GGRNA | NM_001080430.2

LOCUS       NM_001080430            3121 bp    mRNA    linear   PRI 01-JUL-2013
DEFINITION  Homo sapiens TOX high mobility group box family member 3 (TOX3),
            transcript variant 1, mRNA.
ACCESSION   NM_001080430 XM_049037
VERSION     NM_001080430.2  GI:226054294
KEYWORDS    RefSeq.
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 3121)
  AUTHORS   Shan,J., Dsouza,S.P., Bakhru,S., Al-Azwani,E.K., Ascierto,M.L.,
            Sastry,K.S., Bedri,S., Kizhakayil,D., Aigha,I.I., Malek,J.,
            Al-Bozom,I., Gehani,S., Furtado,S., Mathiowitz,E., Wang,E.,
            Marincola,F.M. and Chouchane,L.
  TITLE     TNRC9 downregulates BRCA1 expression and promotes breast cancer
            aggressiveness
  JOURNAL   Cancer Res. 73 (9), 2840-2849 (2013)
   PUBMED   23447579
  REMARK    GeneRIF: TNRC9 gene is amplified and associated with poor prognosis
            in advanced breast cancer. TNRC9 promotes cancer cell
            proliferation, migration, and survival both in vitro and in vivo.
            TNRC9 and BRCA1 expression are inversely correlated.
REFERENCE   2  (bases 1 to 3121)
  AUTHORS   Fernandez-Navarro,P., Pita,G., Santamarina,C., Moreno,M.P.,
            Vidal,C., Miranda-Garcia,J., Ascunce,N., Casanova,F.,
            Collado-Garcia,F., Herraez,B., Gonzalez-Neira,A., Benitez,J. and
            Pollan,M.
  TITLE     Association analysis between breast cancer genetic variants and
            mammographic density in a large population-based study
            (Determinants of Density in Mammographies in Spain) identifies
            susceptibility loci in TOX3 gene
  JOURNAL   Eur. J. Cancer 49 (2), 474-481 (2013)
   PUBMED   23021931
  REMARK    GeneRIF: Evidence of association with mammographic density was
            found for variant rs3803662 (TOX3).
REFERENCE   3  (bases 1 to 3121)
  AUTHORS   Cowper-Sal lari,R., Zhang,X., Wright,J.B., Bailey,S.D., Cole,M.D.,
            Eeckhoute,J., Moore,J.H. and Lupien,M.
  TITLE     Breast cancer risk-associated SNPs modulate the affinity of
            chromatin for FOXA1 and alter gene expression
  JOURNAL   Nat. Genet. 44 (11), 1191-1198 (2012)
   PUBMED   23001124
  REMARK    GeneRIF: risk-associated SNPs modulate the affinity of chromatin
            for FOXA1 at distal regulatory elements, thereby resulting in
            allele-specific gene expression, which is exemplified by the effect
            of the rs4784227 SNP on the TOX3 gene within the 16q12.1 risk
            locus.
REFERENCE   4  (bases 1 to 3121)
  AUTHORS   Orr,N., Lemnrau,A., Cooke,R., Fletcher,O., Tomczyk,K., Jones,M.,
            Johnson,N., Lord,C.J., Mitsopoulos,C., Zvelebil,M., McDade,S.S.,
            Buck,G., Blancher,C., Trainer,A.H., James,P.A., Bojesen,S.E.,
            Bokmand,S., Nevanlinna,H., Mattson,J., Friedman,E., Laitman,Y.,
            Palli,D., Masala,G., Zanna,I., Ottini,L., Giannini,G.,
            Hollestelle,A., Ouweland,A.M., Novakovic,S., Krajc,M.,
            Gago-Dominguez,M., Castelao,J.E., Olsson,H., Hedenfalk,I.,
            Easton,D.F., Pharoah,P.D., Dunning,A.M., Bishop,D.T.,
            Neuhausen,S.L., Steele,L., Houlston,R.S., Garcia-Closas,M.,
            Ashworth,A. and Swerdlow,A.J.
  CONSRTM   KConFab Consortium
  TITLE     Genome-wide association study identifies a common variant in RAD51B
            associated with male breast cancer risk
  JOURNAL   Nat. Genet. 44 (11), 1182-1184 (2012)
   PUBMED   23001122
REFERENCE   5  (bases 1 to 3121)
  AUTHORS   Gudmundsdottir,E.T., Barkardottir,R.B., Arason,A., Gunnarsson,H.,
            Amundadottir,L.T., Agnarsson,B.A., Johannsson,O.T. and
            Reynisdottir,I.
  TITLE     The risk allele of SNP rs3803662 and the mRNA level of its closest
            genes TOX3 and LOC643714 predict adverse outcome for breast cancer
            patients
  JOURNAL   BMC Cancer 12, 621 (2012)
   PUBMED   23270421
  REMARK    GeneRIF: the minor allele of SNP rs3803662 was associated with
            shorter survival in breast cancer patients with luminal A tumours,
            with lower mRNA expression of TOX3
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3121)
  AUTHORS   Stacey,S.N., Manolescu,A., Sulem,P., Rafnar,T., Gudmundsson,J.,
            Gudjonsson,S.A., Masson,G., Jakobsdottir,M., Thorlacius,S.,
            Helgason,A., Aben,K.K., Strobbe,L.J., Albers-Akkers,M.T.,
            Swinkels,D.W., Henderson,B.E., Kolonel,L.N., Le Marchand,L.,
            Millastre,E., Andres,R., Godino,J., Garcia-Prats,M.D., Polo,E.,
            Tres,A., Mouy,M., Saemundsdottir,J., Backman,V.M., Gudmundsson,L.,
            Kristjansson,K., Bergthorsson,J.T., Kostic,J., Frigge,M.L.,
            Geller,F., Gudbjartsson,D., Sigurdsson,H., Jonsdottir,T.,
            Hrafnkelsson,J., Johannsson,J., Sveinsson,T., Myrdal,G.,
            Grimsson,H.N., Jonsson,T., von Holst,S., Werelius,B., Margolin,S.,
            Lindblom,A., Mayordomo,J.I., Haiman,C.A., Kiemeney,L.A.,
            Johannsson,O.T., Gulcher,J.R., Thorsteinsdottir,U., Kong,A. and
            Stefansson,K.
  TITLE     Common variants on chromosomes 2q35 and 16q12 confer susceptibility
            to estrogen receptor-positive breast cancer
  JOURNAL   Nat. Genet. 39 (7), 865-869 (2007)
   PUBMED   17529974
REFERENCE   7  (bases 1 to 3121)
  AUTHORS   Easton,D.F., Pooley,K.A., Dunning,A.M., Pharoah,P.D., Thompson,D.,
            Ballinger,D.G., Struewing,J.P., Morrison,J., Field,H., Luben,R.,
            Wareham,N., Ahmed,S., Healey,C.S., Bowman,R., Meyer,K.B.,
            Haiman,C.A., Kolonel,L.K., Henderson,B.E., Le Marchand,L.,
            Brennan,P., Sangrajrang,S., Gaborieau,V., Odefrey,F., Shen,C.Y.,
            Wu,P.E., Wang,H.C., Eccles,D., Evans,D.G., Peto,J., Fletcher,O.,
            Johnson,N., Seal,S., Stratton,M.R., Rahman,N., Chenevix-Trench,G.,
            Bojesen,S.E., Nordestgaard,B.G., Axelsson,C.K., Garcia-Closas,M.,
            Brinton,L., Chanock,S., Lissowska,J., Peplonska,B., Nevanlinna,H.,
            Fagerholm,R., Eerola,H., Kang,D., Yoo,K.Y., Noh,D.Y., Ahn,S.H.,
            Hunter,D.J., Hankinson,S.E., Cox,D.G., Hall,P., Wedren,S., Liu,J.,
            Low,Y.L., Bogdanova,N., Schurmann,P., Dork,T., Tollenaar,R.A.,
            Jacobi,C.E., Devilee,P., Klijn,J.G., Sigurdson,A.J., Doody,M.M.,
            Alexander,B.H., Zhang,J., Cox,A., Brock,I.W., MacPherson,G.,
            Reed,M.W., Couch,F.J., Goode,E.L., Olson,J.E., Meijers-Heijboer,H.,
            van den Ouweland,A., Uitterlinden,A., Rivadeneira,F., Milne,R.L.,
            Ribas,G., Gonzalez-Neira,A., Benitez,J., Hopper,J.L., McCredie,M.,
            Southey,M., Giles,G.G., Schroen,C., Justenhoven,C., Brauch,H.,
            Hamann,U., Ko,Y.D., Spurdle,A.B., Beesley,J., Chen,X.,
            Mannermaa,A., Kosma,V.M., Kataja,V., Hartikainen,J., Day,N.E.,
            Cox,D.R. and Ponder,B.A.
  CONSRTM   SEARCH collaborators; kConFab; AOCS Management Group
  TITLE     Genome-wide association study identifies novel breast cancer
            susceptibility loci
  JOURNAL   Nature 447 (7148), 1087-1093 (2007)
   PUBMED   17529967
  REMARK    GeneRIF: Observational study and genome-wide association study of
            gene-disease association. (HuGE Navigator)
REFERENCE   8  (bases 1 to 3121)
  AUTHORS   Huijts,P.E., Vreeswijk,M.P., Kroeze-Jansema,K.H., Jacobi,C.E.,
            Seynaeve,C., Krol-Warmerdam,E.M., Wijers-Koster,P.M., Blom,J.C.,
            Pooley,K.A., Klijn,J.G., Tollenaar,R.A., Devilee,P. and van
            Asperen,C.J.
  TITLE     Clinical correlates of low-risk variants in FGFR2, TNRC9, MAP3K1,
            LSP1 and 8q24 in a Dutch cohort of incident breast cancer cases
  JOURNAL   Breast Cancer Res. 9 (6), R78 (2007)
   PUBMED   17997823
  REMARK    GeneRIF: Heterozygote carriers and minor allele homozygote carriers
            for SNP rs3803662 near the TNCR9 gene were more likely to be
            diagnosed before the age of 60 years (P = 0.025) relative to major
            allele homozygote carriers
            GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   9  (bases 1 to 3121)
  AUTHORS   O'Flaherty,E. and Kaye,J.
  TITLE     TOX defines a conserved subfamily of HMG-box proteins
  JOURNAL   BMC Genomics 4 (1), 13 (2003)
   PUBMED   12697058
  REMARK    Publication Status: Online-Only
REFERENCE   10 (bases 1 to 3121)
  AUTHORS   Margolis,R.L., Abraham,M.R., Gatchell,S.B., Li,S.H., Kidwai,A.S.,
            Breschel,T.S., Stine,O.C., Callahan,C., McInnis,M.G. and Ross,C.A.
  TITLE     cDNAs with long CAG trinucleotide repeats from human brain
  JOURNAL   Hum. Genet. 100 (1), 114-122 (1997)
   PUBMED   9225980
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BE501808.1 and AK299202.1.
            On Apr 1, 2009 this sequence version replaced gi:122937252.
            
            Summary: The protein encoded by this gene contains an HMG-box,
            indicating that it may be involved in bending and unwinding of DNA
            and alteration of chromatin structure. The C-terminus of the
            encoded protein is glutamine-rich due to CAG repeats in the coding
            sequence. A minor allele of this gene has been implicated in an
            elevated risk of breast cancer. Two transcript variants encoding
            different isoforms have been found for this gene.[provided by
            RefSeq, Apr 2009].
            
            Transcript Variant: This variant (1) 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##
            RNAseq introns :: single sample supports all introns ERS025084,
                              ERS025088 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-579               BE501808.1         1-579
            580-3121            AK299202.1         582-3123
FEATURES             Location/Qualifiers
     source          1..3121
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="16"
                     /map="16q12.1"
     gene            1..3121
                     /gene="TOX3"
                     /gene_synonym="CAGF9; TNRC9"
                     /note="TOX high mobility group box family member 3"
                     /db_xref="GeneID:27324"
                     /db_xref="HGNC:11972"
                     /db_xref="MIM:611416"
     exon            1..258
                     /gene="TOX3"
                     /gene_synonym="CAGF9; TNRC9"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    97..99
                     /gene="TOX3"
                     /gene_synonym="CAGF9; TNRC9"
                     /note="upstream in-frame stop codon"
     CDS             172..1902
                     /gene="TOX3"
                     /gene_synonym="CAGF9; TNRC9"
                     /note="isoform 1 is encoded by transcript variant 1;
                     trinucleotide repeat containing 9; trinucleotide
                     repeat-containing gene 9 protein; CAG trinucleotide
                     repeat-containing gene F9 protein"
                     /codon_start=1
                     /product="TOX high mobility group box family member 3
                     isoform 1"
                     /protein_id="NP_001073899.2"
                     /db_xref="GI:226054295"
                     /db_xref="CCDS:CCDS54009.1"
                     /db_xref="GeneID:27324"
                     /db_xref="HGNC:11972"
                     /db_xref="MIM:611416"
                     /translation="

MDVRFYPAAAGDPASLDFAQCLGYYGYSKFGNNNNYMNMAEANNAFFAASEQTFHTPSLGDEEFEIPPITPPPESDPALGMPDVLLPFQALSDPLPSQGSEFTPQFPPQSLDLPSITISRNLVEQDGVLHSSGLHMDQSHTQVSQYRQDPSLIMRSIVHMTDAARSGVMPPAQLTTINQSQLSAQLGLNLGGASMPHTSPSPPASKSATPSPSSSINEEDADEANRAIGEKRAAPDSGKKPKTPKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKTEAAKKEYLKALAAYRASLVSKAAAESAEAQTIRSVQQTLASTNLTSSLLLNTPLSQHGTVSASPQTLQQSLPRSIAPKPLTMRLPMNQIVTSVTIAANMPSNIGAPLISSMGTTMVGSAPSTQVSPSVQTQQHQMQLQQQQQQQQQQMQQMQQQQLQQHQMHQQIQQQMQQQHFQHHMQQHLQQQQQHLQQQINQQQLQQQLQQRLQLQQLQHMQHQSQPSPRQHSPVASQITSPIPAIGSPQPASQQHQSQIQSQTQTQVLSQVSIF

"
     misc_feature    949..>1092
                     /gene="TOX3"
                     /gene_synonym="CAGF9; TNRC9"
                     /note="High Mobility Group (HMG)-box is found in a variety
                     of eukaryotic chromosomal proteins and transcription
                     factors. HMGs bind to the minor groove of DNA and have
                     been classified by DNA binding preferences. Two
                     phylogenically distinct groups of Class I...; Region:
                     HMG-box; cd00084"
                     /db_xref="CDD:28965"
     misc_feature    order(949..951,955..960,967..972,979..981,991..993,
                     1030..1032,1039..1041,1048..1050)
                     /gene="TOX3"
                     /gene_synonym="CAGF9; TNRC9"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:28965"
     exon            259..324
                     /gene="TOX3"
                     /gene_synonym="CAGF9; TNRC9"
                     /inference="alignment:Splign:1.39.8"
     exon            325..579
                     /gene="TOX3"
                     /gene_synonym="CAGF9; TNRC9"
                     /inference="alignment:Splign:1.39.8"
     exon            580..849
                     /gene="TOX3"
                     /gene_synonym="CAGF9; TNRC9"
                     /inference="alignment:Splign:1.39.8"
     exon            850..1077
                     /gene="TOX3"
                     /gene_synonym="CAGF9; TNRC9"
                     /inference="alignment:Splign:1.39.8"
     exon            1078..1158
                     /gene="TOX3"
                     /gene_synonym="CAGF9; TNRC9"
                     /inference="alignment:Splign:1.39.8"
     exon            1159..3121
                     /gene="TOX3"
                     /gene_synonym="CAGF9; TNRC9"
                     /inference="alignment:Splign:1.39.8"
     variation       2611
                     /gene="TOX3"
                     /gene_synonym="CAGF9; TNRC9"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:201023725"
ORIGIN

gcggccgcggctcccgagctcctcgggctctgggtcccggcgcccctccggccgcgagtcccacgcgccacccccgggcgccctcgacggtggatctagcggcggcgaggaggcgggtcccggccccggcgaaccccagtcccggcccccggccccgggcccagcttcggcatggatgtgaggttctaccccgcggcggccggggaccctgccagcctggacttcgcgcagtgcctggggtactacggctacagcaagtttggaaataataataactatatgaatatggctgaggcgaacaatgcgttcttcgctgccagtgagcagacattccacacaccaagccttggggacgaggaattcgaaattccaccaatcacgcctcctccagagtcagaccctgccctaggcatgccggatgtactgctaccctttcaagccctcagcgatccattgccttcccagggaagtgaattcacaccccagtttccccctcaaagcctggacctcccttccattacaatctcaagaaatctcgtggaacaagatggcgtgcttcatagcagtgggttgcatatggatcagagccacacacaagtgtcccagtaccggcaggatccctccctgatcatgcggtccatcgtccacatgaccgatgctgcgcgttctggggtcatgcctcctgcccagctcaccaccatcaaccagtctcagctcagcgcccagttggggttgaatttgggaggtgccagtatgcctcacacatctccttcacctccagcaagcaaatcagccactccctccccttccagctccatcaatgaagaggatgctgatgaagccaacagagccattggagagaaaagagctgctccagactctggcaagaagcccaagactccaaagaaaaagaaaaagaaagatcccaatgagccacagaagccagtgtcagcatatgccctgtttttcagagacacacaggctgcaattaaaggtcaaaaccccaatgcaacctttggagaggtctcaaaaattgtagcatctatgtgggacagccttggagaagaacaaaagcaggtatataaaaggaaaacagaagctgccaaaaaagaatacctgaaggccctggcggcatacagggccagcctcgtttctaaggctgctgctgagtcagcagaagcccagaccatccgttctgttcagcagaccctggcgtcgaccaatctaacatcctctctccttctcaacactccactgtctcaacatggaacagtgtcagcatcacctcagactctccagcaatccctccctaggtcaatcgctcccaaacccttaaccatgagactccccatgaaccagattgtcacatcagtcaccattgcagccaacatgccctcgaacattggggctccactgataagctccatgggaacgaccatggttggctcagcaccctccacccaagtgagtccttcggtgcaaacccagcagcatcagatgcaattgcagcagcagcagcagcagcaacaacaacagatgcaacagatgcagcagcagcaactccagcagcaccaaatgcatcagcaaatccagcagcagatgcagcagcagcatttccagcaccacatgcagcagcacctgcagcagcagcagcagcatctccagcagcaaattaatcaacagcagctgcagcagcagctgcagcagcgcctccagctgcagcagctgcaacacatgcagcaccagtctcagccttctcctcggcagcactcccctgtcgcctctcagataacatcccccatccctgccatcgggagcccccagccagcctctcagcagcaccagtcgcaaatacagtctcagacacagactcaagtattatcgcaggtcagtattttctgaagacgcatatggcagacggatttgcgtataccaaggagagtggcataggagggaaaagcatatgtggctgaaacctgtaagttggtgttggttatgcagaaatgtgtaacagatcaaacggtcctctcaagtgtctattagataggcaataagaactgcagtgtagctgagtaacatcttttagctgactataaatcactttgtttttaaacaagaaaagctgtgctcttttatgtgatgccttttttatttattcaggctatacctacaatatgtgaatcaaactgtttaatgaatcctgggacatactgatgactataaactggcctctctgagtcatagaaaaatggccttatttctccagaagtgagtaaaccacacttccaggctatctgaactcctgaagccctaaaaataaaaagcacagttgtaactacctgaaatatgaagatccagtttcatacaaacatttgtatgacgtgaatagttgatggcatttttttgtcatgaaaaaaataatgtaaatcacagacttttgccaaagctcttattttttttcctaaatctctccagaaaaaaaatgcaagtgactaaattcaattattgactaatttccactttttatccatgacttctccaaatcaaaccacagtatatgttgtaacaatatctatgaccactgttagcccattatattcattccaattagaagaaatgtgaatactatattccgtgttttgagtgacaagtttcgaaaaataaaaacactgtatttttaaaagggaaatgcacttaaatgaaaacagttattacaaaagttaagatttaaaaagaaaaagcaagagtttttattatgatgtaataccagtagaatatttaaaaggcacaccacatctgaataatcaatgtaaatattttctttcaaagttgtaagttttcatatcatgtgctgtaaagttttcctaaatgaggctttaacgtaaacactggtgacataaaccattcattgctacgttgcttattgtgtttttatgctgttttatacttttttatgagttatgatagcagcaattaagttgtttgtattttgcttaactaaaacaaaaatgcttttatcttgctatagaataaacacatttcagtaaaaactgtggactgtattttgatgcaacaacaaagaaactgttcacttttcaaataaaatgatatgtcagatttc

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