LOCUS       NM_023924               2665 bp    mRNA    linear   PRI 11-SEP-2024
DEFINITION  Homo sapiens bromodomain containing 9 (BRD9), transcript variant 1,
            mRNA.
ACCESSION   NM_023924
VERSION     NM_023924.5
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 2665)
  AUTHORS   Pehlivanoglu,B., Araya,J.C., Lawrence,S., Roa,J.C., Balci,S.,
            Andersen,J.B., Rashid,A., Hsing,A.W., Zhu,B., Gao,Y.T., Koshiol,J.
            and Adsay,V.
  TITLE     TPPP-BRD9 fusion-related gallbladder carcinomas are frequently
            associated with intracholecystic neoplasia, neuroendocrine
            carcinoma, and a distinctive small tubular-type adenocarcinoma
            commonly accompanied with a syringomatous pattern
  JOURNAL   Hum Pathol 150, 67-73 (2024)
   PUBMED   38972607
  REMARK    GeneRIF: TPPP-BRD9 fusion-related gallbladder carcinomas are
            frequently associated with intracholecystic neoplasia,
            neuroendocrine carcinoma, and a distinctive small tubular-type
            adenocarcinoma commonly accompanied with a syringomatous pattern.
REFERENCE   2  (bases 1 to 2665)
  AUTHORS   Garg,S., Ni,W., Chowdhury,B., Weisberg,E.L., Sattler,M. and
            Griffin,J.D.
  TITLE     BRD9 regulates normal human hematopoietic stem cell function and
            lineage differentiation
  JOURNAL   Cell Death Differ 31 (7), 868-880 (2024)
   PUBMED   38816579
  REMARK    GeneRIF: BRD9 regulates normal human hematopoietic stem cell
            function and lineage differentiation.
REFERENCE   3  (bases 1 to 2665)
  AUTHORS   Chen,Y., Gao,Z., Mohd-Ibrahim,I., Yang,H., Wu,L., Fu,Y. and Deng,Y.
  TITLE     Pan-cancer analyses of bromodomain containing 9 as a novel
            therapeutic target reveals its diagnostic, prognostic potential and
            biological mechanism in human tumours
  JOURNAL   Clin Transl Med 14 (2), e1543 (2024)
   PUBMED   38303608
  REMARK    GeneRIF: Pan-cancer analyses of bromodomain containing 9 as a novel
            therapeutic target reveals its diagnostic, prognostic potential and
            biological mechanism in human tumours.
REFERENCE   4  (bases 1 to 2665)
  AUTHORS   Klein,D.C., Lardo,S.M. and Hainer,S.J.
  TITLE     The ncBAF Complex Regulates Transcription in AML Through H3K27ac
            Sensing by BRD9
  JOURNAL   Cancer Res Commun 4 (1), 237-252 (2024)
   PUBMED   38126767
  REMARK    GeneRIF: The ncBAF Complex Regulates Transcription in AML Through
            H3K27ac Sensing by BRD9.
REFERENCE   5  (bases 1 to 2665)
  AUTHORS   Yang,Q., Vafaei,S., Falahati,A., Khosh,A., Bariani,M.V.,
            Omran,M.M., Bai,T., Siblini,H., Ali,M., He,C., Boyer,T.G. and
            Al-Hendy,A.
  TITLE     Bromodomain-Containing Protein 9 Regulates Signaling Pathways and
            Reprograms the Epigenome in Immortalized Human Uterine Fibroid
            Cells
  JOURNAL   Int J Mol Sci 25 (2), 905 (2024)
   PUBMED   38255982
  REMARK    GeneRIF: Bromodomain-Containing Protein 9 Regulates Signaling
            Pathways and Reprograms the Epigenome in Immortalized Human Uterine
            Fibroid Cells.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2665)
  AUTHORS   Huang,H.T., Chen,S.M., Pan,L.B., Yao,J. and Ma,H.T.
  TITLE     Loss of function of SWI/SNF chromatin remodeling genes leads to
            genome instability of human lung cancer
  JOURNAL   Oncol Rep 33 (1), 283-291 (2015)
   PUBMED   25370573
REFERENCE   7  (bases 1 to 2665)
  AUTHORS   Kadoch,C., Hargreaves,D.C., Hodges,C., Elias,L., Ho,L., Ranish,J.
            and Crabtree,G.R.
  TITLE     Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes
            identifies extensive roles in human malignancy
  JOURNAL   Nat Genet 45 (6), 592-601 (2013)
   PUBMED   23644491
REFERENCE   8  (bases 1 to 2665)
  AUTHORS   Filippakopoulos,P., Picaud,S., Mangos,M., Keates,T., Lambert,J.P.,
            Barsyte-Lovejoy,D., Felletar,I., Volkmer,R., Muller,S., Pawson,T.,
            Gingras,A.C., Arrowsmith,C.H. and Knapp,S.
  TITLE     Histone recognition and large-scale structural analysis of the
            human bromodomain family
  JOURNAL   Cell 149 (1), 214-231 (2012)
   PUBMED   22464331
REFERENCE   9  (bases 1 to 2665)
  AUTHORS   Scotto,L., Narayan,G., Nandula,S.V., Subramaniyam,S.,
            Kaufmann,A.M., Wright,J.D., Pothuri,B., Mansukhani,M.,
            Schneider,A., Arias-Pulido,H. and Murty,V.V.
  TITLE     Integrative genomics analysis of chromosome 5p gain in cervical
            cancer reveals target over-expressed genes, including Drosha
  JOURNAL   Mol Cancer 7, 58 (2008)
   PUBMED   18559093
  REMARK    Publication Status: Online-Only
REFERENCE   10 (bases 1 to 2665)
  AUTHORS   Clark,H.F., Gurney,A.L., Abaya,E., Baker,K., Baldwin,D., Brush,J.,
            Chen,J., Chow,B., Chui,C., Crowley,C., Currell,B., Deuel,B.,
            Dowd,P., Eaton,D., Foster,J., Grimaldi,C., Gu,Q., Hass,P.E.,
            Heldens,S., Huang,A., Kim,H.S., Klimowski,L., Jin,Y., Johnson,S.,
            Lee,J., Lewis,L., Liao,D., Mark,M., Robbie,E., Sanchez,C.,
            Schoenfeld,J., Seshagiri,S., Simmons,L., Singh,J., Smith,V.,
            Stinson,J., Vagts,A., Vandlen,R., Watanabe,C., Wieand,D., Woods,K.,
            Xie,M.H., Yansura,D., Yi,S., Yu,G., Yuan,J., Zhang,M., Zhang,Z.,
            Goddard,A., Wood,W.I., Godowski,P. and Gray,A.
  TITLE     The secreted protein discovery initiative (SPDI), a large-scale
            effort to identify novel human secreted and transmembrane proteins:
            a bioinformatics assessment
  JOURNAL   Genome Res 13 (10), 2265-2270 (2003)
   PUBMED   12975309
  REMARK    Erratum:[Genome Res. 2003 Dec;13(12):2759]
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AK299157.1, AK023503.1 and AK026830.1.
            
            On Nov 23, 2018 this sequence version replaced NM_023924.4.
            
            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 :: AK299157.1, SRR14038191.3182532.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000467963.6/ ENSP00000419765.1
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-905               AK299157.1         24-928
            906-906             AK023503.1         1086-1086
            907-2133            AK299157.1         930-2156
            2134-2665           AK026830.1         1289-1820
FEATURES             Location/Qualifiers
     source          1..2665
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5p15.33"
     gene            1..2665
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /note="bromodomain containing 9"
                     /db_xref="GeneID:65980"
                     /db_xref="HGNC:HGNC:25818"
                     /db_xref="MIM:618465"
     exon            1..196
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     CDS             145..1938
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /note="isoform 1 is encoded by transcript variant 1;
                     bromodomain-containing protein 9; rhabdomyosarcoma antigen
                     MU-RMS-40.8; sarcoma antigen NY-SAR-29"
                     /codon_start=1
                     /product="bromodomain-containing protein 9 isoform 1"
                     /protein_id="NP_076413.3"
                     /db_xref="CCDS:CCDS34127.2"
                     /db_xref="GeneID:65980"
                     /db_xref="HGNC:HGNC:25818"
                     /db_xref="MIM:618465"
                     /translation="MGKKHKKHKAEWRSSYEDYADKPLEKPLKLVLKVGGSEVTELSG
                     SGHDSSYYDDRSDHERERHKEKKKKKKKKSEKEKHLDDEERRKRKEEKKRKREREHCD
                     TEGEADDFDPGKKVEVEPPPDRPVRACRTQPAENESTPIQQLLEHFLRQLQRKDPHGF
                     FAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRP
                     DTVYYKLAKKILHAGFKMMSKQAALLGNEDTAVEEPVPEVVPVQVETAKKSKKPSREV
                     ISCMFEPEGNACSLTDSTAEEHVLALVEHAADEARDRINRFLPGGKMGYLKRNGDGSL
                     LYSVVNTAEPDADEEETHPVDLSSLSSKLLPGFTTLGFKDERRNKVTFLSSATTALSM
                     QNNSVFGDLKSDEMELLYSAYGDETGVQCALSLQEFVKDAGSYSKKVVDDLLDQITGG
                     DHSRTLFQLKQRRNVPMKPPDEAKVGDTLGDSSSSVLEFMSMKSYPDVSVDISMLSSL
                     GKVKKELDPDDSHLNLDETTKLLQDLHEAQAERGGSRPSSNLSSLSNASERDQHHLGS
                     PSRLSVGEQPDVTHDPYEFLQSPEPAASAKT"
     exon            197..411
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     exon            412..544
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     exon            545..605
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     exon            606..750
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     exon            751..861
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     exon            862..977
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     exon            978..1110
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     exon            1111..1186
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     exon            1187..1282
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     exon            1283..1415
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     exon            1416..1527
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     exon            1528..1566
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     exon            1567..1669
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     exon            1670..1837
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     exon            1838..2665
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2644..2649
                     /regulatory_class="polyA_signal_sequence"
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /note="hexamer: CATAAA"
     polyA_site      2665
                     /gene="BRD9"
                     /gene_synonym="LAVS3040; PRO9856; SMARCI2"
                     /note="major polyA site"
ORIGIN      
        1 gtttccggcg cggcccagcg agctcggcaa cctcggcgca gcgagcgcgg gcggccagcc
       61 agggccaggg ggcggtggcg gccaaggtcc gaccgggtgc cagctgttcc cagcccccgc
      121 ctcgggcccg ccgccggcgc cgccatgggc aagaagcaca agaagcacaa ggccgagtgg
      181 cgctcgtcct acgaggatta tgccgacaag cccctggaga agcctctaaa gctagtcctg
      241 aaggtcggag gaagtgaagt gactgaactc tcaggatccg gccacgactc cagttactat
      301 gatgacaggt cagaccatga gcgagagagg cacaaagaaa agaaaaagaa gaagaagaag
      361 aagtccgaga aggagaagca tctggacgat gaggaaagaa ggaagcgaaa ggaagagaag
      421 aagcggaagc gagagaggga gcactgtgac acggagggag aggctgacga ctttgatcct
      481 gggaagaagg tggaggtgga gccgccccca gatcggccag tccgagcgtg ccggacacag
      541 ccagccgaaa atgagagcac acctattcag caactcctgg aacacttcct ccgccagctt
      601 cagagaaaag atccccatgg attttttgct tttcctgtca cggatgcaat tgctcctgga
      661 tattcaatga taataaaaca tcccatggat tttggcacca tgaaagacaa aattgtagct
      721 aatgaataca agtcagttac ggaatttaag gcagatttca agctgatgtg tgataatgca
      781 atgacataca ataggccaga taccgtgtac tacaagttgg cgaagaagat ccttcacgca
      841 ggctttaaga tgatgagcaa acaggcagct cttttgggca atgaagatac agctgttgag
      901 gaacctgtcc ctgaagttgt accagtacaa gtagaaactg ccaagaaatc caaaaagccg
      961 agtagagaag ttatcagctg catgtttgag cctgaaggga atgcctgcag cttgacggac
     1021 agtaccgcag aggagcacgt gctggcgctg gtggagcacg cagctgacga agctcgggac
     1081 aggatcaacc ggttcctccc aggcggcaag atgggctatc tgaagaggaa cggggacggg
     1141 agcctgctct acagcgtggt caacacggcc gagccggacg ctgatgagga ggagacccac
     1201 ccggtggact tgagctcgct ctccagtaag ctactcccag gcttcaccac gctgggcttc
     1261 aaagacgaga gaagaaacaa agtcaccttt ctctccagtg ccactactgc gctttcgatg
     1321 cagaataatt cagtatttgg cgacttgaag tcggacgaga tggagctgct ctactcagcc
     1381 tacggagatg agacaggcgt gcagtgtgcg ctgagcctgc aggagtttgt gaaggatgct
     1441 gggagctaca gcaagaaagt ggtggacgac ctcctggacc agatcacagg cggagaccac
     1501 tctaggacgc tcttccagct gaagcagaga agaaatgttc ccatgaagcc tccagatgaa
     1561 gccaaggttg gggacaccct aggagacagc agcagctctg ttctggagtt catgtcgatg
     1621 aagtcctatc ccgacgtttc tgtggatatc tccatgctca gctctctggg gaaggtgaag
     1681 aaggagctgg accctgacga cagccatttg aacttggatg agacgacgaa gctcctgcag
     1741 gacctgcacg aagcacaggc ggagcgcggc ggctctcggc cgtcgtccaa cctcagctcc
     1801 ctgtccaacg cctccgagag ggaccagcac cacctgggaa gcccttctcg cctgagtgtc
     1861 ggggagcagc cagacgtcac ccacgacccc tatgagtttc ttcagtctcc agagcctgcg
     1921 gcctctgcca agacctaact ctagaccacc ttcagctctt ttattttatt tttttagttt
     1981 tattttgcac gtgtagagtt tttgtcatca gacaaggact ttgatcctgt cccctttggc
     2041 atgcgggaag cagccgcggg gaggtaatga attgtctgtg gtatcatgtc agcagagtct
     2101 ccaagcccca cgaaccctga ggagtggagt catacgcgaa ggccatatgg ccatcgtgtc
     2161 agcagagaga gtctctgtac acagccccgt gaaccctgag gagtggagtc atacacgaag
     2221 ggcgtgtggc catcgtgtca gcagagagag tctctgtaca cagccccgtg aaccctgagg
     2281 agtggagtca tacgcgaagg gtgtgtggcc aggctgcaga gctgcgtgcc gtttgtgtcc
     2341 gagcatcacg tgtggctcca gcccttgttt ctgccagtgt agacacctct gtctgcccca
     2401 ctgtcctggg gtcgctcttg ggaggcacag gcatgggtgt gtctggcctc attctgtatc
     2461 agtccagtgt gttcctgtca tagtttgtgt ctcccaggca ggccatggta ggggcctcgc
     2521 aggggccatt ggggagcaca gggccaggct ggggtgagga gagctcccct gttttctgtt
     2581 taattgatga gcctgggaaa ggagtgtgtt ctgcctgccc gttacagtgg agcgttccgt
     2641 gtccataaaa cgttttctaa ctggg
//
