccaca tccatctgaa tgggtaccca tttcttgatg
     2101 tgaaggatga gttcacccac cgtacgctgg ccactgatgt gatgcggccc cggaggggag
     2161 aaccgccatt atcggtacta acccaggaca gcatgactgt ggaggacgtg gagactctca
     2221 tcaaggagac agactacaac ggctttcctg tgctcgtctc cagagactcg gagcgtctca
     2281 tcgggtttgc ccagaggcgg gagctaatct tggctataaa aaatgccagg cagaggcaag
     2341 agggcattgt gagcaattcc atcatgtact tcacagagga gcctcctgag ctgcctgcca
     2401 acagcccaca tccactgaag ctgaggcgca ttttgaacct gagccctttc acggtcacag
     2461 atcacacccc catggagacg gtggtggaca ttttccggaa actggggctc cgacaatgcc
     2521 tggtgacacg gagtgggaga cttcttggga tcatcacaaa aaaggatgtt ctgagacaca
     2581 tggcccagat ggcaaaccag gaccctgaat ccatcatgtt taattagcaa taagatgggc
     2641 attattttga gaagatcaat aattatatca tttttaaaga aataaccaag tgatacatta
     2701 tgatcctaat gaaaaaactt gcactgaagg cagaaaaaga aaagaaaaga aaaaaagaaa
     2761 aaaaaagaaa gccttatttg aatttgaaac gagggggaaa agggtgaaac ttttttaaaa
     2821 ggcaaaaacc ataaactagt agtcatttta tagctttaac ctcttatgag ttcaaagctg
     2881 tgtttcttaa taaatttatt aactgctttt ggggtatgtg ggagggtgta aatgacatga
     2941 attatacaaa gacatggaac acaggaaaca ttggcacatt tactcaaggt tgatattcgt
     3001 aattttggag tacacatgaa gctttgagtc caaaagacaa aggggtattc gcatgctact
     3061 gttagatatt ggttcctaaa attttgctat gatgttacgg aatcatattg aagatattgc
     3121 attcagagaa aagaaaatta aagttggatg cagtgaaagc tacaagcagg ccctaatagg
     3181 tggtctactc atggccatct catttcttgc ctttgttctc aagcctgttg ttatgtttct
     3241 ttatcagtct gcaccagatt cagtagtgcc caccataatg agcatgaagt gaaagacttc
     3301 tcgacagaag acttcaagac tggactaaat gtttggacta tgaaccatgt agttctatgt
     3361 ggacatttct cttataaaag gggacacatt tttactttga ggggacactt gcgtcatcac
     3421 tgatttgcaa gcccaaagca tcaatttcac ttatttatat ggttacttgt gcatttgacg
     3481 tattgattag tccagcactt cccatggatt attgcccgtg tgctcctaga ttgctgtagt
     3541 gtggttttgt ttctaagtag catgtgcaat acttaaaacc agctatccag tgtttctact
     3601 taactttctt ctcaggtctt ccagatagag ccatgatgag agtgaggcat atgagttctc
     3661 agtgggaact cctccaaatg gattacaaga gaaatagtaa attgattcta aatctgttcc
     3721 attctcttcc ctgtaggata taaaatgtcc agttttaacg cctaagcatg gactttcaaa
     3781 ctagcaatca cagcgcggga cagagtcaca ttttatacag ccaattgaag cactgggtct
     3841 ctttgtgttt gaacttaatg gcaattttat tctttaaatt ctgcacatct gtcttttctt
     3901 caggaaggaa ttagtgtttc aggcccatcg catgatctgt gtaagatttg tgtcacttgc
     3961 catttcactt catctttgcc cctcactttt cactgagtca tcctcctcct tttcaatctt
     4021 actgtcattg ggtatcgttg aatcacgtat gtgcacttga ctgtatgtaa tagatcctga
     4081 cagtgcacct aagaaacctg ggacatggcc agtccaggac tgtctctaca ctattgccag
     4141 ggttccaaat tcttctggta tttcattttc cctcttctta ttctctgtcc tctggcttac
     4201 tgcctcatag ttgtaaaatt gttgcccaga tgccaggtgc gatgtctact ttctgtgagg
     4261 gaaggagggg gagaggcgag tacgaagatg aatgtgtata tctttcccag agatgcgcag
     4321 catacaacca ttggctggaa atctgttata tgccccattc gcctagatgt ctgtaaatac
     4381 aggaaggaaa attgttttag ctatacatta taacacatta ctttctggat ggaatttcga
     4441 ttctgtggat agggaagtgg gattggtatc tgtcatatta aattccaaca tcatgtccct
     4501 gc
//
