LOCUS       NM_152739               2076 bp    mRNA    linear   PRI 07-JUL-2013
DEFINITION  Homo sapiens homeobox A9 (HOXA9), mRNA.
ACCESSION   NM_152739
VERSION     NM_152739.3  GI:84043950
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 2076)
  AUTHORS   Li,Z., Zhang,Z., Li,Y., Arnovitz,S., Chen,P., Huang,H., Jiang,X.,
            Hong,G.M., Kunjamma,R.B., Ren,H., He,C., Wang,C.Z., Elkahloun,A.G.,
            Valk,P.J., Dohner,K., Neilly,M.B., Bullinger,L., Delwel,R.,
            Lowenberg,B., Liu,P.P., Morgan,R., Rowley,J.D., Yuan,C.S. and
            Chen,J.
  TITLE     PBX3 is an important cofactor of HOXA9 in leukemogenesis
  JOURNAL   Blood 121 (8), 1422-1431 (2013)
   PUBMED   23264595
  REMARK    GeneRIF: Collectively, our data suggest that PBX3 is a critical
            cofactor of HOXA9 in leukemogenesis.
REFERENCE   2  (bases 1 to 2076)
  AUTHORS   Ohno,Y., Yasunaga,S., Janmohamed,S., Ohtsubo,M., Saeki,K.,
            Kurogi,T., Mihara,K., Iscove,N.N. and Takihara,Y.
  TITLE     Hoxa9 transduction induces hematopoietic stem and progenitor cell
            activity through direct down-regulation of geminin protein
  JOURNAL   PLoS ONE 8 (1), E53161 (2013)
   PUBMED   23326393
  REMARK    GeneRIF: Data indicate that retroviral transduction-mediated
            overexpression or siRNA-mediated knock-down of Hoxa9 respectively
            down-regulated or up-regulated Geminin in hematopoietic cells.
REFERENCE   3  (bases 1 to 2076)
  AUTHORS   Ko,S.Y., Barengo,N., Ladanyi,A., Lee,J.S., Marini,F., Lengyel,E.
            and Naora,H.
  TITLE     HOXA9 promotes ovarian cancer growth by stimulating
            cancer-associated fibroblasts
  JOURNAL   J. Clin. Invest. 122 (10), 3603-3617 (2012)
   PUBMED   22945634
  REMARK    GeneRIF: HOXA9 expression is associated with poor outcomes in
            epithelial ovarian cancer & and in mouse EOC xenografts. HOXA9
            expression in EOC cells promotes a microenvironment permissive for
            tumor growth, via paracrine TGF-beta-2 action on fibroblasts.
REFERENCE   4  (bases 1 to 2076)
  AUTHORS   Reinert,T., Borre,M., Christiansen,A., Hermann,G.G., Orntoft,T.F.
            and Dyrskjot,L.
  TITLE     Diagnosis of bladder cancer recurrence based on urinary levels of
            EOMES, HOXA9, POU4F2, TWIST1, VIM, and ZNF154 hypermethylation
  JOURNAL   PLoS ONE 7 (10), E46297 (2012)
   PUBMED   23056278
  REMARK    GeneRIF: Methylation levels of EOMES, HOXA9, POU4F2, TWIST1, VIM,
            and ZNF154 in urine specimens are promising diagnostic biomarkers
            for bladder cancer recurrence surveillance
REFERENCE   5  (bases 1 to 2076)
  AUTHORS   Durand,C., Decker,E., Roeth,R., Schneider,K.U. and Rappold,G.
  TITLE     The homeobox transcription factor HOXA9 is a regulator of SHOX in
            U2OS cells and chicken micromass cultures
  JOURNAL   PLoS ONE 7 (9), E45369 (2012)
   PUBMED   23028966
  REMARK    GeneRIF: Data identified the homeodomain protein HOXA9 as a
            positive regulator of SHOX expression in U2OS cells.
REFERENCE   6  (bases 1 to 2076)
  AUTHORS   Borrow,J., Shearman,A.M., Stanton,V.P. Jr., Becher,R., Collins,T.,
            Williams,A.J., Dube,I., Katz,F., Kwong,Y.L., Morris,C.,
            Ohyashiki,K., Toyama,K., Rowley,J. and Housman,D.E.
  TITLE     The t(7;11)(p15;p15) translocation in acute myeloid leukaemia fuses
            the genes for nucleoporin NUP98 and class I homeoprotein HOXA9
  JOURNAL   Nat. Genet. 12 (2), 159-167 (1996)
   PUBMED   8563754
REFERENCE   7  (bases 1 to 2076)
  AUTHORS   Nakamura,T., Largaespada,D.A., Lee,M.P., Johnson,L.A.,
            Ohyashiki,K., Toyama,K., Chen,S.J., Willman,C.L., Chen,I.M.,
            Feinberg,A.P., Jenkins,N.A., Copeland,N.G. and Shaughnessy,J.D. Jr.
  TITLE     Fusion of the nucleoporin gene NUP98 to HOXA9 by the chromosome
            translocation t(7;11)(p15;p15) in human myeloid leukaemia
  JOURNAL   Nat. Genet. 12 (2), 154-158 (1996)
   PUBMED   8563753
REFERENCE   8  (bases 1 to 2076)
  AUTHORS   Scott,M.P.
  TITLE     Vertebrate homeobox gene nomenclature
  JOURNAL   Cell 71 (4), 551-553 (1992)
   PUBMED   1358459
REFERENCE   9  (bases 1 to 2076)
  AUTHORS   McAlpine,P.J. and Shows,T.B.
  TITLE     Nomenclature for human homeobox genes
  JOURNAL   Genomics 7 (3), 460 (1990)
   PUBMED   1973146
REFERENCE   10 (bases 1 to 2076)
  AUTHORS   Acampora,D., D'Esposito,M., Faiella,A., Pannese,M., Migliaccio,E.,
            Morelli,F., Stornaiuolo,A., Nigro,V., Simeone,A. and Boncinelli,E.
  TITLE     The human HOX gene family
  JOURNAL   Nucleic Acids Res. 17 (24), 10385-10402 (1989)
   PUBMED   2574852
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BG258601.1, BC006537.2,
            CA442923.1 and AW612618.1.
            This sequence is a reference standard in the RefSeqGene project.
            On Dec 29, 2005 this sequence version replaced gi:24497557.
            
            Summary: In vertebrates, the genes encoding the class of
            transcription factors called homeobox genes are found in clusters
            named A, B, C, and D on four separate chromosomes. Expression of
            these proteins is spatially and temporally regulated during
            embryonic development. This gene is part of the A cluster on
            chromosome 7 and encodes a DNA-binding transcription factor which
            may regulate gene expression, morphogenesis, and differentiation.
            This gene is highly similar to the abdominal-B (Abd-B) gene of
            Drosophila. A specific translocation event which causes a fusion
            between this gene and the NUP98 gene has been associated with
            myeloid leukemogenesis. Read-through transcription exists between
            this gene and the upstream homeobox A10 (HOXA10) gene.[provided by
            RefSeq, Mar 2011].
            
            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 :: BC006537.2, BQ422016.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           ERS025084, ERS025087 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-20                BG258601.1         1-20
            21-974              BC006537.2         1-954
            975-1589            CA442923.1         19-633              c
            1590-2049           AW612618.1         8-467               c
            2050-2076           BC006537.2         2030-2056
FEATURES             Location/Qualifiers
     source          1..2076
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="7"
                     /map="7p15.2"
     gene            1..2076
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /note="homeobox A9"
                     /db_xref="GeneID:3205"
                     /db_xref="HGNC:5109"
                     /db_xref="HPRD:00844"
                     /db_xref="MIM:142956"
     exon            1..653
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    11..13
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /note="upstream in-frame stop codon"
     CDS             74..892
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /note="homeodomain protein HOXA9; homeobox protein Hox-1G"
                     /codon_start=1
                     /product="homeobox protein Hox-A9"
                     /protein_id="NP_689952.1"
                     /db_xref="GI:23097236"
                     /db_xref="CCDS:CCDS5409.1"
                     /db_xref="GeneID:3205"
                     /db_xref="HGNC:5109"
                     /db_xref="HPRD:00844"
                     /db_xref="MIM:142956"
                     /translation="

MATTGALGNYYVDSFLLGADAADELSVGRYAPGTLGQPPRQAATLAEHPDFSPCSFQSKATVFGASWNPVHAAGANAVPAAVYHHHHHHPYVHPQAPVAAAAPDGRYMRSWLEPTPGALSFAGLPSSRPYGIKPEPLSARRGDCPTLDTHTLSLTDYACGSPPVDREKQPSEGAFSENNAENESGGDKPPIDPNNPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDRAKDE

"
     misc_feature    74..652
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /note="Hox9 activation region; Region: Hox9_act;
                     pfam04617"
                     /db_xref="CDD:191048"
     misc_feature    491..493
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="Symmetric dimethylarginine; propagated from
                     UniProtKB/Swiss-Prot (P31269.4); methylation site"
     misc_feature    560..565
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="Breakpoint for translocation to form MSI2/HOXA9
                     fusion protein; propagated from UniProtKB/Swiss-Prot
                     (P31269.4); other site"
     misc_feature    692..862
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /note="Homeodomain;  DNA binding domains involved in the
                     transcriptional regulation of key eukaryotic developmental
                     processes; may bind to DNA as monomers or as homo- and/or
                     heterodimers, in a sequence-specific manner; Region:
                     homeodomain; cd00086"
                     /db_xref="CDD:28970"
     misc_feature    order(692..706,710..712,761..763,779..781,818..820,
                     824..829,836..841,845..853,857..862)
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:28970"
     misc_feature    order(698..700,707..709,827..829,836..841,848..850)
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:28970"
     variation       181
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:35958560"
     STS             210..276
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /standard_name="Hoxa9"
                     /db_xref="UniSTS:536646"
     STS             232..481
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /standard_name="REN100619"
                     /db_xref="UniSTS:425416"
     variation       418
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:35355140"
     STS             606..856
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /standard_name="Hoxa9"
                     /db_xref="UniSTS:516607"
     exon            654..2057
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /inference="alignment:Splign:1.39.8"
     STS             704..816
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /standard_name="HOX1"
                     /db_xref="UniSTS:71932"
     variation       741
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:35991882"
     STS             747..978
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /standard_name="REN100612"
                     /db_xref="UniSTS:425409"
     STS             858..1429
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /standard_name="Hoxa9"
                     /db_xref="UniSTS:468837"
     STS             958..1222
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /standard_name="REN100611"
                     /db_xref="UniSTS:425408"
     STS             1154..1405
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /standard_name="REN100610"
                     /db_xref="UniSTS:425407"
     STS             1373..1600
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /standard_name="REN100609"
                     /db_xref="UniSTS:425406"
     STS             1487..1636
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /standard_name="RH18061"
                     /db_xref="UniSTS:50049"
     polyA_signal    1567..1572
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
     polyA_site      1589
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /experiment="experimental evidence, no additional details
                     recorded"
     STS             1593..1842
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
                     /standard_name="REN100608"
                     /db_xref="UniSTS:425405"
     polyA_signal    2033..2038
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
     polyA_site      2057
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G"
ORIGIN      

agttgttacatgaaatctgcagtttcataatttccgtgggtcgggccgggcgggccaggcgctgggcacggtgatggccaccactggggccctgggcaactactacgtggactcgttcctgctgggcgccgacgccgcggatgagctgagcgttggccgctatgcgccggggaccctgggccagcctccccggcaggcggcgacgctggccgagcaccccgacttcagcccgtgcagcttccagtccaaggcgacggtgtttggcgcctcgtggaacccagtgcacgcggcgggcgccaacgctgtacccgctgcggtgtaccaccaccatcaccaccacccctacgtgcacccccaggcgcccgtggcggcggcggcgccggacggcaggtacatgcgctcctggctggagcccacgcccggtgcgctctccttcgcgggcttgccctccagccggccttatggcattaaacctgaaccgctgtcggccagaaggggtgactgtcccacgcttgacactcacactttgtccctgactgactatgcttgtggttctcctccagttgatagagaaaaacaacccagcgaaggcgccttctctgaaaacaatgctgagaatgagagcggcggagacaagccccccatcgatcccaataacccagcagccaactggcttcatgcgcgctccactcggaaaaagcggtgcccctatacaaaacaccagaccctggaactggagaaagagtttctgttcaacatgtacctcaccagggaccgcaggtacgaggtggctcgactgctcaacctcaccgagaggcaggtcaagatctggttccagaaccgcaggatgaaaatgaagaaaatcaacaaagaccgagcaaaagacgagtgatgccatttgggcttatttagaaaaaagggtaagctagagagaaaaagaaagaactgtccgtcccccttccgccttctcccttctctcacccccaccctagcctccaccatccccgcacaaagcggctctaaacctcaggccacatcttttccaaggcaaaccctgttcaggctggctcgtaggcctgccgctttgatggaggaggtattgtaagctttccattttctataagaaaaaggaaaagttgaggggggggcattagtgctgatagctgtgtgtgttagcttgtatatatatttttaaaaatctacctgttcctgacttaaaacaaaaggaaagaaactacctttttataatgcacaactgttgatggtaggctgtatagtttttagtctgtgtagttaatttaatttgcagtttgtgcggcagattgctctgccaagatacttgaacactgtgttttattgtggtaattatgttttgtgattcaaacttctgtgtactgggtgatgcacccattgtgattgtggaagatagaattcaatttgaactcaggttgtttatgaggggaaaaaaacagttgcatagagtatagctctgtagtggaatatgtcttctgtataactaggctgttaacctatgattgtaaagtagctgtaagaatttcccagtgaaataaaaaaaaattttaagtgttctcggggatgcatagattcatcattttctccaccttaaaaatgcgggcatttaagtctgtccattatctatatagtcctgtcttgtctattgtatatataatctatatgattaaagaaaatatgcataatcagacaagcttgaatattgtttttgcaccagacgaacagtgaggaaattcggagctatacatatgtgcagaaggttactacctagggtttatgcttaattttaattggaggaaatgaatgctgattgtaacggagttaattttattgataataaattatacactatgaaaccgccattgggctactgtagatttgtatccttgatgaatctggggtttccatcagactgaacttacactgtatattttgcaatagttacctcaaggcctactgaccaaattgttgtgttgagatgatatttaactttttgccaaataaaatatattgattcttttctaaaaaaaaaaaaaaaaaaaa

//

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:3205 -> Molecular function: GO:0003700 [sequence-specific DNA binding transcription factor activity] evidence: IEA
            GeneID:3205 -> Molecular function: GO:0005515 [protein binding] evidence: IPI
            GeneID:3205 -> Molecular function: GO:0019899 [enzyme binding] evidence: IPI
            GeneID:3205 -> Molecular function: GO:0043565 [sequence-specific DNA binding] evidence: IEA
            GeneID:3205 -> Biological process: GO:0006351 [transcription, DNA-dependent] evidence: IEA
            GeneID:3205 -> Biological process: GO:0007275 [multicellular organismal development] evidence: IEA
            GeneID:3205 -> Biological process: GO:0042118 [endothelial cell activation] evidence: IMP
            GeneID:3205 -> Biological process: GO:0045638 [negative regulation of myeloid cell differentiation] evidence: ISS
            GeneID:3205 -> Cellular component: GO:0005634 [nucleus] evidence: IDA