LOCUS       NM_008273               3959 bp    mRNA    linear   ROD 29-OCT-2024
DEFINITION  Mus musculus homeobox D11 (Hoxd11), transcript variant 1, mRNA.
ACCESSION   NM_008273
VERSION     NM_008273.2
KEYWORDS    RefSeq; RefSeq Select.
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 3959)
  AUTHORS   Oikonomakos,I., Tedesco,M., Motamedi,F.J., Peitzsch,M., Nef,S.,
            Bornstein,S.R., Schedl,A., Steenblock,C. and Neirijnck,Y.
  TITLE     In vitro differentiation of mouse pluripotent stem cells into
            corticosteroid-producing adrenocortical cells
  JOURNAL   Stem Cell Reports 19 (9), 1289-1303 (2024)
   PUBMED   39178848
REFERENCE   2  (bases 1 to 3959)
  AUTHORS   Huang,B., Zeng,Z., Kim,S., Fausto,C.C., Koppitch,K., Li,H., Li,Z.,
            Chen,X., Guo,J., Zhang,C.C., Ma,T., Medina,P., Schreiber,M.E.,
            Xia,M.W., Vonk,A.C., Xiang,T., Patel,T., Li,Y., Parvez,R.K.,
            Der,B., Chen,J.H., Liu,Z., Thornton,M.E., Grubbs,B.H., Diao,Y.,
            Dou,Y., Gnedeva,K., Ying,Q., Pastor-Soler,N.M., Fei,T.,
            Hallows,K.R., Lindstrom,N.O., McMahon,A.P. and Li,Z.
  TITLE     Long-term expandable mouse and human-induced nephron progenitor
            cells enable kidney organoid maturation and modeling of plasticity
            and disease
  JOURNAL   Cell Stem Cell 31 (6), 921-939 (2024)
   PUBMED   38692273
REFERENCE   3  (bases 1 to 3959)
  AUTHORS   Soussi,G., Girdziusaite,A., Jhanwar,S., Palacio,V., Notaro,M.,
            Sheth,R., Zeller,R. and Zuniga,A.
  TITLE     TBX3 is essential for establishment of the posterior boundary of
            anterior genes and upregulation of posterior genes together with
            HAND2 during the onset of limb bud development
  JOURNAL   Development 151 (11) (2024)
   PUBMED   38828908
REFERENCE   4  (bases 1 to 3959)
  AUTHORS   Saito,S., Kanazawa,U., Tatsumi,A., Iida,A., Takemoto,T. and
            Suzuki,T.
  TITLE     Functional analysis of a first hindlimb positioning enhancer via
            Gdf11 expression
  JOURNAL   Front Cell Dev Biol 12, 1302141 (2024)
   PUBMED   38559809
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 3959)
  AUTHORS   Chen,Y., Zhou,T., Liao,Z., Gao,W., Wu,J., Zhang,S., Li,Y., Liu,H.,
            Zhou,H., Xu,C. and Su,P.
  TITLE     Hnrnpk is essential for embryonic limb bud development as a
            transcription activator and a collaborator of insulator protein
            Ctcf
  JOURNAL   Cell Death Differ 30 (10), 2293-2308 (2023)
   PUBMED   37608075
REFERENCE   6  (bases 1 to 3959)
  AUTHORS   Dolle,P., Izpisua-Belmonte,J.C., Boncinelli,E. and Duboule,D.
  TITLE     The Hox-4.8 gene is localized at the 5' extremity of the Hox-4
            complex and is expressed in the most posterior parts of the body
            during development
  JOURNAL   Mech Dev 36 (1-2), 3-13 (1991)
   PUBMED   1685889
REFERENCE   7  (bases 1 to 3959)
  AUTHORS   Dolle,P., Izpisua-Belmonte,J.C., Brown,J.M., Tickle,C. and
            Duboule,D.
  TITLE     HOX-4 genes and the morphogenesis of mammalian genitalia
  JOURNAL   Genes Dev 5 (10), 1767-1767 (1991)
   PUBMED   1680771
REFERENCE   8  (bases 1 to 3959)
  AUTHORS   Izpisua-Belmonte,J.C., Falkenstein,H., Dolle,P., Renucci,A. and
            Duboule,D.
  TITLE     Murine genes related to the Drosophila AbdB homeotic genes are
            sequentially expressed during development of the posterior part of
            the body
  JOURNAL   EMBO J 10 (8), 2279-2289 (1991)
   PUBMED   1676674
REFERENCE   9  (bases 1 to 3959)
  AUTHORS   Izpisua-Belmonte,J.C., Dolle,P., Renucci,A., Zappavigna,V.,
            Falkenstein,H. and Duboule,D.
  TITLE     Primary structure and embryonic expression pattern of the mouse
            Hox-4.3 homeobox gene
  JOURNAL   Development 110 (3), 733-745 (1990)
   PUBMED   1982431
REFERENCE   10 (bases 1 to 3959)
  AUTHORS   Duboule,D., Boncinelli,E., DeRobertis,E., Featherstone,M.,
            Lonai,P., Oliver,G. and Ruddle,F.H.
  TITLE     An update of mouse and human HOX gene nomenclature
  JOURNAL   Genomics 7 (3), 458-459 (1990)
   PUBMED   1973145
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BC138115.1, AK054090.1 and AL928644.12.
            
            On Aug 4, 2012 this sequence version replaced NM_008273.1.
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the functional protein.
            
            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 :: BC138115.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849381
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1111              BC138115.1         1-1111
            1112-1908           AK054090.1         520-1316
            1909-1909           AL928644.12        169898-169898
            1910-2193           AK054090.1         1318-1601
            2194-2194           AL928644.12        170183-170183
            2195-2766           AK054090.1         1603-2174
            2767-2767           AL928644.12        170756-170756
            2768-3497           AK054090.1         2176-2905
            3498-3959           AK054090.1         2907-3368
FEATURES             Location/Qualifiers
     source          1..3959
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 44.13 cM"
     gene            1..3959
                     /gene="Hoxd11"
                     /gene_synonym="E230017H14Rik; Hox-4.6; Hox-5.4; Hox-5.5"
                     /note="homeobox D11"
                     /db_xref="GeneID:15431"
                     /db_xref="MGI:MGI:96203"
     exon            1..845
                     /gene="Hoxd11"
                     /gene_synonym="E230017H14Rik; Hox-4.6; Hox-5.4; Hox-5.5"
                     /inference="alignment:Splign:2.1.0"
     CDS             71..1081
                     /gene="Hoxd11"
                     /gene_synonym="E230017H14Rik; Hox-4.6; Hox-5.4; Hox-5.5"
                     /note="homeobox protein Hox-4.6; homeobox protein Hox-5.5;
                     homeo box D11"
                     /codon_start=1
                     /product="homeobox protein Hox-D11"
                     /protein_id="NP_032299.1"
                     /db_xref="CCDS:CCDS16140.1"
                     /db_xref="GeneID:15431"
                     /db_xref="MGI:MGI:96203"
                     /translation="MNDFDECGPSAASMYLPGCAYYVAPSDFASKPSFLSQPSSCQMT
                     FPYSSNLAPHVQPVREVAFRDYGLERAKWPYRGGGGGGAGGGGGGGPGGGGGGSGGYA
                     PYYAAAAAAAAAAAAAEEAAMQRDLLPPAGRRPDVLFKAPEPVCGAPGPPHGPAAAAS
                     NFYSAVGRNGILPQGFDQFYEAAPGPPFAGPQPQPAPAPPQPEGAADKGDPKPGAGGG
                     GGSPCAKATPGPEPKGAAEGGGGEGEGPPGEAGAEKSGGTVAPQRSRKKRCPYTKYQI
                     RELEREFFFNVYINKEKRLQLSRMLNLTDRQVKIWFQNRRMKEKKLNRDRLQYFTGNP
                     LF"
     exon            846..3959
                     /gene="Hoxd11"
                     /gene_synonym="E230017H14Rik; Hox-4.6; Hox-5.4; Hox-5.5"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1532..1537
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hoxd11"
                     /gene_synonym="E230017H14Rik; Hox-4.6; Hox-5.4; Hox-5.5"
                     /note="hexamer: AATAAA"
     polyA_site      1552
                     /gene="Hoxd11"
                     /gene_synonym="E230017H14Rik; Hox-4.6; Hox-5.4; Hox-5.5"
                     /note="major polyA site"
     regulatory      3833..3838
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hoxd11"
                     /gene_synonym="E230017H14Rik; Hox-4.6; Hox-5.4; Hox-5.5"
                     /note="hexamer: AATATA"
     polyA_site      3862
                     /gene="Hoxd11"
                     /gene_synonym="E230017H14Rik; Hox-4.6; Hox-5.4; Hox-5.5"
     regulatory      3900..3905
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hoxd11"
                     /gene_synonym="E230017H14Rik; Hox-4.6; Hox-5.4; Hox-5.5"
                     /note="hexamer: ATTAAA"
     polyA_site      3925
                     /gene="Hoxd11"
                     /gene_synonym="E230017H14Rik; Hox-4.6; Hox-5.4; Hox-5.5"
ORIGIN      
        1 tgcaatcgat ggctcaggtt ggaggcgcgg ggagcggccc gaggcttgcc ggcgtgcacg
       61 ccgcgcagcc atgaacgact ttgacgagtg cggccccagc gcagccagca tgtacctgcc
      121 gggctgcgct tactacgtgg ccccgtcgga cttcgccagc aagccgtcgt tcctctcgca
      181 gccgtcctcg tgccagatga ctttccccta ctcctccaac ctggcgccac acgtccagcc
      241 cgtgcgggag gtggcctttc gcgactacgg cctggagcgc gccaagtggc cgtaccgcgg
      301 cggaggcggc ggtggcgcgg ggggcggcgg cggcggcggt cccggcgggg gtggtggcgg
      361 ctccgggggc tacgctccct actacgccgc ggcagcggcg gcagcggcgg cagcggcggc
      421 ggccgaggag gcggccatgc aacgagatct gctcccgccc gccggccgcc ggccagacgt
      481 gctcttcaag gctcccgagc cggtgtgcgg cgctcccggg ccgccgcacg gtccggcggc
      541 cgcagcctct aacttctaca gcgccgtggg tcgcaacggc atcctgcccc agggctttga
      601 tcagttctac gaggcggcgc ccggaccccc cttcgccggc ccgcagcccc agcccgctcc
      661 cgcgccgcca cagcccgagg gcgccgctga caagggcgac cccaagccag gggctggtgg
      721 cggcgggggc agtccctgcg ccaaggcgac tccgggccca gagcccaagg gggcggcgga
      781 aggcggtggc ggtgaaggcg agggcccccc gggggaggcg ggggccgaaa agagcggcgg
      841 cacagtggcc ccccagaggt cccggaaaaa gcgctgtccc tacaccaagt accagatccg
      901 cgaactggaa cgcgagtttt tctttaatgt atacataaac aaagagaaaa gactccaact
      961 ctctcggatg ctcaacctca ctgaccggca agtcaaaatc tggttccaga atcgcaggat
     1021 gaaagaaaag aaactgaaca gggaccgtct gcaatatttc actggaaacc ccttattttg
     1081 agaactccag gatgtacccc ctccccagag ccccactcac ccaccctcct ccccaccagc
     1141 ctgctctcag caggcccaat gtccttgggt tcaatgacgc ctcttctctg tggaacttca
     1201 cgatttcttc tcgccttcaa ctcgggacct cccagcgacc actacagcct gaggaagagg
     1261 cccggaactt ggctgtgcgg atcctaataa ggggaacatg gtaaatgtaa acatcccttt
     1321 ccaattttac cgccaatgcg ctgttgttcc tctcctccct ctctgagtcc tcaacgcggc
     1381 gagatctgta ggaagttagg ccatggggct agaaggagcc agtgttttgt tttgagttta
     1441 agaaatccct ttctttccct tcagtgaaca cagattattt aaactctggg aaatgtacct
     1501 ttgggcatga gtcactgtct ttttgtgtgt gaataaatgt tttctagcaa aatggaggtc
     1561 ccagcttcaa tacactgcat gaattttact gtttgaagaa gtttagtggc tgatcaggct
     1621 gtcttagtga ccagaaaccc cttcctcatg caactgaaag cccgctggga cactttttaa
     1681 tctcaccata gtaggaattg gtccttcaca ccccctgtag gctacactgg ctctaaaaaa
     1741 tcatgttagt gttacatttc tgaattgatg ctgtgatcca gcagtgctgg ttgtcttttc
     1801 ttcttcttct tcttcttctt cttcttcttc ttcttcttct tcttcttctt cttcttcttc
     1861 ttcttcttct tcttcttcca ggcaatgaga ttgaagcagt aggagtctaa gagcaaattc
     1921 tcaccccacc cccacctcta gtctaatgaa cttggaattt ttggaaggaa aaaacaaatt
     1981 ttaaacttaa ttagaggatc caaatgatct cttaacatgg tgacaaggag ctagagtttc
     2041 ttaagaagaa gaagggggta aaatcctcct tgtgaggcgg gggaagtttg ttaagaggaa
     2101 gttaataggt gcagggactt ggggtctttc tgatgtcatg aagcagggac tgtgaacccc
     2161 cctcactgga ctaaggctgc aaaactgctt ctcaccacat ttatcgcttt aagttaaaga
     2221 atgtggtgag ggctgcagtg ccctttatgt cacaggacca agccaggctg tttacaaaac
     2281 cttgaactgt ctagacaaca ccataaaacc caaagttcta aacagcttaa ttgggttata
     2341 ttatacacct tctggtgggc ccaaaagaga tttccgcaat gtgcaataaa ctggagacgt
     2401 gagaaaacct cctcttgatc tgaccagagt gaagtggatc tcatgactct taacctctca
     2461 gaagcccaaa gtctaaaaat aaatccataa gatgcacagc agctcatgcc tcttctgagg
     2521 aagtatgctt tttaaaatat gaatttttta aattgccaaa gctttggggg gggtaaagaa
     2581 aaacataagt gtataagtgt atgcctttga acttccaaaa tgtcaaggtc atcaccttta
     2641 acctctctga ataattaggc gccttaaagt tcttctgtga tttctaacca ccgcccaggc
     2701 tcatacatcc agacccacac acatatttat gaccatacag attcatactg ggggttcacc
     2761 ataaatctag gaaaattcct aatttcagga tcaataacta taatttccct cccaacattt
     2821 gagtaattta atagcaactg acttcttagg aaaaaaaaaa acacttgtta gattaaaatg
     2881 cccattaact attactagag ctagggtgta ctgagaattt gggaagatct tagaaagagt
     2941 ttctctttgc tgtaatgaag agctgcagtt tttaaaaaga catttgacag agtaaattct
     3001 gattagactt acatcatctc tagcatttga aagcaatttg ccaccctgct aaataaacgc
     3061 tggcacttta taaaatatag aacaaagtaa aatatagtta tattgtttcg taaacgcatt
     3121 tctaaatctt tggtaaagga taaaatagaa acaaagcaga caatcaaagt atttcactca
     3181 gaaagtgatt attttgttta gaattctggg cattggttta cctgtaaata ccctaataat
     3241 atgatctttc tgggatcata ctgtttgttt gaaacaaacc ataaaactgg tttgtttctt
     3301 tttctttatc tttctttttt cttcttcttt taactgggtc taaatgtaca agctgtgtgc
     3361 cagccagcac actccaggca aacgagagaa acactatttt ccatttgtaa gaacttctac
     3421 agccacacga gggcgcgctc atgttccaga aaccttattt gccaagaggc tgcggtacct
     3481 tttttttttt tttttttcca atcctagagt ctaataagga atcttggccc gcccgttaga
     3541 aacaggcagt cgttaaggtg tttgctattt gcttgttcca accagctgtg agtttgagaa
     3601 gttgtagaga gacagaggaa aagaggcaac cagtcttccg aaacaggaga tccccctaat
     3661 cgttgtctcc ttaaagtcgc tatgaaaaag accttggtat ataacctgat ggtgtcaaga
     3721 aaatagtttt aaaagacaaa tagctgtggt ttgaaatacg tcatagccac tgggagttaa
     3781 ttaattagga aaatctattt tcatgttgat ttgagtgtgg agagcgatga caaatataag
     3841 accccttccc atttccccca aaccgcacgc gtcttgtgag ctttcagatg gctgggatga
     3901 ttaaacggct tttgtttaaa acagattagg gcgttggcaa cttagctgag catgtactt
//
