LOCUS       NM_153620               2358 bp    mRNA    linear   PRI 17-APR-2013
DEFINITION  Homo sapiens homeobox A1 (HOXA1), transcript variant 2, mRNA.
ACCESSION   NM_153620
VERSION     NM_153620.2  GI:84697021
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 2358)
  AUTHORS   Zha,T.Z., Hu,B.S., Yu,H.F., Tan,Y.F., Zhang,Y. and Zhang,K.
  TITLE     Overexpression of HOXA1 correlates with poor prognosis in patients
            with hepatocellular carcinoma
  JOURNAL   Tumour Biol. 33 (6), 2125-2134 (2012)
   PUBMED   22864671
  REMARK    GeneRIF: Overexpression of HOXA1 is associated with hepatocellular
            carcinoma.
REFERENCE   2  (bases 1 to 2358)
  AUTHORS   Cho,H.S., Toyokawa,G., Daigo,Y., Hayami,S., Masuda,K., Ikawa,N.,
            Yamane,Y., Maejima,K., Tsunoda,T., Field,H.I., Kelly,J.D.,
            Neal,D.E., Ponder,B.A., Maehara,Y., Nakamura,Y. and Hamamoto,R.
  TITLE     The JmjC domain-containing histone demethylase KDM3A is a positive
            regulator of the G1/S transition in cancer cells via
            transcriptional regulation of the HOXA1 gene
  JOURNAL   Int. J. Cancer 131 (3), E179-E189 (2012)
   PUBMED   22020899
  REMARK    GeneRIF: study demonstrates KDM3A is overexpressed in various types
            of cancer and directly activates transcription of HOXA1 through
            demethylation of histone H3K9 by binding to its promoter region
REFERENCE   3  (bases 1 to 2358)
  AUTHORS   Ohuchida,K., Mizumoto,K., Lin,C., Yamaguchi,H., Ohtsuka,T.,
            Sato,N., Toma,H., Nakamura,M., Nagai,E., Hashizume,M. and Tanaka,M.
  TITLE     MicroRNA-10a is overexpressed in human pancreatic cancer and
            involved in its invasiveness partially via suppression of the HOXA1
            gene
  JOURNAL   Ann. Surg. Oncol. 19 (7), 2394-2402 (2012)
   PUBMED   22407312
  REMARK    GeneRIF: Loss of HOXA1 is associated with pancreatic cancer.
REFERENCE   4  (bases 1 to 2358)
  AUTHORS   Bitu,C.C., Destro,M.F., Carrera,M., da Silva,S.D., Graner,E.,
            Kowalski,L.P., Soares,F.A. and Coletta,R.D.
  TITLE     HOXA1 is overexpressed in oral squamous cell carcinomas and its
            expression is correlated with poor prognosis
  JOURNAL   BMC Cancer 12, 146 (2012)
   PUBMED   22498108
  REMARK    GeneRIF: HOXA1 may contribute to oral carcinogenesis by increasing
            tumor cell proliferation, and suggest that HOXA1 expression might
            be helpful as a prognostic marker for patients with oral squamous
            cell carcinoma.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2358)
  AUTHORS   Song,R.R., Zou,L., Zhong,R., Zheng,X.W., Zhu,B.B., Chen,W., Liu,L.
            and Miao,X.P.
  TITLE     An integrated meta-analysis of two variants in HOXA1/HOXB1 and
            their effect on the risk of autism spectrum disorders
  JOURNAL   PLoS ONE 6 (9), E25603 (2011)
   PUBMED   21980499
  REMARK    GeneRIF: HOXA1 A218G and HOXB1 nINS/INS variants may not contribute
            significantly to autism spectrum disorders risk
REFERENCE   6  (bases 1 to 2358)
  AUTHORS   Green,N.C., Rambaldi,I., Teakles,J. and Featherstone,M.S.
  TITLE     A conserved C-terminal domain in PBX increases DNA binding by the
            PBX homeodomain and is not a primary site of contact for the YPWM
            motif of HOXA1
  JOURNAL   J. Biol. Chem. 273 (21), 13273-13279 (1998)
   PUBMED   9582372
REFERENCE   7  (bases 1 to 2358)
  AUTHORS   Studer,M., Gavalas,A., Marshall,H., Ariza-McNaughton,L.,
            Rijli,F.M., Chambon,P. and Krumlauf,R.
  TITLE     Genetic interactions between Hoxa1 and Hoxb1 reveal new roles in
            regulation of early hindbrain patterning
  JOURNAL   Development 125 (6), 1025-1036 (1998)
   PUBMED   9463349
  REMARK    GeneRIF: In mice, establishing Hoxb1 in rhombomere 4 is dependent
            on the early activation of Hoxa1 and Hoxb1 and that together both
            are essential for patterning the r4 territory.
REFERENCE   8  (bases 1 to 2358)
  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   9  (bases 1 to 2358)
  AUTHORS   Chariot,A., Moreau,L., Senterre,G., Sobel,M.E. and Castronovo,V.
  TITLE     Retinoic acid induces three newly cloned HOXA1 transcripts in MCF7
            breast cancer cells
  JOURNAL   Biochem. Biophys. Res. Commun. 215 (2), 713-720 (1995)
   PUBMED   7488013
REFERENCE   10 (bases 1 to 2358)
  AUTHORS   Hong,Y.S., Kim,S.Y., Bhattacharya,A., Pratt,D.R., Hong,W.K. and
            Tainsky,M.A.
  TITLE     Structure and function of the HOX A1 human homeobox gene cDNA
  JOURNAL   Gene 159 (2), 209-214 (1995)
   PUBMED   7622051
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DB246535.1, S79871.1 and
            BC032547.2.
            On Jan 10, 2006 this sequence version replaced gi:24497508.
            
            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. Two transcript variants encoding two different
            isoforms have been found for this gene, with only one of the
            isoforms containing the homeodomain region. [provided by RefSeq,
            Jul 2008].
            
            Transcript Variant: This variant (2) lacks an alternate coding
            segment compared to variant 1, which causes a frameshift. The
            resulting isoform (b) has a shorter, distinct C-terminus and lacks
            the homeodomain region compared to isoform a.
            
            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 :: S79871.1, AK308067.1 [ECO:0000332]
            RNAseq introns              :: mixed/partial sample support
                                           ERS025083, ERS025084 [ECO:0000350]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-100               DB246535.1         1-100
            101-1240            S79871.1           1-1140
            1241-2358           BC032547.2         1412-2529
FEATURES             Location/Qualifiers
     source          1..2358
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="7"
                     /map="7p15.3"
     gene            1..2358
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /note="homeobox A1"
                     /db_xref="GeneID:3198"
                     /db_xref="HGNC:5099"
                     /db_xref="MIM:142955"
     exon            1..448
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /inference="alignment:Splign:1.39.8"
     variation       complement(29)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:376159031"
     variation       complement(47)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:372667623"
     variation       complement(63)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:199540608"
     misc_feature    89..91
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /note="upstream in-frame stop codon"
     CDS             95..508
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /note="isoform b is encoded by transcript variant 2; homeo
                     box A1; homeobox 1F; Hox 1.6-like protein; lab-like
                     protein; homeobox protein HOX-A1; HOX A1 homeodomain
                     protein; homeobox protein Hox-1F"
                     /codon_start=1
                     /product="homeobox protein Hox-A1 isoform b"
                     /protein_id="NP_705873.2"
                     /db_xref="GI:84697022"
                     /db_xref="CCDS:CCDS5402.2"
                     /db_xref="GeneID:3198"
                     /db_xref="HGNC:5099"
                     /db_xref="MIM:142955"
                     /translation="

MDNARMNSFLEYPILSSGDSGTCSARAYPSDHRITTFQSCAVSANSCGGDDRFLVGRGVQIGSPHHHHHHHHHHPQPATYQTSGNLGVSYSHSSCGPSYGSQNFSAPYSPYALNQEADPPRSLSLPRIGDIFSSADF

"
     variation       complement(122)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:370355386"
     variation       complement(150)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:367605225"
     variation       complement(155)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:374581356"
     STS             160..391
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /standard_name="REN100307"
                     /db_xref="UniSTS:425104"
     variation       170
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:104894018"
     variation       complement(173)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:150376380"
     variation       178
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:104894017"
     variation       complement(181)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:370896322"
     variation       complement(189)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:140318803"
     variation       complement(214)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:200922808"
     variation       complement(236)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:146737549"
     variation       complement(245)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:144288739"
     variation       complement(268)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:77832452"
     variation       complement(282)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:376243279"
     variation       complement(285)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:373107510"
     variation       complement(288)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:146782650"
     variation       complement(304)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:199620262"
     variation       complement(307)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:2074398"
     variation       complement(310..312)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace=""
                     /replace="tcg"
                     /db_xref="dbSNP:368428758"
     variation       complement(312)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:10951154"
     variation       complement(316)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:370583131"
     STS             354..570
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /standard_name="ECD00936"
                     /db_xref="UniSTS:282045"
     variation       complement(388)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:377149193"
     variation       complement(421)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:372765755"
     variation       complement(430)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:111580588"
     variation       complement(433)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:199827755"
     variation       complement(440)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:369218661"
     exon            449..543
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /inference="alignment:Splign:1.39.8"
     variation       complement(453)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:150540921"
     variation       complement(457)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:17500494"
     exon            544..2346
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /inference="alignment:Splign:1.39.8"
     STS             560..837
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /standard_name="STS-U10421"
                     /db_xref="UniSTS:34895"
     variation       complement(570)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:370033913"
     variation       complement(575)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:34462126"
     STS             598..1491
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /standard_name="ECD00702"
                     /db_xref="UniSTS:281811"
     variation       complement(605)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:377716509"
     STS             623..894
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /standard_name="REN100302"
                     /db_xref="UniSTS:425099"
     variation       complement(632)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:143597165"
     variation       complement(643)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:141900601"
     variation       complement(656)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:138651027"
     variation       complement(668)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:183033372"
     variation       complement(669)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:200421049"
     variation       complement(688)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:41311763"
     variation       complement(713)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:373337108"
     variation       complement(765)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:144812662"
     variation       complement(766)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:113439849"
     variation       complement(770)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:375418482"
     variation       complement(772)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:372137447"
     variation       complement(786)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:41303378"
     variation       complement(813)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:41311760"
     variation       complement(842)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:141025500"
     variation       complement(844)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:190754463"
     variation       complement(849)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:199550475"
     variation       complement(871)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:145746454"
     STS             876..1139
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /standard_name="REN100301"
                     /db_xref="UniSTS:425098"
     variation       complement(919)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:374093898"
     variation       complement(939)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:368587915"
     variation       complement(955)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:56012816"
     variation       complement(1020)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:112390813"
     variation       complement(1080)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:145102625"
     variation       complement(1082)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:186304469"
     STS             1135..1406
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /standard_name="REN100300"
                     /db_xref="UniSTS:425097"
     STS             1209..2286
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /standard_name="stSG609305"
                     /db_xref="UniSTS:449405"
     variation       complement(1331)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:143106423"
     variation       complement(1353)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:41305921"
     variation       complement(1369)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:73683592"
     STS             1391..1652
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /standard_name="REN100299"
                     /db_xref="UniSTS:425096"
     STS             1400..2249
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /standard_name="HOXA1__v322"
                     /db_xref="UniSTS:277317"
     variation       complement(1462)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:117011404"
     variation       complement(1548)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:370119189"
     variation       complement(1622)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:183342348"
     STS             1629..1879
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /standard_name="REN100298"
                     /db_xref="UniSTS:425095"
     variation       complement(1650)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:368791817"
     variation       complement(1666)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:41308326"
     variation       complement(1806)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:76826100"
     variation       complement(1811)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:17449017"
     STS             1868..2131
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /standard_name="REN100297"
                     /db_xref="UniSTS:425094"
     variation       complement(1948)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:190587574"
     variation       complement(1958)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:17449010"
     variation       complement(1989)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:7786554"
     polyA_signal    2008..2013
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
     polyA_signal    2012..2017
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
     polyA_site      2026
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /experiment="experimental evidence, no additional details
                     recorded"
     polyA_site      2036
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /experiment="experimental evidence, no additional details
                     recorded"
     variation       complement(2127)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:148827747"
     variation       complement(2207)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:186111902"
     variation       complement(2244)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:114796827"
     variation       complement(2253)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:207467747"
     variation       complement(2290..2291)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
                     /replace=""
                     /replace="t"
                     /db_xref="dbSNP:370674583"
     polyA_site      2346
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F"
ORIGIN      

attcatatcatttttcttctccggccccatggaggaagtgagaaagttggcacagtcacgccgggcttcgcaggaccaggtcactcagtgacagatggacaatgcaagaatgaactccttcctggaataccccatacttagcagtggcgactcggggacctgctcagcccgagcctacccctcggaccataggattacaactttccagtcgtgcgcggtcagcgccaacagttgcggcggcgacgaccgcttcctagtgggcaggggggtgcagatcggttcgccccaccaccaccaccaccaccaccatcaccacccccagccggctacctaccagacttccgggaacctgggggtgtcctactcccactcaagttgtggtccaagctatggctcacagaacttcagtgcgccttacagcccctacgcgttaaatcaggaagcagacccaccaagaagcctgtcgctcccccgcatcggagacatcttctccagcgcagacttttgactggatgaaagtcaaaagaaaccctcccaaaacagggaaagttggagagtacggctacctgggtcaacccaacgcggtgcgcaccaacttcactaccaagcagctcacggaactggagaaggagttccacttcaacaagtacctgacgcgcgcccgcagggtggagatcgctgcatccctgcagctcaacgagacccaagtgaagatctggttccagaaccgccgaatgaagcaaaagaaacgtgagaaggagggtctcttgcccatctctccggccaccccgccaggaaacgacgagaaggccgaggaatcctcagagaagtccagctcttcgccctgcgttccttccccggggtcttctacctcagacactctgactacctcccactgaggcggctccagccccagacaacagcccaggcatctccttgggctgggacttcttacccaaagcacatgcttagcttatctttctttccatttacagtctctttcttcctttctaatcctatctggggagctcctggccaggataatatatttgcagataattctggaccagagacttggtgcggggttaacaccttcatccagattgggtgccagcatacattttctggtgggccttaacatccctcctgcttttaggagaattcacagaacctactgttcctttcagatgaccttttggaaaatagttccctttgccaacagaaacatgccagaaggaatcttctcatcttttatctaactatatgtacagctctcccctcccttgtccttgaaagtaggatatagcgaaaggcgagtccaggagctcaggaagaagagatgcactatatgtttacacaattaattcatcccttaatttaagtcattttcatgtgtgtgagtttgctggttgtaaatactttgtcctaagagatttatctttatacagattttctagaaatgtttaggttactaaaacagggtgggcaaactctctaaactggtacaattttataggtgaaagaaaaaattccctcatttaaacccaatcagatgcctcagagggtagccttgatttgttcttacagttaagaagccctgcagagcacaaacttcagaaacccggcttcctgtgctaagtctttcccaatctctacccctttcttctcgggccaccctctgtttaaaatttgtgctgggttattcagaacctaaaagtattattcaaaccaatttcttccttccacagttatcttagctggatataatgtattttcagctcaattgttaatgtgatggatggcacaatgaatgtatattttgtgttattcgtgaatagtcttttgcatgtcgcacaatgtttgatgtccccaaagtaccacactgagttctatcagttatcctttgtgagcctatgatattccccatttcctgtacaatcatgaacagctctgagatcctggagtgatatgatccagagcagagtttacgggtcttaggatgtctgtaataaataaatatactcaagtttcaggtatgcttaagcatccgtgtatttggctgggctacaatttgttaattcctatgaagttggcacatttcatgaggggaaagggagaagggtggtaaatattttcaaagagatgggccttttcttgaataaaagttaataacagctcctttattataatcaaagctcataatggaaaaaaagactgatgaagaaatttatgaagcagatttatttttgaaacaaacatggatacttcctgggtcaagtgctaaccttttcacctccaactggatgttgacgtatatataaacagaactcccttcaaaagccaaaaaaaaaaaaaaaa

//

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:3198 -> Molecular function: GO:0003700 [sequence-specific DNA binding transcription factor activity] evidence: IEA
            GeneID:3198 -> Molecular function: GO:0005515 [protein binding] evidence: IPI
            GeneID:3198 -> Molecular function: GO:0043565 [sequence-specific DNA binding] evidence: IEA
            GeneID:3198 -> Biological process: GO:0006351 [transcription, DNA-dependent] evidence: IEA
            GeneID:3198 -> Biological process: GO:0007275 [multicellular organismal development] evidence: TAS
            GeneID:3198 -> Biological process: GO:0007605 [sensory perception of sound] evidence: IDA
            GeneID:3198 -> Biological process: GO:0007634 [optokinetic behavior] evidence: IDA
            GeneID:3198 -> Biological process: GO:0008045 [motor neuron axon guidance] evidence: IEA
            GeneID:3198 -> Biological process: GO:0009653 [anatomical structure morphogenesis] evidence: IMP
            GeneID:3198 -> Biological process: GO:0009952 [anterior/posterior pattern specification] evidence: IEA
            GeneID:3198 -> Biological process: GO:0021569 [rhombomere 3 development] evidence: IEA
            GeneID:3198 -> Biological process: GO:0021570 [rhombomere 4 development] evidence: IEA
            GeneID:3198 -> Biological process: GO:0021571 [rhombomere 5 development] evidence: IEA
            GeneID:3198 -> Biological process: GO:0021599 [abducens nerve formation] evidence: IMP
            GeneID:3198 -> Biological process: GO:0021612 [facial nerve structural organization] evidence: IEA
            GeneID:3198 -> Biological process: GO:0021754 [facial nucleus development] evidence: IEA
            GeneID:3198 -> Biological process: GO:0021953 [central nervous system neuron differentiation] evidence: IEA
            GeneID:3198 -> Biological process: GO:0042473 [outer ear morphogenesis] evidence: IDA
            GeneID:3198 -> Biological process: GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] evidence: IEA
            GeneID:3198 -> Biological process: GO:0048702 [embryonic neurocranium morphogenesis] evidence: IMP
            GeneID:3198 -> Biological process: GO:0048839 [inner ear development] evidence: IMP
            GeneID:3198 -> Biological process: GO:0048844 [artery morphogenesis] evidence: IMP
            GeneID:3198 -> Biological process: GO:0050795 [regulation of behavior] evidence: IDA
            GeneID:3198 -> Biological process: GO:0050890 [cognition] evidence: IDA
            GeneID:3198 -> Biological process: GO:0050905 [neuromuscular process] evidence: IDA
            GeneID:3198 -> Biological process: GO:0060840 [artery development] evidence: IMP
            GeneID:3198 -> Biological process: GO:0060876 [semicircular canal formation] evidence: IMP
            GeneID:3198 -> Biological process: GO:0090102 [cochlea development] evidence: IMP
            GeneID:3198 -> Biological process: GO:0090103 [cochlea morphogenesis] evidence: IMP
            GeneID:3198 -> Cellular component: GO:0005634 [nucleus] evidence: IEA