LOCUS       NM_172553               2493 bp    mRNA    linear   ROD 06-OCT-2024
DEFINITION  Mus musculus ALX homeobox 1 (Alx1), transcript variant 1, mRNA.
ACCESSION   NM_172553
VERSION     NM_172553.4
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 2493)
  AUTHORS   Quilez,S., Dumontier,E., Baim,C., Kam,J. and Cloutier,J.F.
  TITLE     Loss of Neogenin alters branchial arch development and leads to
            craniofacial skeletal defects
  JOURNAL   Front Cell Dev Biol 12, 1256465 (2024)
   PUBMED   38404688
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2493)
  AUTHORS   Nguyen,T.T., Mitchell,J.M., Kiel,M.D., Kenny,C.P., Li,H.,
            Jones,K.L., Cornell,R.A., Williams,T.J., Nichols,J.T. and Van
            Otterloo,E.
  TITLE     TFAP2 paralogs regulate midfacial development in part through a
            conserved ALX genetic pathway
  JOURNAL   Development 151 (1) (2024)
   PUBMED   38063857
REFERENCE   3  (bases 1 to 2493)
  AUTHORS   Baxi,A., Jourdeuil,K., Cox,T.C., Clouthier,D.E. and Tavares,A.L.P.
  TITLE     Transcriptomic analysis reveals the role of SIX1 in mouse cranial
            neural crest patterning and bone development
  JOURNAL   Dev Dyn 252 (10), 1303-1315 (2023)
   PUBMED   37183792
REFERENCE   4  (bases 1 to 2493)
  AUTHORS   Deacon,E., Li,A., Boivin,F., Dvorkin-Gheva,A., Cunanan,J. and
            Bridgewater,D.
  TITLE     beta-Catenin in the kidney stroma modulates pathways and genes to
            regulate kidney development
  JOURNAL   Dev Dyn 252 (9), 1224-1239 (2023)
   PUBMED   37227110
REFERENCE   5  (bases 1 to 2493)
  AUTHORS   Qu,F., Li,W., Xu,J., Zhang,R., Ke,J., Ren,X., Meng,X., Qin,L.,
            Zhang,J., Lu,F., Zhou,X., Luo,X., Zhang,Z., Wang,M., Wu,G., Pei,D.,
            Chen,J., Cui,G., Suo,S. and Peng,G.
  TITLE     Three-dimensional molecular architecture of mouse organogenesis
  JOURNAL   Nat Commun 14 (1), 4599 (2023)
   PUBMED   37524711
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2493)
  AUTHORS   Gordon,D.F., Wagner,J., Atkinson,B.L., Chiono,M., Berry,R.,
            Sikela,J. and Gutierrez-Hartmann,A.
  TITLE     Human Cart-1: structural organization, chromosomal localization,
            and functional analysis of a cartilage-specific homeodomain cDNA
  JOURNAL   DNA Cell Biol 15 (7), 531-541 (1996)
   PUBMED   8756334
REFERENCE   7  (bases 1 to 2493)
  AUTHORS   Zhao,Q., Behringer,R.R. and de Crombrugghe,B.
  TITLE     Prenatal folic acid treatment suppresses acrania and
            meroanencephaly in mice mutant for the Cart1 homeobox gene
  JOURNAL   Nat Genet 13 (3), 275-283 (1996)
   PUBMED   8673125
REFERENCE   8  (bases 1 to 2493)
  AUTHORS   Grass,S., Arnold,H.H. and Braun,T.
  TITLE     Alterations in somite patterning of Myf-5-deficient mice: a
            possible role for FGF-4 and FGF-6
  JOURNAL   Development 122 (1), 141-150 (1996)
   PUBMED   8565825
REFERENCE   9  (bases 1 to 2493)
  AUTHORS   Ishibashi,M., Ang,S.L., Shiota,K., Nakanishi,S., Kageyama,R. and
            Guillemot,F.
  TITLE     Targeted disruption of mammalian hairy and Enhancer of split
            homolog-1 (HES-1) leads to up-regulation of neural helix-loop-helix
            factors, premature neurogenesis, and severe neural tube defects
  JOURNAL   Genes Dev 9 (24), 3136-3148 (1995)
   PUBMED   8543157
REFERENCE   10 (bases 1 to 2493)
  AUTHORS   Zhao,G.Q., Eberspaecher,H., Seldin,M.F. and de Crombrugghe,B.
  TITLE     The gene for the homeodomain-containing protein Cart-1 is expressed
            in cells that have a chondrogenic potential during embryonic
            development
  JOURNAL   Mech Dev 48 (3), 245-254 (1994)
   PUBMED   7893605
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC167468.2.
            
            On Oct 19, 2007 this sequence version replaced NM_172553.3.
            
            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.
            
            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 :: AK047846.1, BC052200.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164142 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-397               AC167468.2         19906-20302
            398-702             AC167468.2         23244-23548
            703-831             AC167468.2         26378-26506
            832-2493            AC167468.2         39175-40836
FEATURES             Location/Qualifiers
     source          1..2493
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="10"
                     /map="10 53.56 cM"
     gene            1..2493
                     /gene="Alx1"
                     /gene_synonym="C130005I02; Cart1"
                     /note="ALX homeobox 1"
                     /db_xref="GeneID:216285"
                     /db_xref="MGI:MGI:104621"
     exon            1..397
                     /gene="Alx1"
                     /gene_synonym="C130005I02; Cart1"
                     /inference="alignment:Splign:2.1.0"
     CDS             172..1152
                     /gene="Alx1"
                     /gene_synonym="C130005I02; Cart1"
                     /note="isoform 1 is encoded by transcript variant 1; ALX
                     homeobox protein 1; cartilage homeoprotein 1"
                     /codon_start=1
                     /product="ALX homeobox protein 1 isoform 1"
                     /protein_id="NP_766141.1"
                     /db_xref="CCDS:CCDS24155.1"
                     /db_xref="GeneID:216285"
                     /db_xref="MGI:MGI:104621"
                     /translation="MEFLSEKFALKSPPSKNSDFYMGTGGALEHVMETLDNESFYGKA
                     TAGKCVQAFGPLPRAEHHVRLDRTSPCQDSSVNYGITKVEGQPLHTELNRAMDNCNNL
                     RMSPVKGMPEKSELDELGDKCDSNVSSSKKRRHRTTFTSLQLEELEKVFQKTHYPDVY
                     VREQLALRTELTEARVQVWFQNRRAKWRKRERYGQIQQAKSHFAATYDISVLPRTDSY
                     PQIQNNLWAGNASGGSVVTSCMLPRDASSCMTPYSHSPRTDSSYTGFSNHQNQFSHVP
                     LNNFFTDSLLTGATNGHAFETKPEFERRSSSIAVLRMKAKEHTANISWAM"
     exon            398..702
                     /gene="Alx1"
                     /gene_synonym="C130005I02; Cart1"
                     /inference="alignment:Splign:2.1.0"
     exon            703..831
                     /gene="Alx1"
                     /gene_synonym="C130005I02; Cart1"
                     /inference="alignment:Splign:2.1.0"
     exon            832..2493
                     /gene="Alx1"
                     /gene_synonym="C130005I02; Cart1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1458..1463
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Alx1"
                     /gene_synonym="C130005I02; Cart1"
                     /note="hexamer: AATAAA"
     polyA_site      1476
                     /gene="Alx1"
                     /gene_synonym="C130005I02; Cart1"
                     /note="major polyA site"
     regulatory      2168..2173
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Alx1"
                     /gene_synonym="C130005I02; Cart1"
                     /note="hexamer: AATAAA"
     regulatory      2186..2191
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Alx1"
                     /gene_synonym="C130005I02; Cart1"
                     /note="hexamer: AATACA"
     polyA_site      2191
                     /gene="Alx1"
                     /gene_synonym="C130005I02; Cart1"
     polyA_site      2205
                     /gene="Alx1"
                     /gene_synonym="C130005I02; Cart1"
ORIGIN      
        1 agccgggacg tattaagagt ctgggagctg ggcagctcct ggcgtcgcag gtctcgcttc
       61 ccctttccct cctctctgac cctccctact cccgcccact gctccctcct ccctccgcgc
      121 cctccagcct ccgcacgccc cggagagctc gcggacagcc tttccaggat tatggagttt
      181 ctgagcgaga agtttgccct gaagagcccg ccaagtaaaa acagtgactt ttacatgggc
      241 acaggaggcg cgttggagca cgttatggag acgctggaca atgagtcctt ttacggcaaa
      301 gcgacggctg gcaaatgcgt gcaggccttc gggccgctgc cgcgagcgga gcatcacgtg
      361 cgcctggaca ggacttcgcc ctgtcaggac agcagcgtga actatggaat caccaaagtg
      421 gaaggacagc cccttcacac cgagctgaat agagcaatgg ataactgcaa caatctcagg
      481 atgtctcccg tgaaagggat gccagagaag agcgaactgg atgaacttgg ggacaaatgt
      541 gacagcaatg tatccagcag caaaaagagg agacaccgaa ctacctttac cagtttgcag
      601 ctggaggaac tggagaaagt tttccagaaa acccattacc cagatgtata tgtcagagaa
      661 caacttgccc tgagaacgga gctcactgag gccagggtcc aggtttggtt tcaaaatcga
      721 agggccaagt ggagaaaaag agaacgatac ggccaaatac agcaagctaa aagccatttc
      781 gctgccacgt acgacatatc agtcttacca aggacggaca gctacccaca gatccagaac
      841 aatttgtggg caggaaatgc tagcggtggt tctgtggtta cgtcatgcat gctaccacgt
      901 gacgcgtcct cctgcatgac accttactct cactcgcctc ggacagattc cagttatacg
      961 gggttttcga accaccagaa tcagttcagc cacgtgcccc tcaataattt tttcactgac
     1021 tctcttctca ctggagctac caacggacac gcatttgaaa caaagccgga gtttgaaagg
     1081 aggtcttcca gtatcgctgt tctgagaatg aaggccaagg agcacaccgc caatatttca
     1141 tgggccatgt aacatacagt actcttttat ttttcttttc atagcaaagt aaaacattct
     1201 tatttctcgt atttaaagga taccacaata agctgctgtg tgtggaaggg ctaaaggtca
     1261 agatatacgg tgagaccagc ttacatgaat agttgttatt atttaacatt taaatctaag
     1321 aatggatccc tgaaaggact aaataggttt accatgcacc agcctccaca gactctgttt
     1381 tagtagtaag ttttttggtt tttttttttt tcctattgta caagtcaatg aaatatggtc
     1441 aggcaacttc ttaaaggaat aaatgtatta aacaaatcct tctgtgatag attgatttat
     1501 gcttgttctg tataacaaga aatcccttgt aaagtgatac ctgataaacg aggaaacacc
     1561 ccggggggaa aaaggcagta ttgatacagg gggctttgag agctaatgcc attttcaatt
     1621 ctttggctcc aagacacaat ggtcatacac tctgttgcag cctcaagatt cttttctttt
     1681 aacctttcaa tgttttggtg aatttccact cagtcggaaa aaaaagtcct tctgaactgc
     1741 tctgtatttg catggatatc tgggcacagt ttcttgcaac catgtggtta aaggtgacaa
     1801 ctgaagtatt cgcgtatgat ttaaagtcta gtcaactgga caggatttat aaatccaact
     1861 ttcaattgaa gaggccagca ggcagactgc aattttgtga ttaaaactga gaactcatta
     1921 gtaaacgtgc tgttgctttt atactaaaat catgttgatt caatcgcata caaacgtatc
     1981 ttgcaaataa agggtaactt ttcgattaaa ggagtaacag attggaattt atgtttgttt
     2041 tgtgggccta tgcatgttca aatgcatgcc tgtttggcct tgacactctg tgccttaagc
     2101 atttttgcta ctgtgctatc catagagaat taaaatgtca ggaggtgctc tagaatttct
     2161 tgttaaaaat aaaaagaaga agacaaatac attgcatctg gaaaatggct aacttctttg
     2221 atttccttct actcccttcc ccctgtcaca ttccaagtgt tttcagatga gtgaaatgtc
     2281 agcccccctt gaaagattcc taagttcata aaggcaaagt caattaattg aagcgaagat
     2341 gacttccaat ggctcagatc agagcaacat cgactctttg tactctgtta ggatcttcat
     2401 gtggttccgg tgaacgttag caatcgccca agaagcccta atgggtaaag aacaggagta
     2461 tgtgaatttt gaaaattaaa tttgatataa aag
//
