LOCUS       NM_004070               2491 bp    mRNA    linear   PRI 07-FEB-2025
DEFINITION  Homo sapiens chloride voltage-gated channel Ka (CLCNKA), transcript
            variant 1, mRNA.
ACCESSION   NM_004070
VERSION     NM_004070.4
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 2491)
  AUTHORS   Yun,Y., Park,S.S., Lee,S., Seok,H., Park,S. and Lee,S.Y.
  TITLE     Expanding Genotype-Phenotype Correlation of CLCNKA and CLCNKB
            Variants Linked to Hearing Loss
  JOURNAL   Int J Mol Sci 24 (23), 17077 (2023)
   PUBMED   38069401
  REMARK    GeneRIF: Expanding Genotype-Phenotype Correlation of CLCNKA and
            CLCNKB Variants Linked to Hearing Loss.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2491)
  AUTHORS   Gerbino,A., De Zio,R., Russo,D., Milella,L., Milano,S., Procino,G.,
            Pusch,M., Svelto,M. and Carmosino,M.
  TITLE     Role of PKC in the Regulation of the Human Kidney Chloride Channel
            ClC-Ka
  JOURNAL   Sci Rep 10 (1), 10268 (2020)
   PUBMED   32581267
  REMARK    GeneRIF: Role of PKC in the Regulation of the Human Kidney Chloride
            Channel ClC-Ka.
            Erratum:[Sci Rep. 2020 Sep 30;10(1):16469. doi:
            10.1038/s41598-020-74040-w.. PMID: 32994445]
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2491)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   4  (bases 1 to 2491)
  AUTHORS   Wojciechowski,D., Thiemann,S., Schaal,C., Rahtz,A., de la Roche,J.,
            Begemann,B., Becher,T. and Fischer,M.
  TITLE     Activation of renal ClC-K chloride channels depends on an intact N
            terminus of their accessory subunit barttin
  JOURNAL   J Biol Chem 293 (22), 8626-8637 (2018)
   PUBMED   29674316
  REMARK    GeneRIF: Increasing expression of barttin over that of ClC-K
            partially recovered this insufficiency, indicating that N-terminal
            modifications of barttin alter both binding affinities and gating
            properties
REFERENCE   5  (bases 1 to 2491)
  AUTHORS   Steinke,K.V., Gorinski,N., Wojciechowski,D., Todorov,V., Guseva,D.,
            Ponimaskin,E., Fahlke,C. and Fischer,M.
  TITLE     Human CLC-K Channels Require Palmitoylation of Their Accessory
            Subunit Barttin to Be Functional
  JOURNAL   J Biol Chem 290 (28), 17390-17400 (2015)
   PUBMED   26013830
  REMARK    GeneRIF: R8W and G47R, two naturally occurring barttin mutations
            identified in patients with Bartter syndrome type IV, reduce
            barttin palmitoylation and CLC-K/barttin channel activity.
REFERENCE   6  (bases 1 to 2491)
  AUTHORS   Estevez,R., Boettger,T., Stein,V., Birkenhager,R., Otto,E.,
            Hildebrandt,F. and Jentsch,T.J.
  TITLE     Barttin is a Cl- channel beta-subunit crucial for renal Cl-
            reabsorption and inner ear K+ secretion
  JOURNAL   Nature 414 (6863), 558-561 (2001)
   PUBMED   11734858
REFERENCE   7  (bases 1 to 2491)
  AUTHORS   Jentsch,T.J. and Gunther,W.
  TITLE     Chloride channels: an emerging molecular picture
  JOURNAL   Bioessays 19 (2), 117-126 (1997)
   PUBMED   9046241
  REMARK    Review article
REFERENCE   8  (bases 1 to 2491)
  AUTHORS   Saito-Ohara,F., Uchida,S., Takeuchi,Y., Sasaki,S., Hayashi,A.,
            Marumo,F. and Ikeuchi,T.
  TITLE     Assignment of the genes encoding the human chloride channels,
            CLCNKA and CLCNKB, to 1p36 and of CLCN3 to 4q32-q33 by in situ
            hybridization
  JOURNAL   Genomics 36 (2), 372-374 (1996)
   PUBMED   8812470
REFERENCE   9  (bases 1 to 2491)
  AUTHORS   Takeuchi,Y., Uchida,S., Marumo,F. and Sasaki,S.
  TITLE     Cloning, tissue distribution, and intrarenal localization of ClC
            chloride channels in human kidney
  JOURNAL   Kidney Int 48 (5), 1497-1503 (1995)
   PUBMED   8544406
REFERENCE   10 (bases 1 to 2491)
  AUTHORS   Kieferle,S., Fong,P., Bens,M., Vandewalle,A. and Jentsch,T.J.
  TITLE     Two highly homologous members of the ClC chloride channel family in
            both rat and human kidney
  JOURNAL   Proc Natl Acad Sci U S A 91 (15), 6943-6947 (1994)
   PUBMED   8041726
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BC053869.1 and Z30643.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_004070.3.
            
            Summary: This gene is a member of the CLC family of voltage-gated
            chloride channels. The encoded protein is predicted to have 12
            transmembrane domains, and requires a beta subunit called barttin
            to form a functional channel. It is thought to function in salt
            reabsorption in the kidney and potassium recycling in the inner
            ear. The gene is highly similar to CLCNKB, which is located 10 kb
            downstream from this gene. Multiple transcript variants encoding
            different isoforms have been found for this gene. [provided by
            RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest 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 :: AK290814.1, Z30643.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968832, SAMEA1968968
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000331433.5/ ENSP00000332771.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-15                BC053869.1         94-108
            16-2149             Z30643.1           3-2136
            2150-2491           BC053869.1         2240-2581
FEATURES             Location/Qualifiers
     source          1..2491
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1p36.13"
     gene            1..2491
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /note="chloride voltage-gated channel Ka"
                     /db_xref="GeneID:1187"
                     /db_xref="HGNC:HGNC:2026"
                     /db_xref="MIM:602024"
     exon            1..28
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            29..135
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     CDS             36..2099
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /note="isoform 1 is encoded by transcript variant 1;
                     chloride channel, kidney, A; chloride channel protein
                     ClC-Ka; chloride channel Ka; chloride channel,
                     voltage-sensitive Ka"
                     /codon_start=1
                     /product="chloride channel protein ClC-Ka isoform 1"
                     /protein_id="NP_004061.3"
                     /db_xref="CCDS:CCDS167.1"
                     /db_xref="GeneID:1187"
                     /db_xref="HGNC:HGNC:2026"
                     /db_xref="MIM:602024"
                     /translation="MEELVGLREGFSGDPVTLQELWGPCPHIRRAIQGGLEWLKQKVF
                     RLGEDWYFLMTLGVLMALVSYAMNFAIGCVVRAHQWLYREIGDSHLLRYLSWTVYPVA
                     LVSFSSGFSQSITPSSGGSGIPELKTMLAGVILEDYLDIKNFGAKVVGLSCTLATGST
                     LFLGKVGPFVHLSVMIAAYLGRVRTTTIGEPENKSKQNEMLVAAAAVGVATVFAAPFS
                     GVLFSIEVMSSHFSVRDYWRGFFAATCGAFIFRLLAVFNSEQETITSLYKTSFRVDVP
                     FDLPEIFFFVALGGICGVLSCAYLFCQRTFLSFIKTNRYSSKLLATSKPVYSALATLL
                     LASITYPPGVGHFLASRLSMKQHLDSLFDNHSWALMTQNSSPPWPEELDPQHLWWEWY
                     HPRFTIFGTLAFFLVMKFWMLILATTIPMPAGYFMPIFILGAAIGRLLGEALAVAFPE
                     GIVTGGVTNPIMPGGYALAGAAAFSGAVTHTISTALLAFELTGQIVHALPVLMAVLAA
                     NAIAQSCQPSFYDGTIIVKKLPYLPRILGRNIGSHHVRVEHFMNHSITTLAKDTPLEE
                     VVKVVTSTDVTEYPLVESTESQILVGIVQRAQLVQALQAEPPSRAPGHQQCLQDILAR
                     GCPTEPVTLTLFSETTLHQAQNLFKLLNLQSLFVTSRGRAVGCVSWVEMKKAISNLTN
                     PPAPK"
     exon            136..264
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            265..393
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            394..533
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            534..611
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            612..690
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            691..816
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            817..901
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            902..1003
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            1004..1088
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            1089..1262
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            1263..1332
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            1333..1443
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            1444..1657
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            1658..1791
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            1792..1880
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            1881..1964
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            1965..2051
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     exon            2052..2491
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2473..2478
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /note="hexamer: AATAAA"
     polyA_site      2491
                     /gene="CLCNKA"
                     /gene_synonym="ClC-K1; CLCK1; hClC-Ka"
                     /note="major polyA site"
ORIGIN      
        1 agttcagccg cagcaggagg actgacaggg gcctgatgga ggagttggtg gggctgcgtg
       61 agggcttctc aggggaccct gtgactctgc aggagctgtg gggcccctgt ccccacatcc
      121 gccgagccat ccaaggtggc ctggagtggc taaagcagaa ggtgttccgc ctgggagaag
      181 actggtactt cctgatgacc ctcggggtgc tcatggccct ggtcagctat gccatgaact
      241 ttgccatcgg gtgtgtggtc cgagcacacc agtggctgta cagggagatt ggggacagcc
      301 acctgctccg gtatctttcc tggactgtgt accctgtggc cctcgtctct ttctcctcag
      361 gcttctccca gagcatcacg ccctcctctg gaggttctgg aatcccggag ctgaagacca
      421 tgttggcggg tgtgatcttg gaggactacc tggatatcaa gaactttggg gccaaggtgg
      481 tgggcctctc ctgcaccctg gccaccggca gcaccctgtt cctgggcaaa gtgggccctt
      541 tcgtgcacct gtctgtaatg atcgctgcct acctgggccg tgtgcgcacc acgaccatcg
      601 gggagcctga gaacaagagc aagcaaaacg aaatgctggt ggcagcggcg gcagtgggcg
      661 tggccacagt ctttgcagct cccttcagcg gcgtcctgtt cagcatcgag gtcatgtctt
      721 cccacttctc tgtccgggat tactggaggg gcttctttgc ggccacctgc ggggccttca
      781 tattccggct cctggcagtc ttcaacagcg agcaggagac catcacctcc ctctacaaga
      841 ccagtttccg ggtggacgtt cccttcgacc tgcctgagat cttctttttt gtggcgctgg
      901 gtggcatctg cggcgtcctg agctgtgctt acctcttctg tcagcgaacc ttcctcagct
      961 tcatcaagac caatcggtac agctccaaac tgctggctac tagcaagcct gtgtactccg
     1021 ctctggccac cttgcttctc gcctccatca cctacccgcc tggtgtgggc cacttcctag
     1081 cttctcggct gtccatgaag cagcatctgg actcgctgtt cgacaaccac tcctgggcgc
     1141 tgatgaccca gaactccagc ccaccctggc ccgaggagct cgacccccag cacctttggt
     1201 gggaatggta ccacccgcgg ttcaccatct ttgggaccct tgccttcttc ctggttatga
     1261 agttctggat gctgattctg gccaccacca tccccatgcc tgccgggtac ttcatgccca
     1321 tctttatcct tggagctgcc atcgggcgcc tcttgggaga ggctcttgcc gtcgccttcc
     1381 ctgagggcat tgtgactgga ggggttacca atcccatcat gcccgggggg tatgctctgg
     1441 caggggctgc agccttctca ggggctgtga cccacaccat ctccacggcg ctgctggcct
     1501 ttgagctgac cggccagata gtgcatgcac tgcccgtgct gatggcggtg ctggcagcca
     1561 acgccattgc acagagctgc cagccctcct tctatgatgg caccatcatt gtcaagaagc
     1621 tgccatacct gccacggatt ctgggccgca acatcggctc ccaccatgtg agggtggagc
     1681 acttcatgaa ccacagcatc accacactgg ccaaggacac gccgctggag gaggtggtca
     1741 aggttgtgac ctccacagac gtgaccgagt atcccctggt ggagagcaca gagtcccaga
     1801 tcctggtagg catcgtgcag agggcccagc tggtgcaggc cctccaggct gagcctcctt
     1861 ccagggctcc aggacaccag cagtgtctcc aggacatctt ggccaggggc tgccccacgg
     1921 aaccagtgac cctgacgcta ttctcagaga ccaccttgca ccaggcacaa aacctcttta
     1981 agctgttgaa ccttcagtcc ctcttcgtga catcgcgggg cagagctgtg ggctgcgtgt
     2041 cctgggtgga gatgaagaaa gcaatttcca acctgacaaa tccgccagct ccaaagtgag
     2101 ccggcccagc aagatgaaac agggcacccc agctgacctg gtactgaggt tgggctgaga
     2161 ccctgcttct cttcccccat caccacctgc ccctccctcc agcccagctc cattctttgg
     2221 cataacaggc aactctaacc tagcccagaa gaggatggct catcctgggt gggacgatgg
     2281 ctcctgcctt gaaagacaaa aatcccacct tgggcagagc tgagtgtgag aagatggaaa
     2341 accagtatct gccaggtgct cagtgactgg ccatcacatt aatgaatgac gagattggag
     2401 tacactgtca ccaagggcag gcaaagatgc cctctggggt tgtctggttc ccagtgagag
     2461 gctcctgaga aaaataaagc tggttcccag a
//
