LOCUS       NM_006521               3291 bp    mRNA    linear   PRI 15-OCT-2024
DEFINITION  Homo sapiens transcription factor binding to IGHM enhancer 3
            (TFE3), transcript variant 1, mRNA.
ACCESSION   NM_006521
VERSION     NM_006521.6
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 3291)
  AUTHORS   Patel,A.A., Kim,H., Ramesh,R., Marquez,A., Faraj,M.M.,
            Antikainen,H., Lee,A.S., Torres,A., Khawaja,I.M., Heffernan,C.,
            Bonder,E.M., Maurel,P., Svaren,J., Son,Y.J., Dobrowolski,R. and
            Kim,H.A.
  TITLE     TFEB/3 Govern Repair Schwann Cell Generation and Function Following
            Peripheral Nerve Injury
  JOURNAL   J Neurosci 44 (35), e0198242024 (2024)
   PUBMED   39054068
  REMARK    GeneRIF: TFEB/3 Govern Repair Schwann Cell Generation and Function
            Following Peripheral Nerve Injury.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3291)
  AUTHORS   Qin,Y., Yang,L., Zhang,H.J., Wei,J., Liu,Y.X., Zhang,W.H., Wen,Z.,
            Wang,Z. and Fan,L.N.
  TITLE     [TFE3-rearranged perivascular epithelioid cell tumors: a
            clinicopathological analysis of eight cases]
  JOURNAL   Zhonghua Bing Li Xue Za Zhi 53 (8), 822-829 (2024)
   PUBMED   39103264
  REMARK    GeneRIF: [TFE3-rearranged perivascular epithelioid cell tumors: a
            clinicopathological analysis of eight cases].
REFERENCE   3  (bases 1 to 3291)
  AUTHORS   Lee,C.R., Suh,J., Jang,D., Jin,B.Y., Cho,J., Lee,M., Sim,H.,
            Kang,M., Lee,J., Park,J.H., Lee,K.H., Hwang,G.S., Moon,K.C.,
            Song,C., Ku,J.H., Kwak,C., Kim,H.H., Cho,S.Y., Choi,M. and
            Jeong,C.W.
  TITLE     Comprehensive molecular characterization of TFE3-rearranged renal
            cell carcinoma
  JOURNAL   Exp Mol Med 56 (8), 1807-1815 (2024)
   PUBMED   39085357
  REMARK    GeneRIF: Comprehensive molecular characterization of
            TFE3-rearranged renal cell carcinoma.
REFERENCE   4  (bases 1 to 3291)
  AUTHORS   Clark,J., Lu,Y.J., Sidhar,S.K., Parker,C., Gill,S., Smedley,D.,
            Hamoudi,R., Linehan,W.M., Shipley,J. and Cooper,C.S.
  TITLE     Fusion of splicing factor genes PSF and NonO (p54nrb) to the TFE3
            gene in papillary renal cell carcinoma
  JOURNAL   Oncogene 15 (18), 2233-2239 (1997)
   PUBMED   9393982
REFERENCE   5  (bases 1 to 3291)
  AUTHORS   Weterman,M.A., Wilbrink,M. and Geurts van Kessel,A.
  TITLE     Fusion of the transcription factor TFE3 gene to a novel gene, PRCC,
            in t(X;1)(p11;q21)-positive papillary renal cell carcinomas
  JOURNAL   Proc Natl Acad Sci U S A 93 (26), 15294-15298 (1996)
   PUBMED   8986805
REFERENCE   6  (bases 1 to 3291)
  AUTHORS   Sidhar,S.K., Clark,J., Gill,S., Hamoudi,R., Crew,A.J., Gwilliam,R.,
            Ross,M., Linehan,W.M., Birdsall,S., Shipley,J. and Cooper,C.S.
  TITLE     The t(X;1)(p11.2;q21.2) translocation in papillary renal cell
            carcinoma fuses a novel gene PRCC to the TFE3 transcription factor
            gene
  JOURNAL   Hum Mol Genet 5 (9), 1333-1338 (1996)
   PUBMED   8872474
REFERENCE   7  (bases 1 to 3291)
  AUTHORS   Macchi,P., Notarangelo,L., Giliani,S., Strina,D., Repetto,M.,
            Sacco,M.G., Vezzoni,P. and Villa,A.
  TITLE     The genomic organization of the human transcription factor 3 (TFE3)
            gene
  JOURNAL   Genomics 28 (3), 491-494 (1995)
   PUBMED   7490085
REFERENCE   8  (bases 1 to 3291)
  AUTHORS   Henthorn,P.S., Stewart,C.C., Kadesch,T. and Puck,J.M.
  TITLE     The gene encoding human TFE3, a transcription factor that binds the
            immunoglobulin heavy-chain enhancer, maps to Xp11.22
  JOURNAL   Genomics 11 (2), 374-378 (1991)
   PUBMED   1685140
REFERENCE   9  (bases 1 to 3291)
  AUTHORS   Puck,J.M., Stewart,C.C. and Henthorn,P.S.
  TITLE     A high-frequency RFLP at the human TFE3 locus on the X chromosome
  JOURNAL   Nucleic Acids Res 19 (3), 684 (1991)
   PUBMED   1672758
REFERENCE   10 (bases 1 to 3291)
  AUTHORS   Beckmann,H., Su,L.K. and Kadesch,T.
  TITLE     TFE3: a helix-loop-helix protein that activates transcription
            through the immunoglobulin enhancer muE3 motif
  JOURNAL   Genes Dev 4 (2), 167-179 (1990)
   PUBMED   2338243
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from HY157114.1, BM904206.1,
            BC026027.1 and AL161985.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_006521.5.
            
            Summary: This gene encodes a basic helix-loop-helix
            domain-containing transcription factor that binds MUE3-type E-box
            sequences in the promoter of genes. The encoded protein promotes
            the expression of genes downstream of transforming growth factor
            beta (TGF-beta) signaling. This gene may be involved in chromosomal
            translocations in renal cell carcinomas and other cancers,
            resulting in the production of fusion proteins. Translocation
            partners include PRCC (papillary renal cell carcinoma), NONO
            (non-POU domain containing, octamer-binding), and ASPSCR1 (alveolar
            soft part sarcoma chromosome region, candidate 1), among other
            genes. Alternative splicing results in multiple transcript
            variants. [provided by RefSeq, Aug 2013].
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the longer 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 :: BC026027.1, X96717.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000315869.8/ ENSP00000314129.7
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-36                HY157114.1         161-196
            37-662              BM904206.1         49-674
            663-1453            BC026027.1         770-1560
            1454-3291           AL161985.1         1450-3287
FEATURES             Location/Qualifiers
     source          1..3291
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xp11.23"
     gene            1..3291
                     /gene="TFE3"
                     /gene_synonym="bHLHe33; MRXSPF; RCCP2; RCCX1; TFEA"
                     /note="transcription factor binding to IGHM enhancer 3"
                     /db_xref="GeneID:7030"
                     /db_xref="HGNC:HGNC:11752"
                     /db_xref="MIM:314310"
     exon            1..247
                     /gene="TFE3"
                     /gene_synonym="bHLHe33; MRXSPF; RCCP2; RCCX1; TFEA"
                     /inference="alignment:Splign:2.1.0"
     CDS             132..1859
                     /gene="TFE3"
                     /gene_synonym="bHLHe33; MRXSPF; RCCP2; RCCX1; TFEA"
                     /note="isoform 1 is encoded by transcript variant 1;
                     transcription factor for IgH enhancer; transcription
                     factor E family, member A; transcription factor E3; class
                     E basic helix-loop-helix protein 33; transcription factor
                     for immunoglobulin heavy-chain enhancer 3"
                     /codon_start=1
                     /product="transcription factor E3 isoform 1"
                     /protein_id="NP_006512.2"
                     /db_xref="CCDS:CCDS14315.3"
                     /db_xref="GeneID:7030"
                     /db_xref="HGNC:HGNC:11752"
                     /db_xref="MIM:314310"
                     /translation="MSHAAEPARDGVEASAEGPRAVFVLLEERRPADSAQLLSLNSLL
                     PESGIVADIELENVLDPDSFYELKSQPLPLRSSLPISLQATPATPATLSASSSAGGSR
                     TPAMSSSSSSRVLLRQQLMRAQAQEQERRERREQAAAAPFPSPAPASPAISVVGVSAG
                     GHTLSRPPPAQVPREVLKVQTHLENPTRYHLQQARRQQVKQYLSTTLGPKLASQALTP
                     PPGPASAQPLPAPEAAHTTGPTGSAPNSPMALLTIGSSSEKEIDDVIDEIISLESSYN
                     DEMLSYLPGGTTGLQLPSTLPVSGNLLDVYSSQGVATPAITVSNSCPAELPNIKREIS
                     ETEAKALLKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSSDPEMRWNKGTILKAS
                     VDYIRKLQKEQQRSKDLESRQRSLEQANRSLQLRIQELELQAQIHGLPVPPTPGLLSL
                     ATTSASDSLKPEQLDIEEEGRPGAATFHVGGGPAQNAPHQQPPAPPSDALLDLHFPSD
                     HLGDLGDPFHLGLEDILMEEEEGVVGGLSGGALSPLRAASDPLLSSVSPAVSKASSRR
                     SSFSMEEES"
     exon            248..361
                     /gene="TFE3"
                     /gene_synonym="bHLHe33; MRXSPF; RCCP2; RCCX1; TFEA"
                     /inference="alignment:Splign:2.1.0"
     exon            362..665
                     /gene="TFE3"
                     /gene_synonym="bHLHe33; MRXSPF; RCCP2; RCCX1; TFEA"
                     /inference="alignment:Splign:2.1.0"
     exon            666..911
                     /gene="TFE3"
                     /gene_synonym="bHLHe33; MRXSPF; RCCP2; RCCX1; TFEA"
                     /inference="alignment:Splign:2.1.0"
     exon            912..1016
                     /gene="TFE3"
                     /gene_synonym="bHLHe33; MRXSPF; RCCP2; RCCX1; TFEA"
                     /inference="alignment:Splign:2.1.0"
     exon            1017..1134
                     /gene="TFE3"
                     /gene_synonym="bHLHe33; MRXSPF; RCCP2; RCCX1; TFEA"
                     /inference="alignment:Splign:2.1.0"
     exon            1135..1191
                     /gene="TFE3"
                     /gene_synonym="bHLHe33; MRXSPF; RCCP2; RCCX1; TFEA"
                     /inference="alignment:Splign:2.1.0"
     exon            1192..1267
                     /gene="TFE3"
                     /gene_synonym="bHLHe33; MRXSPF; RCCP2; RCCX1; TFEA"
                     /inference="alignment:Splign:2.1.0"
     exon            1268..1415
                     /gene="TFE3"
                     /gene_synonym="bHLHe33; MRXSPF; RCCP2; RCCX1; TFEA"
                     /inference="alignment:Splign:2.1.0"
     exon            1416..3291
                     /gene="TFE3"
                     /gene_synonym="bHLHe33; MRXSPF; RCCP2; RCCX1; TFEA"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3249..3254
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TFE3"
                     /gene_synonym="bHLHe33; MRXSPF; RCCP2; RCCX1; TFEA"
                     /note="hexamer: AATAAA"
     polyA_site      3291
                     /gene="TFE3"
                     /gene_synonym="bHLHe33; MRXSPF; RCCP2; RCCX1; TFEA"
                     /note="major polyA site"
ORIGIN      
        1 gcagtgctag ctccatggct tagcggagga ggcggcggtg gcgagctggg gggagggggg
       61 actcttattt tgttaggggg accgggccga ggcccgaccg gcctggcagg gctcgcccgg
      121 ggccgggcgt catgtctcat gcggccgaac cagctcggga tggcgtagag gccagcgcgg
      181 agggccctcg agccgtgttc gtgctgttgg aggagcgcag gccggccgac tcggctcagc
      241 tgctcagcct gaactctttg cttccggaat ccgggattgt tgctgacata gaattagaaa
      301 acgtccttga tcctgacagc ttctacgagc tcaaaagcca acccttaccc cttcgctcaa
      361 gcctcccaat atcactgcag gccacaccag ccaccccagc tacactctct gcatcgtctt
      421 ctgcaggggg ctccaggacc cctgccatgt cgtcatcttc ttcatcgagg gtcttgctgc
      481 ggcagcagct aatgcgggcc caggcgcagg agcaggagag gcgtgagcgt cgggaacagg
      541 ccgccgcggc tcccttcccc agtcctgcac ctgcctctcc tgccatctct gtggttggcg
      601 tctctgctgg gggccacaca ttgagccgtc caccccctgc tcaggtgccc agggaggtgc
      661 tcaaggtgca gacccatctg gagaacccaa cgcgctacca cctgcagcag gcgcgccggc
      721 agcaggtgaa acagtacctg tccaccacac tcgggcccaa gctggcttcc caggccctca
      781 ccccaccgcc ggggcccgca agtgcccagc cactgcctgc ccctgaggct gcccacacta
      841 ccggccccac aggcagtgcg cccaacagcc ccatggcgct gctcaccatc gggtccagct
      901 cagagaagga gattgatgat gtcattgatg agatcatcag cctggagtcc agttacaatg
      961 atgaaatgct cagctatctg cccggaggca ccacaggact gcagctcccc agcacgctgc
     1021 ctgtgtcagg gaatctgctt gatgtgtaca gtagtcaagg cgtggccaca ccagccatca
     1081 ctgtcagcaa ctcctgccca gctgagctgc ccaacatcaa acgggagatc tctgagaccg
     1141 aggcaaaggc ccttttgaag gaacggcaga agaaagacaa tcacaaccta attgagcgtc
     1201 gcaggcgatt caacattaac gacaggatca aggaactggg cactctcatc cctaagtcca
     1261 gtgacccgga gatgcgctgg aacaagggca ccatcctgaa ggcctctgtg gattatatcc
     1321 gcaagctgca gaaggagcag cagcgctcca aagacctgga gagccggcag cgatccctgg
     1381 agcaggccaa ccgcagcctg cagctccgaa ttcaggaact agaactgcag gcccagatcc
     1441 atggcctgcc agtacctccc actccagggc tgctttcctt ggccacgact tcggcttctg
     1501 acagcctcaa gccagagcag ctggacattg aggaggaggg caggccaggc gcagcaacgt
     1561 tccatgtagg ggggggacct gcccagaatg ctccccatca gcagccccct gcaccgccct
     1621 cagatgccct tctggacctg cactttccca gcgaccacct gggggacctg ggagacccct
     1681 tccacctggg gctggaggac attctgatgg aggaggagga gggggtggtg ggaggactgt
     1741 cggggggtgc cctgtcccca ctgcgggctg cctccgatcc cctgctctct tcagtgtccc
     1801 ctgctgtctc caaggccagc agccgccgca gcagcttcag catggaagag gagtcctgat
     1861 caggcctcac ccctcccctg ggactttccc acccaggaaa ggaggaccag tcaggatgag
     1921 gccccgcctt ttcccccacc ctcccatgag actgccctgc ccaggtatcc tgggggaaga
     1981 ggagatgtga tcaggcccca cccctgtaat caggcaagga ggaggagtca gatgaggccc
     2041 tgcaccttcc ccaaaggaac cgcccagtgc aggtatttca gaaggagaag gctggagaag
     2101 gacatgagat cagggcctgc cccctgggga tcacagcctc acccctgccc ctgtgggact
     2161 catccttgcc caggtgaggg aaggagacag gatgaggtct cgaccctgtc ccctagggac
     2221 tgtcctagcc aggtctcctg ggaaagggag atgtcaggat gttgctccat cctttgtctt
     2281 ggaaccacca gtctagtccg tcctggcaca gaagaggagt caagtaatgg aggtcccagc
     2341 cctgggggtt taagctctgc cccttcccca tgaaccctgc cctgctctgc ccaggcaagg
     2401 aacagaagtg aggatgagac ccagcccctt cccctgggaa ctctcctggc cttctaggaa
     2461 tggaggagcc aggccccacc ccttccctat aggaacagcc cagcacaggt atttcaggtg
     2521 tgaaagaatc agtaggacca ggccaccgct agtgcttgtg gagatcacag ccccaccctt
     2581 gtccctcagc aacatcccat ctaagcattc cacactgcag ggaggagtgg tacttaagct
     2641 cccctgcctt aacctgggac caacctgacc taacctagga gggctctgag ccaaccttgc
     2701 tcttggggaa ggggacagat tatgaaattt catggatgaa ttttccagac ctatatctgg
     2761 agtgagaggc ccccaccctt gggcagagtc ctgccttctt ccttgagggg cagtttggga
     2821 aggtgatggg tattagtggg ggactgagtt caggttacca gaaccagtac ctcagtattc
     2881 tttttcaaca tgtagggcaa gaggatgaag gaaggggcta tcctgggacc tccccagccc
     2941 aggaaaaact ggaagccttc ccccagcaag gcagaagctt ggaggagggt tgtaaaagca
     3001 tattgtaccc cctcatttgt ttatctgatt tttttattgc tccgcatact gagaatctag
     3061 gccaccccaa cctctgttcc ccacccagtt cttcatttgg aggaatcacc ccatttcaga
     3121 gttatcaaga gacactcccc cctccattcc cacccctcat acctacaccc aaggttgtca
     3181 gctttggatt gctggggcca ggccccatgg agggtatact gaggggtcta taggtttgtg
     3241 attaaaataa taaaagctag gcgtgtttga tgcgctttta actttggcaa a
//
