LOCUS       NM_006735               1791 bp    mRNA    linear   PRI 07-JUL-2013
DEFINITION  Homo sapiens homeobox A2 (HOXA2), mRNA.
ACCESSION   NM_006735
VERSION     NM_006735.3  GI:37596298
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 1791)
  AUTHORS   Monks,D.C., Jahangir,A., Shanske,A.L., Samanich,J., Morrow,B.E. and
            Babcock,M.
  TITLE     Mutational analysis of HOXA2 and SIX2 in a Bronx population with
            isolated microtia
  JOURNAL   Int. J. Pediatr. Otorhinolaryngol. 74 (8), 878-882 (2010)
   PUBMED   20542577
  REMARK    GeneRIF: Lack of mutations in the coding region of HOXA2 among the
            sporadic microtia patients.
REFERENCE   2  (bases 1 to 1791)
  AUTHORS   Ester,A.R., Weymouth,K.S., Burt,A., Wise,C.A., Scott,A.,
            Gurnett,C.A., Dobbs,M.B., Blanton,S.H. and Hecht,J.T.
  TITLE     Altered transmission of HOX and apoptotic SNPs identify a potential
            common pathway for clubfoot
  JOURNAL   Am. J. Med. Genet. A 149A (12), 2745-2752 (2009)
   PUBMED   19938081
  REMARK    GeneRIF: Observational study of gene-disease association and
            gene-gene interaction. (HuGE Navigator)
REFERENCE   3  (bases 1 to 1791)
  AUTHORS   Yerges LM, Klei L, Cauley JA, Roeder K, Kammerer CM, Moffett SP,
            Ensrud KE, Nestlerode CS, Marshall LM, Hoffman AR, Lewis C, Lang
            TF, Barrett-Connor E, Ferrell RE, Orwoll ES and Zmuda JM.
  CONSRTM   MrOS Research Group
  TITLE     High-density association study of 383 candidate genes for
            volumetric BMD at the femoral neck and lumbar spine among older men
  JOURNAL   J. Bone Miner. Res. 24 (12), 2039-2049 (2009)
   PUBMED   19453261
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   4  (bases 1 to 1791)
  AUTHORS   Alasti,F., Sadeghi,A., Sanati,M.H., Farhadi,M., Stollar,E.,
            Somers,T. and Van Camp,G.
  TITLE     A mutation in HOXA2 is responsible for autosomal-recessive microtia
            in an Iranian family
  JOURNAL   Am. J. Hum. Genet. 82 (4), 982-991 (2008)
   PUBMED   18394579
  REMARK    GeneRIF: A missense mutation in the HOXA2 in a consanguineous
            iranian family with bilateral microtia was reported.
            Erratum:[Am J Hum Genet. 2008 Sep;83(3):424]
REFERENCE   5  (bases 1 to 1791)
  AUTHORS   Kosaki,K., Kosaki,R., Suzuki,T., Yoshihashi,H., Takahashi,T.,
            Sasaki,K., Tomita,M., McGinnis,W. and Matsuo,N.
  TITLE     Complete mutation analysis panel of the 39 human HOX genes
  JOURNAL   Teratology 65 (2), 50-62 (2002)
   PUBMED   11857506
REFERENCE   6  (bases 1 to 1791)
  AUTHORS   Apiou,F., Flagiello,D., Cillo,C., Malfoy,B., Poupon,M.F. and
            Dutrillaux,B.
  TITLE     Fine mapping of human HOX gene clusters
  JOURNAL   Cytogenet. Cell Genet. 73 (1-2), 114-115 (1996)
   PUBMED   8646877
REFERENCE   7  (bases 1 to 1791)
  AUTHORS   Scott,M.P.
  TITLE     Vertebrate homeobox gene nomenclature
  JOURNAL   Cell 71 (4), 551-553 (1992)
   PUBMED   1358459
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BF509655.1, AW292406.1,
            BE465040.1, AI581335.1 and AI796505.1.
            This sequence is a reference standard in the RefSeqGene project.
            On Oct 9, 2003 this sequence version replaced gi:24497510.
            
            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.
            The encoded protein may be involved in the placement of hindbrain
            segments in the proper location along the anterior-posterior axis
            during development. [provided by RefSeq, Jul 2008].
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC130571.1, BE465040.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           ERS025090, ERS025099 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-490               BF509655.1         1-490               c
            491-609             AW292406.1         7-125
            610-1091            BE465040.1         75-556
            1092-1439           AI581335.1         1-348               c
            1440-1791           AI796505.1         1-352               c
FEATURES             Location/Qualifiers
     source          1..1791
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="7"
                     /map="7p15.2"
     gene            1..1791
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /note="homeobox A2"
                     /db_xref="GeneID:3199"
                     /db_xref="HGNC:5103"
                     /db_xref="HPRD:05252"
                     /db_xref="MIM:604685"
     exon            1..666
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /inference="alignment:Splign:1.39.8"
     STS             46..1522
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /db_xref="UniSTS:486643"
     STS             113..351
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /standard_name="REN100339"
                     /db_xref="UniSTS:425136"
     STS             143..1470
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /db_xref="UniSTS:491328"
     STS             241..1436
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /db_xref="UniSTS:481967"
     STS             247..1741
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /db_xref="UniSTS:494538"
     misc_feature    252..254
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /note="upstream in-frame stop codon"
     CDS             276..1406
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /note="homeobox protein Hox-1K"
                     /codon_start=1
                     /product="homeobox protein Hox-A2"
                     /protein_id="NP_006726.1"
                     /db_xref="GI:10140847"
                     /db_xref="CCDS:CCDS5403.1"
                     /db_xref="GeneID:3199"
                     /db_xref="HGNC:5103"
                     /db_xref="HPRD:05252"
                     /db_xref="MIM:604685"
                     /translation="

MNYEFEREIGFINSQPSLAECLTSFPPVADTFQSSSIKTSTLSHSTLIPPPFEQTIPSLNPGSHPRHGAGGRPKPSPAGSRGSPVPAGALQPPEYPWMKEKKAAKKTALLPAAAAAATAAATGPACLSHKESLEIADGSGGGSRRLRTAYTNTQLLELEKEFHFNKYLCRPRRVEIAALLDLTERQVKVWFQNRRMKHKRQTQCKENQNSEGKCKSLEDSEKVEEDEEEKTLFEQALSVSGALLEREGYTFQQNALSQQQAPNGHNGDSQSFPVSPLTSNEKNLKHFQHQSPTVPNCLSTMGQNCGAGLNNDSPEALEVPSLQDFSVFSTDSCLQLSDAVSPSLPGSLDSPVDISADSLDFFTDTLTTIDLQHLNY

"
     misc_feature    555..572
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="propagated from UniProtKB/Swiss-Prot (O43364.1);
                     Region: Antp-type hexapeptide"
     misc_feature    705..878
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /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(705..719,723..725,774..776,792..794,831..833,
                     837..842,849..854,858..866,870..875)
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:28970"
     misc_feature    order(711..713,720..722,840..842,849..854,861..863)
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:28970"
     STS             328..402
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /standard_name="Hoxa2"
                     /db_xref="UniSTS:536640"
     STS             330..578
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /standard_name="REN100338"
                     /db_xref="UniSTS:425135"
     exon            667..1778
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /inference="alignment:Splign:1.39.8"
     STS             710..959
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /standard_name="REN100333"
                     /db_xref="UniSTS:425130"
     STS             717..1114
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /standard_name="MARC_12745-12746:1030738152:1"
                     /db_xref="UniSTS:267439"
     variation       860..861
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:941002"
     STS             954..1214
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /standard_name="REN100332"
                     /db_xref="UniSTS:425129"
     STS             1012..1162
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /standard_name="Hoxa2"
                     /db_xref="UniSTS:143365"
     STS             1034..1165
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /standard_name="SHGC-57559"
                     /db_xref="UniSTS:27278"
     STS             1197..1442
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /standard_name="REN100331"
                     /db_xref="UniSTS:425128"
     STS             1256..1521
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /standard_name="stSG609312"
                     /db_xref="UniSTS:449411"
     STS             1419..1663
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /standard_name="REN100330"
                     /db_xref="UniSTS:425127"
     polyA_signal    1754..1759
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
     polyA_site      1778
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
ORIGIN      

tcttttgattaaagcccaaattgtcattgggcagaagcaatcatgtgacagccaattcggtccaatttcaaccttgtctccatgaattcaatagtttaatagtagcgcggtccccatacggctgtaatcagtgaattagaaaaaaaacaccctagcagcgatattctatgatagattttttttcctctgcgctcgcctttttcctaggccttgcccccccaaagcccctccaaaagagggaactttttctctgagggggctccaaggagaaggccatgaattacgaatttgagcgagagattggttttatcaatagccagccgtcgctcgctgagtgcctgacatcttttccccctgtcgctgatacatttcaaagttcatcaatcaagacctcgacgctttcacactcgacactgattcctcctccttttgagcagaccattcccagcctgaaccccggcagtcaccctcgccacggcgctggcggccgccccaagccgagccccgcgggcagccgcggcagcccggtgcccgccggcgccctgcagccgcccgagtacccctggatgaaggagaagaaggcggccaagaaaaccgcacttctgccggccgccgccgccgccgccaccgccgcagccaccggccctgcttgcctcagccacaaagaatccctggaaatcgccgatggcagcggcgggggatcgcggcgcctgagaactgcttacaccaacacacagcttctagagctggaaaaagaatttcatttcaacaagtacctttgcagaccccgaagggtggagattgcagcgctgctggatttgactgagagacaagtgaaagtgtggtttcagaaccggaggatgaagcacaagaggcagacccagtgcaaggaaaaccaaaacagcgaagggaaatgtaaaagccttgaggactccgagaaagtagaggaggacgaggaagagaagacgctctttgagcaagcccttagcgtctctggggcccttctggagagggaaggctacacttttcagcaaaatgccctctctcagcagcaggctcccaatggacacaatggcgactcccaaagtttcccagtctcgcctttaaccagcaatgagaaaaatctgaaacattttcagcaccagtcacccactgttcccaactgcttgtcaacaatgggccagaactgtggagctggcctaaacaatgacagtcctgaggcccttgaggtcccctctttgcaggactttagcgttttctccacagattcctgcctgcagctttcagatgcagtttcacccagtttgccaggttccctcgacagtcccgtagatatttcagctgacagcttagacttttttacagacacactcaccacaatcgacttgcagcatctgaattactaaaaacattaaagcaaaacaaagcatcaccaaacaaaaactcctttgaccaggtggttttgccttcttttatttgggagtttattttttattttcttcttgacctaccccttccctcctttaagtgttgaggattttctgtttagtgattccctgacccagtttcaaacagagccatcttttacagattattttggagttttagttgttttaaacctaactcaacaaccctttatgtgattcctgagagcagtatgaggcctgcaagaaagtgatcatataattgtatcttcactttctttttatttttgtattacattgggatgcattgtcatgcatattttttgtagaataaattctcctttgctataagtaaaaaaaaaaaaaa

//

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:3199 -> Molecular function: GO:0003700 [sequence-specific DNA binding transcription factor activity] evidence: IEA
            GeneID:3199 -> Molecular function: GO:0043565 [sequence-specific DNA binding] evidence: IEA
            GeneID:3199 -> Biological process: GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] evidence: IEA
            GeneID:3199 -> Biological process: GO:0001709 [cell fate determination] evidence: IEA
            GeneID:3199 -> Biological process: GO:0002076 [osteoblast development] evidence: IEA
            GeneID:3199 -> Biological process: GO:0006351 [transcription, DNA-dependent] evidence: IEA
            GeneID:3199 -> Biological process: GO:0007379 [segment specification] evidence: IEA
            GeneID:3199 -> Biological process: GO:0008045 [motor neuron axon guidance] evidence: IEA
            GeneID:3199 -> Biological process: GO:0009952 [anterior/posterior pattern specification] evidence: IEA
            GeneID:3199 -> Biological process: GO:0009953 [dorsal/ventral pattern formation] evidence: IEA
            GeneID:3199 -> Biological process: GO:0021568 [rhombomere 2 development] evidence: IEA
            GeneID:3199 -> Biological process: GO:0021658 [rhombomere 3 morphogenesis] evidence: IEA
            GeneID:3199 -> Biological process: GO:0035284 [brain segmentation] evidence: IEA
            GeneID:3199 -> Biological process: GO:0042474 [middle ear morphogenesis] evidence: IEA
            GeneID:3199 -> Biological process: GO:0045665 [negative regulation of neuron differentiation] evidence: IEA
            GeneID:3199 -> Biological process: GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] evidence: IEA
            GeneID:3199 -> Biological process: GO:0048703 [embryonic viscerocranium morphogenesis] evidence: IEA
            GeneID:3199 -> Cellular component: GO:0005634 [nucleus] evidence: IDA
            GeneID:3199 -> Cellular component: GO:0005730 [nucleolus] evidence: IDA