LOCUS       NM_006019               2668 bp    mRNA    linear   PRI 12-FEB-2025
DEFINITION  Homo sapiens T cell immune regulator 1, ATPase H+ transporting V0
            subunit a3 (TCIRG1), transcript variant 1, mRNA.
ACCESSION   NM_006019
VERSION     NM_006019.4
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 2668)
  AUTHORS   Jodeh,W., Katz,A.J., Hart,M., Warden,S.J., Niziolek,P., Alam,I.,
            Ing,S., Polgreen,L.E., Imel,E.A. and Econs,M.J.
  TITLE     Autosomal Dominant Osteopetrosis (ADO) Caused by a Missense Variant
            in the TCIRG1 Gene
  JOURNAL   J Clin Endocrinol Metab 109 (7), 1726-1732 (2024)
   PUBMED   38261998
  REMARK    GeneRIF: Autosomal Dominant Osteopetrosis (ADO) Caused by a
            Missense Variant in the TCIRG1 Gene.
REFERENCE   2  (bases 1 to 2668)
  AUTHORS   El-Kamah,G.Y., Mehrez,M.I., Taher,M.B., El-Bassyouni,H.T.,
            Gaber,K.R. and Amr,K.S.
  TITLE     Outlining the Clinical Profile of TCIRG1 14 Variants including 5
            Novels with Overview of ARO Phenotype and Ethnic Impact in 20
            Egyptian Families
  JOURNAL   Genes (Basel) 14 (4), 900 (2023)
   PUBMED   37107657
  REMARK    GeneRIF: Outlining the Clinical Profile of TCIRG1 14 Variants
            including 5 Novels with Overview of ARO Phenotype and Ethnic Impact
            in 20 Egyptian Families.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2668)
  AUTHORS   Capo,V., Abinun,M. and Villa,A.
  TITLE     Osteoclast rich osteopetrosis due to defects in the TCIRG1 gene
  JOURNAL   Bone 165, 116519 (2022)
   PUBMED   35981697
  REMARK    GeneRIF: Osteoclast rich osteopetrosis due to defects in the TCIRG1
            gene.
REFERENCE   4  (bases 1 to 2668)
  AUTHORS   Smirnova,A.S., Morgun,A., Shulzhenko,N., Silva,I.D. and
            Gerbase-DeLima,M.
  TITLE     Identification of new alternative splice events in the TCIRG1 gene
            in different human tissues
  JOURNAL   Biochem Biophys Res Commun 330 (3), 943-949 (2005)
   PUBMED   15809087
  REMARK    GeneRIF: we validated by RT-PCR six new alternative splice events
            in TCIRG1 in most of the 28 human tissues studied
REFERENCE   5  (bases 1 to 2668)
  AUTHORS   Smith,A.N., Lovering,R.C., Futai,M., Takeda,J., Brown,D. and
            Karet,F.E.
  TITLE     Revised nomenclature for mammalian vacuolar-type H+ -ATPase subunit
            genes
  JOURNAL   Mol Cell 12 (4), 801-803 (2003)
   PUBMED   14580332
REFERENCE   6  (bases 1 to 2668)
  AUTHORS   Heinemann,T., Bulwin,G.C., Randall,J., Schnieders,B., Sandhoff,K.,
            Volk,H.D., Milford,E., Gullans,S.R. and Utku,N.
  TITLE     Genomic organization of the gene coding for TIRC7, a novel membrane
            protein essential for T cell activation
  JOURNAL   Genomics 57 (3), 398-406 (1999)
   PUBMED   10329006
REFERENCE   7  (bases 1 to 2668)
  AUTHORS   Finbow,M.E. and Harrison,M.A.
  TITLE     The vacuolar H+-ATPase: a universal proton pump of eukaryotes
  JOURNAL   Biochem J 324 (Pt 3) (Pt 3), 697-712 (1997)
   PUBMED   9210392
  REMARK    Review article
REFERENCE   8  (bases 1 to 2668)
  AUTHORS   Stevens,T.H. and Forgac,M.
  TITLE     Structure, function and regulation of the vacuolar (H+)-ATPase
  JOURNAL   Annu Rev Cell Dev Biol 13, 779-808 (1997)
   PUBMED   9442887
  REMARK    Review article
REFERENCE   9  (bases 1 to 2668)
  AUTHORS   Li,Y.P., Chen,W. and Stashenko,P.
  TITLE     Molecular cloning and characterization of a putative novel human
            osteoclast-specific 116-kDa vacuolar proton pump subunit
  JOURNAL   Biochem Biophys Res Commun 218 (3), 813-821 (1996)
   PUBMED   8579597
REFERENCE   10 (bases 1 to 2668)
  AUTHORS   Dautry-Varsat,A.
  TITLE     Receptor-mediated endocytosis: the intracellular journey of
            transferrin and its receptor
  JOURNAL   Biochimie 68 (3), 375-381 (1986)
   PUBMED   2874839
  REMARK    Review article
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AP002807.3.
            
            On Nov 23, 2018 this sequence version replaced NM_006019.3.
            
            Summary: This gene encodes a subunit of a large protein complex
            known as a vacuolar H+-ATPase (V-ATPase). The protein complex acts
            as a pump to move protons across the membrane. This movement of
            protons helps regulate the pH of cells and their surrounding
            environment. V-ATPase dependent organelle acidification is
            necessary for such intracellular processes as protein sorting,
            zymogen activation, and receptor-mediated endocytosis. V-ATPase is
            comprised of a cytosolic V1 domain and a transmembrane V0 domain.
            Alternative splicing results in multiple transcript variants.
            Mutations in this gene are associated with infantile malignant
            osteopetrosis. [provided by RefSeq, May 2017].
            
            Transcript Variant: This variant (1) encodes isoform a, also known
            as the OC116 protein because it is one of three V-ATPase 116 kD
            subunits. It is also referred to as the a3 isoform and is induced
            on osteoclast differentiation. This variant contains a unique 5'
            end and lacks an internal segment compared to variant 2, which
            results in an isoform (a) with a different N-terminus than that of
            isoform b.
            
            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 :: BC018133.1, SRR1803613.46571.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000265686.8/ ENSP00000265686.3
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-95                AP002807.3         10437-10531
            96-216              AP002807.3         12680-12800
            217-295             AP002807.3         13165-13243
            296-516             AP002807.3         14055-14275
            517-602             AP002807.3         14358-14443
            603-729             AP002807.3         14783-14909
            730-812             AP002807.3         14983-15065
            813-906             AP002807.3         15226-15319
            907-1119            AP002807.3         15544-15756
            1120-1264           AP002807.3         16370-16514
            1265-1404           AP002807.3         18845-18984
            1405-1562           AP002807.3         19059-19216
            1563-1653           AP002807.3         19294-19384
            1654-1772           AP002807.3         20291-20409
            1773-1986           AP002807.3         20493-20706
            1987-2112           AP002807.3         21075-21200
            2113-2217           AP002807.3         21374-21478
            2218-2335           AP002807.3         21549-21666
            2336-2513           AP002807.3         21899-22076
            2514-2668           AP002807.3         22153-22307
FEATURES             Location/Qualifiers
     source          1..2668
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="11"
                     /map="11q13.2"
     gene            1..2668
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /note="T cell immune regulator 1, ATPase H+ transporting
                     V0 subunit a3"
                     /db_xref="GeneID:10312"
                     /db_xref="HGNC:HGNC:11647"
                     /db_xref="MIM:604592"
     exon            1..95
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            96..216
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     CDS             100..2592
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /EC_number="7.1.2.1"
                     /note="isoform a is encoded by transcript variant 1;
                     T-cell immune response cDNA 7; T-cell, immune regulator 1,
                     ATPase, H+ transporting, lysosomal V0 protein a; T-cell,
                     immune regulator 1, ATPase, H+ transporting, lysosomal V0
                     subunit A3; ATPase, H+ transporting, 116kD; V-ATPase
                     116-kDa; osteoclastic proton pump 116 kDa subunit;
                     vacuolar proton translocating ATPase 116 kDa subunit A;
                     specific 116-kDa vacuolar proton pump subunit; V-type
                     proton ATPase 116 kDa subunit a; V-ATPase 116 kDa subunit
                     a 3; V-ATPase 116 kDa subunit a3; V-type proton ATPase 116
                     kDa subunit a3; V-ATPase subunit a3; V-type proton ATPase
                     116 kDa subunit a 3"
                     /codon_start=1
                     /product="V-type proton ATPase 116 kDa subunit a 3 isoform
                     a"
                     /protein_id="NP_006010.2"
                     /db_xref="CCDS:CCDS8177.1"
                     /db_xref="GeneID:10312"
                     /db_xref="HGNC:HGNC:11647"
                     /db_xref="MIM:604592"
                     /translation="MGSMFRSEEVALVQLFLPTAAAYTCVSRLGELGLVEFRDLNASV
                     SAFQRRFVVDVRRCEELEKTFTFLQEEVRRAGLVLPPPKGRLPAPPPRDLLRIQEETE
                     RLAQELRDVRGNQQALRAQLHQLQLHAAVLRQGHEPQLAAAHTDGASERTPLLQAPGG
                     PHQDLRVNFVAGAVEPHKAPALERLLWRACRGFLIASFRELEQPLEHPVTGEPATWMT
                     FLISYWGEQIGQKIRKITDCFHCHVFPFLQQEEARLGALQQLQQQSQELQEVLGETER
                     FLSQVLGRVLQLLPPGQVQVHKMKAVYLALNQCSVSTTHKCLIAEAWCSVRDLPALQE
                     ALRDSSMEEGVSAVAHRIPCRDMPPTLIRTNRFTASFQGIVDAYGVGRYQEVNPAPYT
                     IITFPFLFAVMFGDVGHGLLMFLFALAMVLAENRPAVKAAQNEIWQTFFRGRYLLLLM
                     GLFSIYTGFIYNECFSRATSIFPSGWSVAAMANQSGWSDAFLAQHTMLTLDPNVTGVF
                     LGPYPFGIDPIWSLAANHLSFLNSFKMKMSVILGVVHMAFGVVLGVFNHVHFGQRHRL
                     LLETLPELTFLLGLFGYLVFLVIYKWLCVWAARAASAPSILIHFINMFLFSHSPSNRL
                     LYPRQEVVQATLVVLALAMVPILLLGTPLHLLHRHRRRLRRRPADRQEENKAGLLDLP
                     DASVNGWSSDEEKAGGLDDEEEAELVPSEVLMHQAIHTIEFCLGCVSNTASYLRLWAL
                     SLAHAQLSEVLWAMVMRIGLGLGREVGVAAVVLVPIFAAFAVMTVAILLVMEGLSAFL
                     HALRLHWVEFQNKFYSGTGYKLSPFTFAATDD"
     exon            217..295
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            296..516
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            517..602
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            603..729
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            730..812
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            813..906
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            907..1119
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            1120..1264
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            1265..1404
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            1405..1562
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            1563..1653
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            1654..1772
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            1773..1986
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            1987..2112
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            2113..2217
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            2218..2335
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            2336..2513
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     exon            2514..2668
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2646..2651
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /note="hexamer: AATAAA"
     polyA_site      2668
                     /gene="TCIRG1"
                     /gene_synonym="a3; Atp6i; ATP6N1C; ATP6V0A3; OC-116kDa;
                     OC116; OPTB1; Stv1; TIRC7; Vph1"
                     /note="major polyA site"
ORIGIN      
        1 agtcccgggc tggcgggagt gcagttctga gtcccgcccg gcgtgcgcgg agcggggcag
       61 ccagcagcgg aggcgcggcg cgcagcacac ccggggacca tgggctccat gttccggagc
      121 gaggaggtgg ccctggtcca gctctttctg cccacagcgg ctgcctacac ctgcgtgagt
      181 cggctgggcg agctgggcct cgtggagttc agagacctca acgcctcggt gagcgccttc
      241 cagagacgct ttgtggttga tgttcggcgc tgtgaggagc tggagaagac cttcaccttc
      301 ctgcaggagg aggtgcggcg ggctgggctg gtcctgcccc cgccaaaggg gaggctgccg
      361 gcacccccac cccgggacct gctgcgcatc caggaggaga cggagcgcct ggcccaggag
      421 ctgcgggatg tgcggggcaa ccagcaggcc ctgcgggccc agctgcacca gctgcagctc
      481 cacgccgccg tgctacgcca gggccatgaa cctcagctgg cagccgccca cacagatggg
      541 gcctcagaga ggacgcccct gctccaggcc cccggggggc cgcaccagga cctgagggtc
      601 aactttgtgg caggtgccgt ggagccccac aaggcccctg ccctagagcg cctgctctgg
      661 agggcctgcc gcggcttcct cattgccagc ttcagggagc tggagcagcc gctggagcac
      721 cccgtgacgg gcgagccagc cacgtggatg accttcctca tctcctactg gggtgagcag
      781 atcggacaga agatccgcaa gatcacggac tgcttccact gccacgtctt cccgtttctg
      841 cagcaggagg aggcccgcct cggggccctg cagcagctgc aacagcagag ccaggagctg
      901 caggaggtcc tcggggagac agagcggttc ctgagccagg tgctaggccg ggtgctgcag
      961 ctgctgccgc cagggcaggt gcaggtccac aagatgaagg ccgtgtacct ggccctgaac
     1021 cagtgcagcg tgagcaccac gcacaagtgc ctcattgccg aggcctggtg ctctgtgcga
     1081 gacctgcccg ccctgcagga ggccctgcgg gacagctcga tggaggaggg agtgagtgcc
     1141 gtggctcacc gcatcccctg ccgggacatg ccccccacac tcatccgcac caaccgcttc
     1201 acggccagct tccagggcat cgtggatgcc tacggcgtgg gccgctacca ggaggtcaac
     1261 cccgctccct acaccatcat caccttcccc ttcctgtttg ctgtgatgtt cggggatgtg
     1321 ggccacgggc tgctcatgtt cctgttcgcc ctggccatgg tccttgcgga gaaccgaccg
     1381 gctgtgaagg ccgcgcagaa cgagatctgg cagactttct tcaggggccg ctacctgctc
     1441 ctgcttatgg gcctgttctc catctacacc ggcttcatct acaacgagtg cttcagtcgc
     1501 gccaccagca tcttcccctc gggctggagt gtggccgcca tggccaacca gtctggctgg
     1561 agtgatgcat tcctggccca gcacacgatg cttaccctgg atcccaacgt caccggtgtc
     1621 ttcctgggac cctacccctt tggcatcgat cctatttgga gcctggctgc caaccacttg
     1681 agcttcctca actccttcaa gatgaagatg tccgtcatcc tgggcgtcgt gcacatggcc
     1741 tttggggtgg tcctcggagt cttcaaccac gtgcactttg gccagaggca ccggctgctg
     1801 ctggagacgc tgccggagct caccttcctg ctgggactct tcggttacct cgtgttccta
     1861 gtcatctaca agtggctgtg tgtctgggct gccagggccg cctcggcccc cagcatcctc
     1921 atccacttca tcaacatgtt cctcttctcc cacagcccca gcaacaggct gctctacccc
     1981 cggcaggagg tggtccaggc cacgctggtg gtcctggcct tggccatggt gcccatcctg
     2041 ctgcttggca cacccctgca cctgctgcac cgccaccgcc gccgcctgcg gaggaggccc
     2101 gctgaccgac aggaggaaaa caaggccggg ttgctggacc tgcctgacgc atctgtgaat
     2161 ggctggagct ccgatgagga aaaggcaggg ggcctggatg atgaagagga ggccgagctc
     2221 gtcccctccg aggtgctcat gcaccaggcc atccacacca tcgagttctg cctgggctgc
     2281 gtctccaaca ccgcctccta cctgcgcctg tgggccctga gcctggccca cgcccagctg
     2341 tccgaggttc tgtgggccat ggtgatgcgc ataggcctgg gcctgggccg ggaggtgggc
     2401 gtggcggctg tggtgctggt ccccatcttt gccgcctttg ccgtgatgac cgtggctatc
     2461 ctgctggtga tggagggact ctcagccttc ctgcacgccc tgcggctgca ctgggtggaa
     2521 ttccagaaca agttctactc aggcacgggc tacaagctga gtcccttcac cttcgctgcc
     2581 acagatgact agggcccact gcaggtcctg ccagacctcc ttcctgacct ctgaggcagg
     2641 agaggaataa agacggtccg ccctggca
//
