LOCUS       NM_001379110            4684 bp    mRNA    linear   PRI 06-MAR-2025
DEFINITION  Homo sapiens solute carrier family 9 member A6 (SLC9A6), transcript
            variant 7, mRNA.
ACCESSION   NM_001379110
VERSION     NM_001379110.1
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 4684)
  AUTHORS   Prasad,H.
  TITLE     Genes for endosomal pH regulators NHE6 and NHE9 are dysregulated in
            the substantia nigra in Parkinson's disease
  JOURNAL   Gene 927, 148737 (2024)
   PUBMED   38945311
  REMARK    GeneRIF: Genes for endosomal pH regulators NHE6 and NHE9 are
            dysregulated in the substantia nigra in Parkinson's disease.
REFERENCE   2  (bases 1 to 4684)
  AUTHORS   Wang,Y., Tian,X., Wang,Z., Liu,D., Zhao,X., Sun,X., Tu,Z., Li,Z.,
            Zhao,Y., Zheng,S. and Yao,J.
  TITLE     A novel peptide encoded by circ-SLC9A6 promotes lipid
            dyshomeostasis through the regulation of H4K16ac-mediated CD36
            transcription in NAFLD
  JOURNAL   Clin Transl Med 14 (8), e1801 (2024)
   PUBMED   39107881
  REMARK    GeneRIF: A novel peptide encoded by circ-SLC9A6 promotes lipid
            dyshomeostasis through the regulation of H4K16ac-mediated CD36
            transcription in NAFLD.
REFERENCE   3  (bases 1 to 4684)
  AUTHORS   Wu,Q., Ma,L., Joesch-Cohen,L., Schmidt,M., Uzun,E.D.G. and
            Morrow,E.M.
  TITLE     Targeting NHE6 gene expression identifies lysosome and
            neurodevelopmental mechanisms in a haploid in vitro cell model
  JOURNAL   Biol Open 12 (11) (2023)
   PUBMED   37747131
  REMARK    GeneRIF: Targeting NHE6 gene expression identifies lysosome and
            neurodevelopmental mechanisms in a haploid in vitro cell model.
REFERENCE   4  (bases 1 to 4684)
  AUTHORS   Hussain,S.I., Muhammad,N., Shah,S.U.D., Fardous,F., Khan,S.A.,
            Khan,N., Rehman,A.U., Siddique,M., Wasan,S.A., Niaz,R., Ullah,H.,
            Khan,N., Muhammad,N., Mirza,M.U., Wasif,N. and Khan,S.
  TITLE     Structural and functional implications of SLC13A3 and SLC9A6
            mutations: an in silico approach to understanding intellectual
            disability
  JOURNAL   BMC Neurol 23 (1), 353 (2023)
   PUBMED   37794328
  REMARK    GeneRIF: Structural and functional implications of SLC13A3 and
            SLC9A6 mutations: an in silico approach to understanding
            intellectual disability.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 4684)
  AUTHORS   Ohgaki,R., Matsushita,M., Kanazawa,H., Ogihara,S., Hoekstra,D. and
            van Ijzendoorn,S.C.
  TITLE     The Na+/H+ exchanger NHE6 in the endosomal recycling system is
            involved in the development of apical bile canalicular surface
            domains in HepG2 cells
  JOURNAL   Mol Biol Cell 21 (7), 1293-1304 (2010)
   PUBMED   20130086
  REMARK    GeneRIF: NHE6 in the endosomal recycling system is involved in the
            development of apical bile canalicular surface domains in HepG2
            cells
REFERENCE   6  (bases 1 to 4684)
  AUTHORS   Numata,M. and Orlowski,J.
  TITLE     Molecular cloning and characterization of a novel (Na+,K+)/H+
            exchanger localized to the trans-Golgi network
  JOURNAL   J Biol Chem 276 (20), 17387-17394 (2001)
   PUBMED   11279194
REFERENCE   7  (bases 1 to 4684)
  AUTHORS   Christianson,A.L., Stevenson,R.E., van der Meyden,C.H., Pelser,J.,
            Theron,F.W., van Rensburg,P.L., Chandler,M. and Schwartz,C.E.
  TITLE     X linked severe mental retardation, craniofacial dysmorphology,
            epilepsy, ophthalmoplegia, and cerebellar atrophy in a large South
            African kindred is localised to Xq24-q27
  JOURNAL   J Med Genet 36 (10), 759-766 (1999)
   PUBMED   10528855
REFERENCE   8  (bases 1 to 4684)
  AUTHORS   Numata,M., Petrecca,K., Lake,N. and Orlowski,J.
  TITLE     Identification of a mitochondrial Na+/H+ exchanger
  JOURNAL   J Biol Chem 273 (12), 6951-6959 (1998)
   PUBMED   9507001
REFERENCE   9  (bases 1 to 4684)
  AUTHORS   Morrow,E.M. and Pescosolido,M.F.
  TITLE     Christianson Syndrome
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   29334451
REFERENCE   10 (bases 1 to 4684)
  AUTHORS   Perlman,S.
  TITLE     Hereditary Ataxia Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301317
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL732579.5.
            This sequence is a reference standard in the RefSeqGene project.
            
            Summary: This gene encodes a sodium-hydrogen exchanger that is
            amember of the solute carrier family 9. The encoded protein
            localizes to early and recycling endosomes and may be involved in
            regulating endosomal pH and volume. Defects in this gene are
            associated with X-linked syndromic cognitive disability,
            Christianson type. Alternate splicing results in multiple
            transcript variants.[provided by RefSeq, Apr 2010].
            
            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##
            RNAseq introns :: single sample supports all introns SAMN03465403
                              [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000630721.3/ ENSP00000487486.2
            RefSeq Select criteria :: based on manual assertion, conservation
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-43                AL732579.5         22388-22430
            44-268              AL732579.5         22556-22780
            269-468             AL732579.5         31739-31938
            469-546             AL732579.5         35061-35138
            547-623             AL732579.5         35435-35511
            624-736             AL732579.5         35809-35921
            737-842             AL732579.5         39061-39166
            843-984             AL732579.5         47395-47536
            985-1090            AL732579.5         49902-50007
            1091-1179           AL732579.5         50302-50390
            1180-1293           AL732579.5         53598-53711
            1294-1405           AL732579.5         59539-59650
            1406-1559           AL732579.5         61283-61436
            1560-1649           AL732579.5         65839-65928
            1650-1680           AL732579.5         67085-67115
            1681-1760           AL732579.5         70367-70446
            1761-1866           AL732579.5         77029-77134
            1867-4684           AL732579.5         81405-84222
FEATURES             Location/Qualifiers
     source          1..4684
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xq26.3"
     gene            1..4684
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /note="solute carrier family 9 member A6"
                     /db_xref="GeneID:10479"
                     /db_xref="HGNC:HGNC:11079"
                     /db_xref="MIM:300231"
     exon            1..43
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            44..268
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     CDS             100..2139
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /note="isoform 5 is encoded by transcript variant 7;
                     solute carrier family 9, subfamily A (NHE6, cation proton
                     antiporter 6), member 6; Na(+)/H(+) exchanger 6; solute
                     carrier family 9 (sodium/hydrogen exchanger), member 6"
                     /codon_start=1
                     /product="sodium/hydrogen exchanger 6 isoform 5"
                     /protein_id="NP_001366039.1"
                     /db_xref="CCDS:CCDS94676.1"
                     /db_xref="GeneID:10479"
                     /db_xref="HGNC:HGNC:11079"
                     /db_xref="MIM:300231"
                     /translation="MDEEIVSEKQAEESHRQDSANLLIFILLLTLTILTIWLFKHRRA
                     RFLHETGLAMIYGLLVGLVLRYGIHVPSDVNNVTLSCEVQSSPTTLLVNVSGKFYEYM
                     LKGEISSHELNNVQDNEMLRKVTFDPEVFFNILLPPIIFYAGYSLKRRHFFRNLGSIL
                     AYAFLGTAISCFVIGSIMYGCVTLMKVTGQLAGDFYFTDCLLFGAIVSATDPVTVLAI
                     FHELQVDVELYALLFGESVLNDAVAIVLSSSIVAYQPAGDNSHTFDVTAMFKSIGIFL
                     GIFSGSFAMGAATGVVTALVTKFTKLREFQLLETGLFFLMSWSTFLLAEAWGFTGVVA
                     VLFCGITQAHYTYNNLSTESQHRTKQLFELLNFLAENFIFSYMGLTLFTFQNHVFNPT
                     FVVGAFVAIFLGRAANIYPLSLLLNLGRRSKIGSNFQHMMMFAGLRGAMAFALAIRDT
                     ATYARQMMFSTTLLIVFFTVWVFGGGTTAMLSCLHIRYCARLWGYRDELRHGLYPQGT
                     HSLFGETDRVGVDSDQEHLGVPENERRTTKAESAWLFRMWYNFDHNYLKPLLTHSGPP
                     LTTTLPACCGPIARCLTSPQAYENQEQLKDDDSDLILNDGDISLTYGDSTVNTEPATS
                     SAPRRFMGNSSEDALDRELAFGDHELVIRGTRLVLPMDDSEPPLNLLDNTRHGPA"
     exon            269..468
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            469..546
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            547..623
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            624..736
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            737..842
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            843..984
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            985..1090
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            1091..1179
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            1180..1293
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            1294..1405
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            1406..1559
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            1560..1649
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            1650..1680
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            1681..1760
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            1761..1866
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     exon            1867..4684
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4515..4520
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /note="hexamer: ATTAAA"
     polyA_site      4542
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /note="major polyA site"
     regulatory      4658..4663
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
                     /note="hexamer: AACAAA"
     polyA_site      4684
                     /gene="SLC9A6"
                     /gene_synonym="MRSA; MRXSCH; NDPACX; NHE6"
ORIGIN      
        1 gagccctcgg ggagtggtcc gaccgcgggc ggccgccggt gagtgggcgt ctttgactgg
       61 gcaggggctt cggacggcgg cggcggagag gctagagcca tggacgagga gatcgtgtcc
      121 gagaagcaag ccgaggagag ccaccggcag gacagcgcca acctgctcat cttcatcctg
      181 ctgctcaccc tcaccattct cacaatctgg ctcttcaagc accgccgggc ccgcttcctg
      241 cacgaaaccg gcctggctat gatttatggt cttttggtgg gccttgtgct tcggtatggc
      301 attcatgttc cgagtgatgt aaataatgtg accctgagct gtgaagtgca gtcaagtcca
      361 actaccttac tggtaaatgt tagtggaaaa ttttatgagt atatgctgaa aggagagatt
      421 agttcacatg aactcaataa tgttcaagat aatgaaatgc ttagaaaggt tacttttgat
      481 ccagaagtat ttttcaacat attacttcct cctatcatat tttatgcagg ttatagcctg
      541 aaaaggagac atttttttcg aaatcttggg tctatcctag catacgcttt tcttggaaca
      601 gcaatttctt gtttcgttat tgggtcaata atgtatggct gtgtaacgct gatgaaggta
      661 acgggacaac ttgcaggaga tttttacttt acagattgcc tactgtttgg tgccattgta
      721 tcagcaactg atccagtgac tgttcttgct atattccacg agcttcaagt tgatgttgaa
      781 ctctatgcac ttctttttgg tgaaagtgtc ctcaatgatg ctgttgccat agtgctgtcc
      841 tcctcaatag tggcatacca gccagctgga gacaacagtc acacctttga tgtcacagcg
      901 atgttcaagt ctattgggat cttccttgga atcttcagtg gatcttttgc aatgggtgct
      961 gctactggag tggtgacagc tttagtgaca aagttcacca aattacggga gttccagttg
     1021 ttggagacag gcctgttctt cttgatgtcc tggagtacct tcctcttggc tgaagcatgg
     1081 ggcttcacag gtgtagttgc agtattgttt tgtggcatca cacaagcaca ttatacgtat
     1141 aataatttgt ccacggagtc tcagcataga actaaacagt tgtttgagct tctcaatttc
     1201 ttggcagaga atttcatctt ctcctacatg gggctgacac tgttcacctt ccagaaccat
     1261 gtctttaacc caacatttgt agtaggagca tttgttgcta ttttcttggg aagagctgcc
     1321 aatatttacc ccttgtccct cttacttaat ttgggtagaa gaagtaagat tggatcaaat
     1381 tttcaacaca tgatgatgtt tgctggcctt cgtggtgcaa tggcatttgc cttggccatt
     1441 cgagatactg ccacttatgc acggcaaatg atgttcagca ccacgcttct gattgtgttt
     1501 tttaccgtgt gggtatttgg tggtggcacc actgcaatgc tgtcatgctt gcatatcagg
     1561 tactgtgcta gactctgggg atacagagat gaattgagac atggccttta ccctcaagga
     1621 actcacagtc tttttgggga gactgacagg gttggtgttg attcagacca agaacacttg
     1681 ggtgttcctg aaaatgaaag gagaactacc aaagcagaga gtgcttggct tttccggatg
     1741 tggtacaact ttgatcataa ctatctgaag cctctgctga cccacagcgg gcctccgctg
     1801 acaacaacac tccctgcctg ctgtggaccc atcgccaggt gcctcaccag cccccaggct
     1861 tacgaaaacc aggaacagtt gaaagatgat gattctgatc ttattctcaa tgatggtgac
     1921 atcagtttga catatggaga ttctactgtg aacactgaac cggccacatc cagcgcccca
     1981 aggagattta tgggaaacag ttctgaagat gccttggatc gggagcttgc atttggggac
     2041 catgaactgg tcattcgagg aacacgcctg gttcttccaa tggatgattc tgaacccccg
     2101 ctaaatttgt tagataatac gagacatggt ccagcctaag cttactaata ctcacttagt
     2161 gatttgtaaa atttgcacat gtgattgtga agaaatttgt actacctaaa agtcccagtg
     2221 catgtctctg aatgtgtaag ctatataaat gctatttata tggcatagaa agaatataaa
     2281 tatcctgtac acggcagatt gtgaacaaac tatattcctt taagttttcc tggttgcact
     2341 ctgtagactg gatctgtttt aggaagttac tttcacagtg atgttgtgtg ttctgttagt
     2401 tttatgtctc agttaaagtg taaaaagtga cggattttct ctttcttaaa cttacctgac
     2461 acttaaccag agtaccagtt ctcgtgatgt gaattaattt ttttgtgtgc taggggaggg
     2521 agagtgagga gggagtgtta tttccttggg aacctaggga ggagaggttc ctttgttggg
     2581 aaacttttgt tgatagctgc tgcctttgtc ctgatcgttt tctttccctt ttctctggtg
     2641 gcctgttgtg gtgcaacgag ctgatggcat ttgatcttgc cccattcagg ttggggagtg
     2701 aagtgtgagg acccttttcc cccgcttgct gtgaaagcac agattcattg actacagtac
     2761 actgttgttc agaaaagaag gctgcaaatg acttctgaga ctttatgtct tttcttccag
     2821 accaagaccg tagaaggagt cacatctagc cggcttagcc aaagtacagg tgtatatagt
     2881 tcagggcact tgatttagat ttggaggggc tggggtgggc agagagcaag aggcgagtaa
     2941 agagaatggt ggtttcagag atctctcttc ccaaatgtgt aaatattcta taccagataa
     3001 gtttaaataa gaaatttaat tgctgcttaa tttttgatta tgtactttat ctgtatagca
     3061 ggctttgtcg tcagaagttt ttatatcgat ttaaattgct gctctttagc agccaaacag
     3121 gagcaaaatg taaaattttt gaacttactg tgtctaatca tcatttgtta gtctgtagtt
     3181 aatgtcaaca gttaatttat gaacccacga tcgttccaca ctgcaccaaa gtcagtcata
     3241 agagaaatcg aatattctgg agcactgatt gcagcagggt ggctcctttg tgtgcagcag
     3301 gtgtagtagt cttcattttc atggtacgtt ttaatattaa ttacctaagc tgccatgcat
     3361 tttttttttt acagttctca aggaagagca cagaacaatt tctcatttca tatttggagt
     3421 atgaaagtag attctatttt gtaatgctga taatacctaa agatgcattg aatgcttgga
     3481 agaatgcttt ttgatgttga ttttgacctg ttcatgattc agaagaaaaa caaacttttt
     3541 tggatttttt ttccctcagg tctgagtagc attgccttaa atcttatcca gttagaacat
     3601 tgatttattt acatgatgtt cagattttcc agtgaaaaat acccttctga acaaaacatg
     3661 tacttactct ccgaaaggca tctatctgtg ctattgcaaa cactccttga gattttaggg
     3721 gaattctaat gttgtaccct ttcgtggcag ctttgactgt tggcatagcc atttgttatg
     3781 tagtggtagc gactttcctg ctatgcagga atccctccca tgacgtgtat gttttacatg
     3841 atgtgtgcct cttcacgcag taaatagttt cttgttaatg tatgtttgag gagtttgaac
     3901 gtcagtgtca cttacccaca aagttattca agttgtaaaa ggttatacaa taatttaaca
     3961 actacctttt ttattctgtc gggttactga cctcacttta tgtaaatact tcgcatgaca
     4021 aattcagtaa ctcgtctatt tcagcatgca taagactttt cactagggaa actgataaag
     4081 cttgagtcaa ctaaatctgc cttcatactt tatcaagggg aaccaagcct gctgtgctta
     4141 catcagcatc tggaagactt tcctctcctc taatctgtgt acacatctcc aagcaaggaa
     4201 gaaaaaacaa actctgctca gacgcctatg aaacacctga atgaactttg atgaagtaca
     4261 gtctgagtta ccatcatgca caagtagaac tgctcttgga cttgttttcc tgttgtttgt
     4321 ggaacctacg cgtttgaatg gcttgaacgt tgcatctttt aaagttattt tttaaggttt
     4381 cttggcattt atcctagttg tccgtgtttg gcaatgtgct gttaaagtaa tagactttta
     4441 atctttatgt attttttgtt ttctctggag tacttggaca gatgttatag tggtttcttt
     4501 taggaaaatc tgtcattaaa aaagttatag ccttgcaaat aaccactcac agtatttgag
     4561 tcacagttta ttttagtgag acgtaaagag tgctgacttc atttattttt ctacctatat
     4621 acctagtgga aaaggggaag actaatgttt tcaaataaac aaacagaaac ctaacagaac
     4681 ttaa
//
