LOCUS       NM_013075               2219 bp    mRNA    linear   ROD 01-APR-2024
DEFINITION  Rattus norvegicus homeobox A1 (Hoxa1), transcript variant 1, mRNA.
ACCESSION   NM_013075 XM_008762937 XM_008775736
VERSION     NM_013075.3
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 2219)
  AUTHORS   Li,M., Gai,F. and Chen,H.
  TITLE     MiR-30b-5p Influences Chronic Exercise Arthritic Injury by
            Targeting Hoxa1
  JOURNAL   Int J Sports Med 42 (13), 1199-1208 (2021)
   PUBMED   33930933
  REMARK    GeneRIF: MiR-30b-5p Influences Chronic Exercise Arthritic Injury by
            Targeting Hoxa1.
REFERENCE   2  (bases 1 to 2219)
  AUTHORS   Kovacs,I.A., Luck,K., Spirohn,K., Wang,Y., Pollis,C., Schlabach,S.,
            Bian,W., Kim,D.K., Kishore,N., Hao,T., Calderwood,M.A., Vidal,M.
            and Barabasi,A.L.
  TITLE     Network-based prediction of protein interactions
  JOURNAL   Nat Commun 10 (1), 1240 (2019)
   PUBMED   30886144
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2219)
  AUTHORS   Maamar,H., Cabili,M.N., Rinn,J. and Raj,A.
  TITLE     linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in
            cis
  JOURNAL   Genes Dev 27 (11), 1260-1271 (2013)
   PUBMED   23723417
REFERENCE   4  (bases 1 to 2219)
  AUTHORS   Jolma,A., Yan,J., Whitington,T., Toivonen,J., Nitta,K.R.,
            Rastas,P., Morgunova,E., Enge,M., Taipale,M., Wei,G., Palin,K.,
            Vaquerizas,J.M., Vincentelli,R., Luscombe,N.M., Hughes,T.R.,
            Lemaire,P., Ukkonen,E., Kivioja,T. and Taipale,J.
  TITLE     DNA-binding specificities of human transcription factors
  JOURNAL   Cell 152 (1-2), 327-339 (2013)
   PUBMED   23332764
REFERENCE   5  (bases 1 to 2219)
  AUTHORS   Yu,H., Tardivo,L., Tam,S., Weiner,E., Gebreab,F., Fan,C.,
            Svrzikapa,N., Hirozane-Kishikawa,T., Rietman,E., Yang,X.,
            Sahalie,J., Salehi-Ashtiani,K., Hao,T., Cusick,M.E., Hill,D.E.,
            Roth,F.P., Braun,P. and Vidal,M.
  TITLE     Next-generation sequencing to generate interactome datasets
  JOURNAL   Nat Methods 8 (6), 478-480 (2011)
   PUBMED   21516116
REFERENCE   6  (bases 1 to 2219)
  AUTHORS   Li,J., Tabor,H.K., Nguyen,L., Gleason,C., Lotspeich,L.J.,
            Spiker,D., Risch,N. and Myers,R.M.
  TITLE     Lack of association between HoxA1 and HoxB1 gene variants and
            autism in 110 multiplex families
  JOURNAL   Am J Med Genet 114 (1), 24-30 (2002)
   PUBMED   11840501
REFERENCE   7  (bases 1 to 2219)
  AUTHORS   Rossel,M. and Capecchi,M.R.
  TITLE     Mice mutant for both Hoxa1 and Hoxb1 show extensive remodeling of
            the hindbrain and defects in craniofacial development
  JOURNAL   Development 126 (22), 5027-5040 (1999)
   PUBMED   10529420
REFERENCE   8  (bases 1 to 2219)
  AUTHORS   Helmbacher,F., Pujades,C., Desmarquet,C., Frain,M., Rijli,F.M.,
            Chambon,P. and Charnay,P.
  TITLE     Hoxa1 and Krox-20 synergize to control the development of
            rhombomere 3
  JOURNAL   Development 125 (23), 4739-4748 (1998)
   PUBMED   9806922
REFERENCE   9  (bases 1 to 2219)
  AUTHORS   Dolle,P., Lufkin,T., Krumlauf,R., Mark,M., Duboule,D. and
            Chambon,P.
  TITLE     Local alterations of Krox-20 and Hox gene expression in the
            hindbrain suggest lack of rhombomeres 4 and 5 in homozygote null
            Hoxa-1 (Hox-1.6) mutant embryos
  JOURNAL   Proc Natl Acad Sci U S A 90 (16), 7666-7670 (1993)
   PUBMED   8102800
REFERENCE   10 (bases 1 to 2219)
  AUTHORS   Baron,A., Featherstone,M.S., Hill,R.E., Hall,A., Galliot,B. and
            Duboule,D.
  TITLE     Hox-1.6: a mouse homeo-box-containing gene member of the Hox-1
            complex
  JOURNAL   EMBO J 6 (10), 2977-2986 (1987)
   PUBMED   2891503
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000004.1.
            
            On Mar 27, 2023 this sequence version replaced NM_013075.2.
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the longer isoform (1).
            
            Sequence Note:.
            
            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 :: U93092.1, SRR26643292.17949.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760400, SAMEA5760476
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-747               JAXUCZ010000004.1  82588463-82589209   c
            748-2219            JAXUCZ010000004.1  82586505-82587976   c
FEATURES             Location/Qualifiers
     source          1..2219
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="4"
                     /map="4q24"
     gene            1..2219
                     /gene="Hoxa1"
                     /gene_synonym="Hoxa1l"
                     /note="homeobox A1"
                     /db_xref="GeneID:103690132"
                     /db_xref="RGD:11414885"
     exon            1..747
                     /gene="Hoxa1"
                     /gene_synonym="Hoxa1l"
                     /inference="alignment:Splign:2.1.0"
     CDS             99..1103
                     /gene="Hoxa1"
                     /gene_synonym="Hoxa1l"
                     /note="isoform 1 is encoded by transcript variant 1;
                     homeobox protein Hox-A1; homeo box A1"
                     /codon_start=1
                     /product="homeobox protein Hox-A1 isoform 1"
                     /protein_id="NP_037207.2"
                     /db_xref="GeneID:103690132"
                     /db_xref="RGD:11414885"
                     /translation="MDNARMNSFLEYPILGSGDSGTCSARVYSSDHGITTFQSCAVSA
                     NSCGGDDRFLGGRGVQITSPHHHHHHHHHPQPATYQTSGNLGVSYSHSSCGPSYGAQN
                     FSAPYGPYGLNQEADVSGGYPPCAPAVYSGNLSSPMVQHHHHHQGYAGGTVGSPQYIH
                     HSYGQEHQSLALATYNNSLSPLHASHQEACRSPASETSSPAQTFDWMKVKRNPPKTGK
                     VGEYGYVGQPNAVRTNFTTKQLTELEKEFHFNKYLTRARRVEIAASLQLNETQVKIWF
                     QNRRMKQKKREKEGLLPISPATPPGSDEKTEESSEKSSSSPSAPSPASSTSDTLTTSH
                     "
     exon            748..2219
                     /gene="Hoxa1"
                     /gene_synonym="Hoxa1l"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 gtacattcat atcatttttc ttctctggtc ctatggagga agtgagaaag ttggcacggt
       61 cacccagggc ttcgcaggac ccagtcactc agtgacagat ggacaatgca agaatgaact
      121 cctttctgga ataccccatc cttggcagtg gcgattctgg gacctgctcg gcgcgagttt
      181 actcctctga ccatggaatt acaactttcc aatcctgcgc ggtcagtgcc aacagctgcg
      241 gcggcgacga ccgcttccta gggggcaggg gggtgcagat cacctcgccc catcaccacc
      301 accaccacca tcaccatccc cagccggcta cttaccagac ttctgggaac cttggggttt
      361 cttattccca ctcgagttgt ggtccaagct atggcgcgca gaacttcagt gcgccttatg
      421 gcccctatgg attaaatcag gaagcagacg taagtggtgg gtaccccccg tgcgctcccg
      481 ctgtttactc tggaaacctc tcgtctccca tggtccagca tcaccaccac caccagggtt
      541 atgctggggg cacagtgggc tcgccccagt acattcacca ctcatatgga caagagcacc
      601 agagtctggc cctggccacg tataataact ccttatcccc tctccacgcc agccaccaag
      661 aagcctgtcg ttcccctgct tcagagacgt cttctccagc gcagaccttt gactggatga
      721 aagttaaaag aaaccctccc aaaacaggga aagttggaga gtatggctac gtgggtcaac
      781 ccaacgcagt gcgcaccaac ttcaccacca agcagctcac agagctggag aaggagttcc
      841 acttcaacaa gtacctaaca agagcccgca gggtggagat agccgcgtcc ctgcaactca
      901 atgagaccca ggtgaagatc tggttccaga atcgccgcat gaagcagaag aagcgcgaga
      961 aagaggggct cttgcccatt tcacccgcca cccctcctgg aagcgatgag aaaactgaag
     1021 aatcatctga gaaatccagc tcctcgccca gcgccccttc tcccgcatca tctacctcag
     1081 atactctgac tacctcccac tgaggctgcc ccagcccaac tctgcagccc aggcttctcc
     1141 ctgggctgag atttcttacc caaagcacat tcttagctta tcttcctttc tttccagact
     1201 ctctcttcct ttctggtccc atctggggag ctcctggcta agataagata tttccagaga
     1261 attctggaga cttggttgga agttaactcc ttattctata ccaggtgccc acatcaattt
     1321 ctgatggtcc ccaacgccct ttctttactg tcttgagatt tttttacaca acctatggtt
     1381 cctttactgt ccgttggaga acagttccct ttgccaacag atatctgcag aagggaggtg
     1441 tctcgccttt gtatctatgt attgttctgc tccacctggc ctttaagtag gacatagagg
     1501 agggagggtg tccaaaggct catgaggaag agatgctcca tgtttacaca attcacccct
     1561 tgattgctgg gtatgaatgc tttctcttca gagatttatc tttatacaca tttcgtagaa
     1621 atatgtaagt cactaaatca aacagggtgg acaaattctc aaaactggca caggccatgt
     1681 gtgattatgg gtgaaaggag aaaacctctc tcattctgag tcagatactt cagaaggtgg
     1741 ccttggttgg ttctttcaga gtttaggcct acaaagcaca aggttcagaa cctttcctgt
     1801 gccgagtctt cccaaactct aaccaattct tcctgcttct ctggccaccc tgcatttaaa
     1861 aaagttatgc tggactattt gtaacctaaa ggaattcttt tcaaccaccc tttcttttca
     1921 cagtatcttg tatcttggct ggagacaagt gtattttcag ctaattgttt gttaatgtga
     1981 tgtatggcac aacgaatgta tattttgtgt ggttcgtgaa tagtcttctg catgtcgcac
     2041 aatgttttga cctccctgaa atagcacact gagttctatc agttgtcctt tgtgagccta
     2101 agatagtccc catttcctgt acaatcatga gcagctctga gatcctggag tgacgtggtc
     2161 cagagcagag tttacgggtc ttacttaaga tgtctgtaat aaaatattca agtttcagg
//
