LOCUS       NM_010467               1878 bp    mRNA    linear   ROD 02-JUN-2024
DEFINITION  Mus musculus homeobox D1 (Hoxd1), mRNA.
ACCESSION   NM_010467
VERSION     NM_010467.2
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 1878)
  AUTHORS   Hintermann,A., Guerreiro,I., Lopez-Delisle,L., Bolt,C.C., Gitto,S.,
            Duboule,D. and Beccari,L.
  TITLE     Developmental and evolutionary comparative analysis of a regulatory
            landscape in mouse and chicken
  JOURNAL   Development 149 (12) (2022)
   PUBMED   35770682
REFERENCE   2  (bases 1 to 1878)
  AUTHORS   Sun,J., Ha,N., Liu,Z., Bian,Q. and Wang,X.
  TITLE     A Neural Crest-specific Overexpression Mouse Model Reveals the
            Transcriptional Regulatory Effects of Dlx2 During Maxillary Process
            Development
  JOURNAL   Front Physiol 13, 855959 (2022)
   PUBMED   35514355
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1878)
  AUTHORS   Amandio,A.R., Beccari,L., Lopez-Delisle,L., Mascrez,B., Zakany,J.,
            Gitto,S. and Duboule,D.
  TITLE     Sequential in cis mutagenesis in vivo reveals various functions for
            CTCF sites at the mouse HoxD cluster
  JOURNAL   Genes Dev 35 (21-22), 1490-1509 (2021)
   PUBMED   34711654
REFERENCE   4  (bases 1 to 1878)
  AUTHORS   Higashijima,Y., Nagai,N., Yamamoto,M., Kitazawa,T., Kawamura,Y.K.,
            Taguchi,A., Nakada,N., Nangaku,M., Furukawa,T., Aburatani,H.,
            Kurihara,H., Wada,Y. and Kanki,Y.
  TITLE     Lysine demethylase 7a regulates murine anterior-posterior
            development by modulating the transcription of Hox gene cluster
  JOURNAL   Commun Biol 3 (1), 725 (2020)
   PUBMED   33257809
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1878)
  AUTHORS   Sato,T., Kataoka,K., Ito,Y., Yokoyama,S., Inui,M., Mori,M.,
            Takahashi,S., Akita,K., Takada,S., Ueno-Kudoh,H. and Asahara,H.
  TITLE     Lin28a/let-7 pathway modulates the Hox code via Polycomb regulation
            during axial patterning in vertebrates
  JOURNAL   Elife 9, e53608 (2020)
   PUBMED   32479258
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1878)
  AUTHORS   Scott,M.P.
  TITLE     Vertebrate homeobox gene nomenclature
  JOURNAL   Cell 71 (4), 551-553 (1992)
   PUBMED   1358459
REFERENCE   7  (bases 1 to 1878)
  AUTHORS   Frohman,M.A. and Martin,G.R.
  TITLE     Isolation and analysis of embryonic expression of Hox-4.9, a member
            of the murine labial-like gene family
  JOURNAL   Mech Dev 38 (1), 55-67 (1992)
   PUBMED   1356009
REFERENCE   8  (bases 1 to 1878)
  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 1878)
  AUTHORS   Hunt,P., Gulisano,M., Cook,M., Sham,M.H., Faiella,A., Wilkinson,D.,
            Boncinelli,E. and Krumlauf,R.
  TITLE     A distinct Hox code for the branchial region of the vertebrate head
  JOURNAL   Nature 353 (6347), 861-864 (1991)
   PUBMED   1682814
REFERENCE   10 (bases 1 to 1878)
  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
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL928733.14, BC120537.1 and BE956647.1.
            
            On Aug 23, 2006 this sequence version replaced NM_010467.1.
            
            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 :: X60034.1, BC120537.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849381, SAMN01164131
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-101               AL928733.14        30042-30142
            102-1613            BC120537.1         1-1512
            1614-1688           AL928733.14        31956-32030
            1689-1878           BE956647.1         1-190               c
FEATURES             Location/Qualifiers
     source          1..1878
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 44.13 cM"
     gene            1..1878
                     /gene="Hoxd1"
                     /gene_synonym="Hox-4.9"
                     /note="homeobox D1"
                     /db_xref="GeneID:15429"
                     /db_xref="MGI:MGI:96201"
     exon            1..774
                     /gene="Hoxd1"
                     /gene_synonym="Hox-4.9"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    60..62
                     /gene="Hoxd1"
                     /gene_synonym="Hox-4.9"
                     /note="upstream in-frame stop codon"
     CDS             123..1109
                     /gene="Hoxd1"
                     /gene_synonym="Hox-4.9"
                     /note="homeobox protein Hox-4.9; homeo box D1"
                     /codon_start=1
                     /product="homeobox protein Hox-D1"
                     /protein_id="NP_034597.2"
                     /db_xref="CCDS:CCDS16147.1"
                     /db_xref="GeneID:15429"
                     /db_xref="MGI:MGI:96201"
                     /translation="

MSSYLEYVSCAAGGGSGGVGGDVLGFAPKFCRADARPVALQPAFPLGSGDGAFVSCLPLATARPTPSPPAGPAQSPVPQPAAPRYAPCTLEGAYERGAAPASAAEYGFLGSGPAFDFPGALGRAADEGGAHVHYATSAVFSGGGSFLLSGQVDFAAFGEPGPFPACLKEPADGHPGPFQTVSPAPGACPKPASPTSSLPAAHSTFEWMKVKRNAPKKSKLSEYGATSPPSAIRTNFSTKQLTELEKEFHFNKYLTRARRIEIANCLQLNDTQVKIWFQNRRMKQKKREREGLLATAASVASIKLPRSETSPIKSGRNLGSPSQAQEPS"

     misc_feature    <153..773
                     /gene="Hoxd1"
                     /gene_synonym="Hox-4.9"
                     /note="DNA polymerase III subunit gamma/tau; Region:
                     PRK12323; cl46901"
                     /db_xref="CDD:481241"
     misc_feature    732..749
                     /gene="Hoxd1"
                     /gene_synonym="Hox-4.9"
                     /note="propagated from UniProtKB/Swiss-Prot (Q01822.2);
                     Region: Antp-type hexapeptide"
     misc_feature    819..980
                     /gene="Hoxd1"
                     /gene_synonym="Hox-4.9"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    1032..1106
                     /gene="Hoxd1"
                     /gene_synonym="Hox-4.9"
                     /note="propagated from UniProtKB/Swiss-Prot (Q01822.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            775..1862
                     /gene="Hoxd1"
                     /gene_synonym="Hox-4.9"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1843..1848
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hoxd1"
                     /gene_synonym="Hox-4.9"
                     /note="hexamer: AATAAA"
     polyA_site      1862
                     /gene="Hoxd1"
                     /gene_synonym="Hox-4.9"
                     /note="major polyA site"
ORIGIN      

atatgaagccactatttacctcgggctcgctcgccatggctcggcgagggcagcgggggtagcgggaaggcggagctgcgcagacctgcagggtgcggcgcctaggtcgtgcggagcgagccatgagctcttacctggagtacgtgtcgtgcgccgcgggcggtggcagcggaggggtaggcggcgacgtgctcggcttcgcacccaagttctgccgcgccgacgcgcgccctgtggccctgcagccggccttccccctgggcagcggagacggcgccttcgtgagctgcctgcccctggccaccgctcggcccacgccgtcgcctcccgcaggccccgctcagtccccggtcccacagcccgccgcgccccggtacgcgccctgcaccctggaaggcgcctacgagcggggcgccgcacctgcctctgccgccgagtatggcttcttggggtccgggccggcgtttgacttcccgggcgcacttgggagagcggcggacgagggcggggcgcacgtccactatgccacctcggcggtcttctccggcgggggatcattcctgctcagcggccaggtggacttcgctgcctttggcgagcctggccccttccccgcgtgtctcaaggagcccgcagacggccaccccgggccctttcagactgtgtccccggcccctggagcctgccccaagccggcctctcccacctccagcctcccggccgcccacagcactttcgagtggatgaaagtgaagaggaacgcccccaagaaaagcaaactgtccgaatatggagccacaagccctcccagtgccatccgcacaaatttcagcaccaagcaactgacagagctagagaaagagtttcatttcaataagtacctaactagagcccgacgcatcgagatagccaactgtttacagctgaatgacacccaggtcaaaatctggttccagaaccgtaggatgaagcagaagaagagggaacgagaggggcttctggccacagctgcctctgtggcctcgattaagcttccccggtcagaaacaagtcccatcaaatctggccggaatctaggaagcccttctcaggctcaagagccttcctgaggcccactcttaaggctgaggaccttgggtctacagaagtcacagactgctccccacctttgaatagacttgagagcttagtttgggctggaggtgggcatgggtagaaattaatacggattttacttggcaaaggaattgtctaaattggcttctgagttccagaggctgtgtatagagatatatatttgatatcttttattcgcatattatttttgcctcatggggaggaaaggtgtcttagctacctgcctaaacgctgctatgtgagccacttaaaattctcgggtgcagagtggcaggccttcttagtctagtgtggtcagaaacgtatctctctgaagttgtttcagttttaatttcctggacagactacatatattcagcttcctgagatgatcaaagctagctagggtttcctctatgtagctaagctgcttcaatgatgatcttcatattgtgctccagtttgtttatttaaagtggcgctcctacctcttcgtgtgcctgggtgaagaaacacaatcactgtttagttagtagcggaacaaatccacagggtaggtaaggattagaatctgaattataccttggcatcagttactcaaacttgaagtgtaaatatatacagtatgtatattttttaaagatttgcttgcagtgaaccttatatatgacatttaatgtcatgcatagcatgtaaagattttgactttttttttttttttttggtaataaaagttacagaatctaaaaaaaaaaaaaaaaa

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