LOCUS       NM_010469               2560 bp    mRNA    linear   ROD 02-JUN-2024
DEFINITION  Mus musculus homeobox D4 (Hoxd4), mRNA.
ACCESSION   NM_010469
VERSION     NM_010469.2
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 2560)
  AUTHORS   Kumar,S., Alam,S.S., Bareke,E., Beauchamp,M.C., Dong,Y., Chan,W.,
            Majewski,J. and Jerome-Majewska,L.A.
  TITLE     Sf3b4 regulates chromatin remodeler splicing and Hox expression
  JOURNAL   Differentiation 131, 59-73 (2023)
   PUBMED   37167859
REFERENCE   2  (bases 1 to 2560)
  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   3  (bases 1 to 2560)
  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 2560)
  AUTHORS   Lopez-Delgado,A.C., Delgado,I., Cadenas,V., Sanchez-Cabo,F. and
            Torres,M.
  TITLE     Axial skeleton anterior-posterior patterning is regulated through
            feedback regulation between Meis transcription factors and retinoic
            acid
  JOURNAL   Development 148 (1) (2021)
   PUBMED   33298461
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2560)
  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   6  (bases 1 to 2560)
  AUTHORS   Scott,M.P.
  TITLE     Vertebrate homeobox gene nomenclature
  JOURNAL   Cell 71 (4), 551-553 (1992)
   PUBMED   1358459
REFERENCE   7  (bases 1 to 2560)
  AUTHORS   Lufkin,T., Mark,M., Hart,C.P., Dolle,P., LeMeur,M. and Chambon,P.
  TITLE     Homeotic transformation of the occipital bones of the skull by
            ectopic expression of a homeobox gene
  JOURNAL   Nature 359 (6398), 835-841 (1992)
   PUBMED   1359423
REFERENCE   8  (bases 1 to 2560)
  AUTHORS   Popperl,H. and Featherstone,M.S.
  TITLE     An autoregulatory element of the murine Hox-4.2 gene
  JOURNAL   EMBO J 11 (10), 3673-3680 (1992)
   PUBMED   1356763
REFERENCE   9  (bases 1 to 2560)
  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   10 (bases 1 to 2560)
  AUTHORS   Simon-Chazottes,D., Matsubara,S., Miyauchi,T., Muramatsu,T. and
            Guenet,J.L.
  TITLE     Chromosomal localization of two cell surface-associated molecules
            of potential importance in development: midkine (Mdk) and basigin
            (Bsg)
  JOURNAL   Mamm Genome 2 (4), 269-271 (1992)
   PUBMED   1347477
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL928644.12.
            
            On Oct 19, 2007 this sequence version replaced NM_010469.1.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            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##
            CDS exon combination :: BC139206.1, AK135479.1 [ECO:0000331]
            RNAseq introns       :: single sample supports all introns
                                    SAMN00849374, SAMN00849380 [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
            1-200               AL928644.12        206910-207109
            201-279             AL928644.12        207485-207563
            280-315             AL928644.12        208264-208299
            316-831             AL928644.12        210395-210910
            832-1661            AL928644.12        211808-212637
            1662-2560           AL928644.12        213194-214092
FEATURES             Location/Qualifiers
     source          1..2560
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 44.13 cM"
     gene            1..2560
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /note="homeobox D4"
                     /db_xref="GeneID:15436"
                     /db_xref="MGI:MGI:96208"
     exon            1..200
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /inference="alignment:Splign:2.1.0"
     exon            201..279
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /inference="alignment:Splign:2.1.0"
     exon            280..315
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /inference="alignment:Splign:2.1.0"
     exon            316..831
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /inference="alignment:Splign:2.1.0"
     exon            832..1661
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    1073..1075
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /note="upstream in-frame stop codon"
     CDS             1235..1987
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /note="homeobox protein Hox-4.2; homeobox protein Hox-5.1;
                     homeo box D4"
                     /codon_start=1
                     /product="homeobox protein Hox-D4"
                     /protein_id="NP_034599.2"
                     /db_xref="CCDS:CCDS16145.1"
                     /db_xref="GeneID:15436"
                     /db_xref="MGI:MGI:96208"
                     /translation="

MAMSSYMVNSKYVDPKFPPCEEYLQGGYLGEQGADYYGSGAQGADFQPSGLYPRPDFGEQPFGGGGPGPGSALPARGHGQEPSGPGSHYGAPGERCPAPPPAPLPGARACSQPTGPKQPPPGTALKQPAVVYPWMKKVHVNSVNPNYTGGEPKRSRTAYTRQQVLELEKEFHFNRYLTRRRRIEIAHTLCLSERQIKIWFQNRRMKWKKDHKLPNTKGRSSSSSSCSSSAAPGQHLQPMAKDHHTDLTTL"

     misc_feature    1325..1612
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /note="propagated from UniProtKB/Swiss-Prot (P10628.3);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    1625..1642
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /note="propagated from UniProtKB/Swiss-Prot (P10628.3);
                     Region: Antp-type hexapeptide"
     misc_feature    1691..1861
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    1862..1984
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /note="propagated from UniProtKB/Swiss-Prot (P10628.3);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            1662..2560
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2252..2257
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /note="hexamer: ATTAAA"
     polyA_site      2271
                     /gene="Hoxd4"
                     /gene_synonym="6030436D05Rik; Hox-4.2; Hox-5.1"
                     /note="major polyA site"
ORIGIN      

cgtgattccaataaactttgttttatggcttgagagttgacaagccaaaatataattcccaccataaattaggttaagagcatacaagtgcagatgcttggttcctgtagcagcgataggcaagtgagaggctccagccagcgccccgggctcaggagacagctctcctctaagcttctctaccaacgaaaagaaacccaaagactaaaaacttgaagatggacatgagtgccctgggaaccactgttctctttgatcggtctgtaggttctcctgcaggttttggagcgtcagggagaacgagggagaaccactctcgacagtctcagcccagggaggctcggtggccgcaaacagcgcctgcctccgggtctgcagcagcagtcatagcagcagcagaagcagcagcagcgggatccgaaagtccggcggggctgagggcccagaaaggtaaatgctcgaattctaggaggactagctgtgaccactcacttggcttaggttctggtgaagactattccttttgcctttttcaaaactccctttctgctgctgagggcctttgcttctttttgggaaataccacttgataagggggcgggagatttgggttctgagaaggggcaattaagccgccatctctggggtgaaaaaaaaactccccttcttttcttttcttttttttttttttaagaagaagaaggtcctggctgctcagctacttggtggcccccatcctggcaagccgatgagggaactcattgctgtagcgagcagcaatacttagaaatgcaccgagcctacctgcaccatctctgaaagccaggcttgtaggagaattcactcttctttgaactatgtccattctgggggctgcttcaggcgatggtgagtaaggagggcatgggaggttagcaaagtcagtggaagacaaaagccgagattacctgccggaaattgggaccccggggatagaattagaactctattagcatctgtcagggactctcaaatgtggcatggcaagtcacttgattacacgtatgttatttagttaaatttgtgaaaattatgagatgctcaccaacccggtgataaacatgctttcttcctattggctggcctggtcacatggccgcccaactttattcagttgacagcaagtaggagggcccaatggaaggagaaaaaagacaacacgagaaaaattagtattttctaccttctgaaattaatggccatgagttcgtatatggtgaactctaagtacgtggaccccaagtttcctccgtgcgaggaatatttgcagggtggctacctaggcgagcagggagccgactactacggcagcggtgcacagggcgccgacttccagccctcggggctctacccacggcccgacttcggcgagcaacccttcggaggcggcgggcccgggcctggctcagcgctgcccgcgaggggtcacggacaggagccgagcggcccgggaagtcattacggtgccccgggagagcggtgcccagcgcccccgcctgcgcccctgcctggcgctcgggcctgcagccagcccaccggccccaagcagccgccccccgggacagcactcaagcagcccgctgtggtctacccttggatgaagaaggtgcacgtgaattcggtgaaccccaactacaccggcggggagcccaagcgctcccggacggcctacaccagacagcaagtcctagaactggaaaaggaatttcattttaacaggtatctgaccaggcgccgtcggattgaaatcgctcacaccctgtgtctgtctgagcgccagatcaagatctggttccagaaccggaggatgaagtggaaaaaagaccacaaactgcccaacaccaagggcaggtcttcttcctcatcttcctgctcctcttcagctgccccgggccagcatttgcagccaatggccaaggaccaccatacggacctgacgaccttatagaagtggggaccctgggcctatcccttcttgcactccaggttgaggcgaagctgcgggtgcaggcggggcctgctgtcacctcactgggctctaaggtactgtgggggtggacctgggacctgcaggccgccctcggactaggttaccttcctgcccgagggcagccccctccctaaagtggggaagggtgggagggtgggcgggcttctttaagtagattatcatatggcaggagctactgagaacataaacccttggcgagtcattaaactcctgaaaatctctgctggtggattgaatttgcaaatgaaggttggaggctttaccccagtgggaaccgggatggtctcctccacaccacccccttcagggagctgtgtggcttagtaactgtgggggagttgaggcagaaggccagccagtgctaggtgctttcagtgcaagcaggagaggctgagccagaatcccagaactttctggattatctatagaatttcttctgtgatttaaaaaaaaaaaaaaaagaaagaaagaaattgtttgcttccagtggcccatgcccaaagaaataaa

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