LOCUS       NM_001109884            2068 bp    mRNA    linear   ROD 27-JUN-2025
DEFINITION  Rattus norvegicus homeo box C4 (Hoxc4), mRNA.
ACCESSION   NM_001109884 XM_235703
VERSION     NM_001109884.1
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 2068)
  AUTHORS   Schmidt,J.A., Avarbock,M.R., Tobias,J.W. and Brinster,R.L.
  TITLE     Identification of glial cell line-derived neurotrophic
            factor-regulated genes important for spermatogonial stem cell
            self-renewal in the rat
  JOURNAL   Biol Reprod 81 (1), 56-66 (2009)
   PUBMED   19339709
REFERENCE   2  (bases 1 to 2068)
  AUTHORS   Calonge,W.M., Martinez,L., Lacadena,J., Fernandez-Dumont,V.,
            Matesanz,R. and Tovar,J.A.
  TITLE     Expression of homeotic genes Hoxa3, Hoxb3, Hoxd3 and Hoxc4 is
            decreased in the lungs but not in the hearts of adriamycin-exposed
            mice
  JOURNAL   Pediatr Surg Int 23 (5), 419-424 (2007)
   PUBMED   17211587
REFERENCE   3  (bases 1 to 2068)
  AUTHORS   Wissmuller,S., Kosian,T., Wolf,M., Finzsch,M. and Wegner,M.
  TITLE     The high-mobility-group domain of Sox proteins interacts with
            DNA-binding domains of many transcription factors
  JOURNAL   Nucleic Acids Res 34 (6), 1735-1744 (2006)
   PUBMED   16582099
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2068)
  AUTHORS   Kim,E.C., Edmonston,C.R., Wu,X., Schaffer,A. and Casali,P.
  TITLE     The HoxC4 homeodomain protein mediates activation of the
            immunoglobulin heavy chain 3' hs1,2 enhancer in human B cells.
            Relevance to class switch DNA recombination
  JOURNAL   J Biol Chem 279 (40), 42258-42269 (2004)
   PUBMED   15252056
REFERENCE   5  (bases 1 to 2068)
  AUTHORS   Boulet,A.M. and Capecchi,M.R.
  TITLE     Targeted disruption of hoxc-4 causes esophageal defects and
            vertebral transformations
  JOURNAL   Dev Biol 177 (1), 232-249 (1996)
   PUBMED   8660891
REFERENCE   6  (bases 1 to 2068)
  AUTHORS   Saegusa,H., Takahashi,N., Noguchi,S. and Suemori,H.
  TITLE     Targeted disruption in the mouse Hoxc-4 locus results in axial
            skeleton homeosis and malformation of the xiphoid process
  JOURNAL   Dev Biol 174 (1), 55-64 (1996)
   PUBMED   8626021
REFERENCE   7  (bases 1 to 2068)
  AUTHORS   Chung,S.Y., Dai,P.H., Lei,J., Riviere,M., Levan,G., Szpirer,J. and
            Szpirer,C.
  TITLE     Chromosomal assignment of seven rat homeobox genes to rat
            chromosomes 3, 4, 7, and 10
  JOURNAL   Mamm Genome 4 (9), 537-540 (1993)
   PUBMED   7906969
REFERENCE   8  (bases 1 to 2068)
  AUTHORS   Falzon,M. and Chung,S.Y.
  TITLE     The expression of rat homeobox-containing genes is developmentally
            regulated and tissue specific
  JOURNAL   Development 103 (3), 601-610 (1988)
   PUBMED   2907739
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from
            JAXUCZ010000007.1.
            
            On Oct 10, 2007 this sequence version replaced XM_235703.3.
            
            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.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26643288.32650.1, FN802484.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760434, SAMN06621351
                                           [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
            1-866               JAXUCZ010000007.1  136049059-136049924
            867-2068            JAXUCZ010000007.1  136050400-136051601
FEATURES             Location/Qualifiers
     source          1..2068
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="7"
                     /map="7q36"
     gene            1..2068
                     /gene="Hoxc4"
                     /gene_synonym="Hox3r3"
                     /note="homeo box C4"
                     /db_xref="GeneID:24459"
                     /db_xref="RGD:1586210"
     exon            1..866
                     /gene="Hoxc4"
                     /gene_synonym="Hox3r3"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    356..358
                     /gene="Hoxc4"
                     /gene_synonym="Hox3r3"
                     /note="upstream in-frame stop codon"
     CDS             428..1222
                     /gene="Hoxc4"
                     /gene_synonym="Hox3r3"
                     /note="homeobox protein R3; Homeobox gene C4"
                     /codon_start=1
                     /product="homeobox protein Hox-C4"
                     /protein_id="NP_001103354.1"
                     /db_xref="GeneID:24459"
                     /db_xref="RGD:1586210"
                     /translation="

MIMSSYLMDSNYIDPKFPPCEEYSQNSYIPEHSPEYYGRTRESGFQHHHQELYPPPPPRPSYPERQYSCTSLQGPGNSRAHGPAQAGHHHPEKSQPLCEPAPLSGASASPSPAPPACSQPAPDHPSSAASKQPIVYPWMKKIHVSTVNPNYNGGEPKRSRTAYTRQQVLELEKEFHYNRYLTRRRRIEIAHSLCLSERQIKIWFQNRRMKWKKDHRLPNTKVRSAPPAGAAPSTLSAATPGTSEDHSQSATPPEQQRAEDITRL"

     misc_feature    896..1066
                     /gene="Hoxc4"
                     /gene_synonym="Hox3r3"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     exon            867..2068
                     /gene="Hoxc4"
                     /gene_synonym="Hox3r3"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

tggaaaggcactggagccgaggcccaccgggtccactgaaggccggagaggagactctgggtgggggctgaatcacagcctaccaacagcccccaatgcccagacattggagtcgagctgggagccacccatcttctgcaagggaggattgtcagtctggtggggtgtgcaatggtgagcaccccagcttctgccagccatccccccaccccaccccctcagcagcagcagcaccacacacacaaaaaattggatacattttgaataaagcgattcggttccttatccggggactgagttgctcggtgtgattggccggcggagtcacatggtgaaagtaactttacagggtcgctagctagtaggagggctttatggagcagaaaaacgacaaagcgagaaaaattattttccactccagaaattaatgatcatgagctcgtatttgatggactctaactacatcgatccgaaatttcctccatgcgaagaatattcgcaaaatagctacatccctgaacacagtccggaatattacggccggaccagggaatcgggattccagcatcaccaccaggagctgtacccaccaccgcctccgcgccctagctaccctgagcgtcagtatagctgcaccagtctccaggggcccggcaattcgcgagcccacgggccggcccaggcgggccaccaccaccctgagaaatcgcagccgctctgcgagccggcgcctctctcaggcgcctctgcctccccgtccccagccccgccagcctgcagccagccagcccctgaccatccctccagcgccgccagcaagcagcccatagtctacccttggatgaaaaaaattcacgttagcacggtgaaccccaattataacggaggggagcccaagcgctcgaggacagcctacacccggcagcaggtcctggaattagagaaagagtttcattacaaccgctacctgacccgaaggagaaggatcgagatcgcccactcgctgtgcctctctgagaggcagatcaaaatctggttccaaaaccgtcgcatgaaatggaagaaggaccaccgactccccaacaccaaagtgaggtcagcgcccccggccggcgctgcacccagcaccctctcggcagccacccccggcacttctgaagaccactcccagagcgccacgccgccggagcagcaacgggcagaggacatcaccaggttataagacataacttacacccctgcccccaccctgtgctccgtgccccctcacacacaaattgactcttatttatagaatttaatatatatatatttttggttctttttttctctctcttcctcctgtctcctcccttgtcagttccaaacagacaaaacagataaacaaacaagccccttgcccttttccctttgctgttaaggacccctttaagcatgtggtgttgtcttagcatggtacctgctgggttttattttttgttgttttgttttgttttgctttgctttgcttttaaggccattggggggtatttattttttaaggaaaaaaagctgcaaaaattatatattgcaaggtgtgatggtctggtttgggtgaatttcaggggaaatgaggaacagaaaaaggaaagggagatttgtaagtggattctcatcctctctcctcctcaccccccctccctttccttaggccttttgcattgaaaatgcaccaggggaggttagtgaggggggggagtcattttaaggagaacaaagctatgaagttcttttgtattcttgtgggggggtggtaggaggggggaggacagcaaacaaagctaaatgcatctggagagcctctgggagctgttcagtttgaggagccaaaaaataaataaataaataaaaatgaactttcagttcagagaggcagtctataggtagatgctcccctacccccatcgtggttattgtgtttttggactgaatttacttgattattgtaaaacttgcaataaagaattttagtgttgatgtgaaatgcccccgtgatcaataataaaccagtggctgtgaattagtttta

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