LOCUS       NM_001311118            2047 bp    mRNA    linear   ROD 08-JUL-2025
DEFINITION  Mus musculus homeobox A1 (Hoxa1), transcript variant 2, mRNA.
ACCESSION   NM_001311118 XM_006505608
VERSION     NM_001311118.2
KEYWORDS    RefSeq.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 2047)
  AUTHORS   Escamilla-Vega,E., Seton,L.W.G., Kyomen,S., Murillo-Rincon,A.P.,
            Petersen,J., Tautz,D. and Kaucka,M.
  TITLE     Evolution of the essential gene MN1 during the macroevolutionary
            transition toward patterning the vertebrate hindbrain
  JOURNAL   Proc Natl Acad Sci U S A 122 (22), e2416061122 (2025)
   PUBMED   40424121
REFERENCE   2  (bases 1 to 2047)
  AUTHORS   Frenette,B., Gueno,J., Houde,N., Landry-Truchon,K., Giguere,A.,
            Ashok,T., Ryckman,A., Morton,B.R., Mansfield,J.H. and Jeannotte,L.
  TITLE     Loss of Hoxa5 function affects Hox gene expression in different
            biological contexts
  JOURNAL   Sci Rep 14 (1), 30903 (2024)
   PUBMED   39730789
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2047)
  AUTHORS   Wang,H., Liu,X., Liu,Y., Yang,C., Ye,Y., Yu,X., Sheng,N., Zhang,S.,
            Mao,B. and Ma,P.
  TITLE     The E3 ubiquitin ligase RNF220 maintains hindbrain Hox expression
            patterns through regulation of WDR5 stability
  JOURNAL   Elife 13, 94657 (2024)
   PUBMED   39526890
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2047)
  AUTHORS   Yang,J., Hu,W. and Zhao,J.
  TITLE     Overexpression of Homeobox A1 Relieves Ovalbumin-Induced Asthma in
            Mice and Is Associated with Blocking of the NF-kappaB Signaling
            Pathway
  JOURNAL   Crit Rev Immunol 44 (3), 25-35 (2024)
   PUBMED   38421703
  REMARK    GeneRIF: Overexpression of Homeobox A1 Relieves Ovalbumin-Induced
            Asthma in Mice and Is Associated with Blocking of the NF-kappaB
            Signaling Pathway.
REFERENCE   5  (bases 1 to 2047)
  AUTHORS   Petrelli,B., Ozturk,A., Pind,M., Ayele,H., Fainsod,A. and
            Hicks,G.G.
  TITLE     Genetically programmed retinoic acid deficiency during gastrulation
            phenocopies most known developmental defects due to acute prenatal
            alcohol exposure in FASD
  JOURNAL   Front Cell Dev Biol 11, 1208279 (2023)
   PUBMED   37397253
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2047)
  AUTHORS   Scott,M.P.
  TITLE     Vertebrate homeobox gene nomenclature
  JOURNAL   Cell 71 (4), 551-553 (1992)
   PUBMED   1358459
REFERENCE   7  (bases 1 to 2047)
  AUTHORS   Langston,A.W. and Gudas,L.J.
  TITLE     Identification of a retinoic acid responsive enhancer 3' of the
            murine homeobox gene Hox-1.6
  JOURNAL   Mech Dev 38 (3), 217-227 (1992)
   PUBMED   1360810
REFERENCE   8  (bases 1 to 2047)
  AUTHORS   Nazarali,A., Kim,Y. and Nirenberg,M.
  TITLE     Hox-1.11 and Hox-4.9 homeobox genes
  JOURNAL   Proc Natl Acad Sci U S A 89 (7), 2883-2887 (1992)
   PUBMED   1348361
REFERENCE   9  (bases 1 to 2047)
  AUTHORS   Chisaka,O., Musci,T.S. and Capecchi,M.R.
  TITLE     Developmental defects of the ear, cranial nerves and hindbrain
            resulting from targeted disruption of the mouse homeobox gene
            Hox-1.6
  JOURNAL   Nature 355 (6360), 516-520 (1992)
   PUBMED   1346922
REFERENCE   10 (bases 1 to 2047)
  AUTHORS   Fowlis,G.A., Adelman,S., Knight,A.M. and Simpson,E.
  TITLE     PCR-analyzed microsatellites of the mouse genome--additional
            polymorphisms among ten inbred mouse strains
  JOURNAL   Mamm Genome 3 (4), 192-196 (1992)
   PUBMED   1611214
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC091106.17.
            
            On Mar 18, 2023 this sequence version replaced NM_001311118.1.
            
            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##
            Transcript exon combination :: AK143943.1, SRR7652917.180246.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849375, SAMN00849381
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-455               AC091106.17        30662-31116
            456-550             AC091106.17        31320-31414
            551-2047            AC091106.17        31892-33388
FEATURES             Location/Qualifiers
     source          1..2047
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="6"
                     /map="6 25.4 cM"
     gene            1..2047
                     /gene="Hoxa1"
                     /gene_synonym="ERA1; Hox-1.6"
                     /note="homeobox A1"
                     /db_xref="GeneID:15394"
                     /db_xref="MGI:MGI:96170"
     exon            1..455
                     /gene="Hoxa1"
                     /gene_synonym="ERA1; Hox-1.6"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    93..95
                     /gene="Hoxa1"
                     /gene_synonym="ERA1; Hox-1.6"
                     /note="upstream in-frame stop codon"
     CDS             99..515
                     /gene="Hoxa1"
                     /gene_synonym="ERA1; Hox-1.6"
                     /note="isoform 2 is encoded by transcript variant 2;
                     homeobox protein Hox-A1; early retinoic acid 1; homeobox
                     protein Hox-1.6; homeotic protein ERA-1-993; homeoboxless
                     protein ERA-1-399"
                     /codon_start=1
                     /product="homeobox protein Hox-A1 isoform 2"
                     /protein_id="NP_001298047.1"
                     /db_xref="CCDS:CCDS80534.1"
                     /db_xref="GeneID:15394"
                     /db_xref="MGI:MGI:96170"
                     /translation="

MDNARMNSFLEYPILGSGDSGTCSARAYPSDHGITTFQSCAVSANSCGGDDRFLVGRGVQISSPHHHHHHHHHHHPQTATYQTSGNLGISYSHSSCGPSYGAQNFSAPYGPYGLNQEADPPRSLSFPCFRDVFSSADL"

     exon            456..550
                     /gene="Hoxa1"
                     /gene_synonym="ERA1; Hox-1.6"
                     /inference="alignment:Splign:2.1.0"
     exon            551..2047
                     /gene="Hoxa1"
                     /gene_synonym="ERA1; Hox-1.6"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2027..2032
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hoxa1"
                     /gene_synonym="ERA1; Hox-1.6"
                     /note="hexamer: AATAAA"
     polyA_site      2047
                     /gene="Hoxa1"
                     /gene_synonym="ERA1; Hox-1.6"
                     /note="major polyA site"
ORIGIN      

gtacattcatatcatttttcttctctggtcctatggaggaagtgagaaagttggcacggtcacccagggcttcgcaggatccaatcactcagtgacagatggacaatgcaagaatgaactcctttctggaataccccatccttggcagtggcgactctgggacctgctcggcgcgagcttacccctctgaccatgggattacaactttccaatcctgcgcggtcagtgccaacagctgcggcggcgacgaccgcttcctagtgggcaggggggtgcagatcagctcgccccaccaccaccaccaccaccaccaccatcaccacccccagacggctacttaccagacttctggaaaccttgggatttcttattcccactcgagttgtggtccaagctatggcgcgcagaacttcagtgcgccttatggcccctatggattaaatcaggaagcagacccaccaagaagcctgtcgttcccctgcttcagagacgtcttctccagcgcagacctttgactggatgaaagttaaaagaaaccctcccaaaacagggaaagttggagagtacggctacgtgggtcaacccaacgcagtgcgcaccaatttcaccaccaagcagctcacagagctggagaaggagttccacttcaacaagtaccttacacgagcgcgcagggtggagattgccgcgtccctacagctcaatgagacccaggtgaagatctggttccagaatcgccgcatgaagcagaagaagcgtgagaaggaggggctcctgcccatctcccctgccactcctcctggcagcgatgagaaaacggaagaatcatctgagaaatctagcccctcgcccagtgccccttctccggcatcgtctacctcagacactctgactacctcccactgaggctactccagcccaactctgcagcccaggcttctccctgggctgggatttcttacccaaagcacattcttagcttatcttcctttctttacagactctctcttcctttctcgtcccatctggggagctcctggccaagataaggtatttccagagaattctggagccttggttggaagttaactccttcatccacatcgggtgtccacatcaattgctgatggctcccaacatcctttccttcactgttgtgagatttttttctccccacaacctatgattccttttagatgtcggctggagaacagttagttccctttgccatcagacatttgcaggaaggaggcatctctccttttatctatgtattgttcttctccacctagcccttaagtaggacatagaggagagagagtgtccaaagactcatgaagaagagatgcactgtgtttacacaattaattcaccccctaacttagctggtttcatgtgtgtgagtttgctggttgtaaatgctttcccgtcagagatttatctttatacacattttatagaaatatgtaggtcactaaatcaaacagggtggacaaattctcaaaactggtacagttcatgtgtgattatgggcgaaagaagaaaacctctttcattcaaacagagtcagatgcctcagaagttggcctcaattggttctttcagagttaagaaggcctgccaagcactttgcctgtgccaggtcttcccaaactctaaccaattcttcctgcttctctggccaccctgcatttaaaaatcatgctggatcatttgtaacccaaaggtattcattctttcagtcaccctttccttccacactgtcttgtatcatggctggatccagtgtatttccagctaattgttaatgtgatggatggcacaatgaatgtatattttgtgtgattcgtgactagtcttctgcatgtcgcacaatgttctgatgtccctgaaatatcacactgagttctatcagttattctttgtgagcctatgatagtctccatttactgtacaatcatgaacagctctgagatcctggagtgatgtggtccagagcagagtttacgggtcttaagatgtctgtaataaaagtattcaagtttta

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