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    Alx1 ALX homeobox 1 [ Mus musculus (house mouse) ]

    Gene ID: 216285, updated on 9-Dec-2024

    Summary

    Official Symbol
    Alx1provided by MGI
    Official Full Name
    ALX homeobox 1provided by MGI
    Primary source
    MGI:MGI:104621
    See related
    Ensembl:ENSMUSG00000036602 AllianceGenome:MGI:104621
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Cart1; C130005I02
    Summary
    Enables DNA-binding transcription factor activity and sequence-specific DNA binding activity. Acts upstream of or within several processes, including embryonic morphogenesis; mesenchymal cell development; and positive regulation of transcription by RNA polymerase II. Located in nucleus. Part of transcription regulator complex. Is expressed in several structures, including branchial arch; embryo mesenchyme; genitourinary system; limb primordium; and nose. Used to study frontonasal dysplasia 3. Human ortholog(s) of this gene implicated in frontonasal dysplasia 3. Orthologous to human ALX1 (ALX homeobox 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in testis adult (RPKM 6.2), CNS E11.5 (RPKM 2.3) and 3 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Alx1 in Genome Data Viewer
    Location:
    10 D1; 10 53.56 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (102834564..102865501, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (103007847..103029549, complement)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene Ras association (RalGDS/AF-6) domain family (N-terminal) member 9 Neighboring gene predicted gene 5175 Neighboring gene predicted gene, 34298 Neighboring gene leucine-rich repeats and IQ motif containing 1 Neighboring gene predicted gene, 25376 Neighboring gene STARR-seq mESC enhancer starr_27747 Neighboring gene STARR-seq mESC enhancer starr_27748 Neighboring gene STARR-seq mESC enhancer starr_27749 Neighboring gene STARR-seq mESC enhancer starr_27750 Neighboring gene STARR-seq mESC enhancer starr_27751 Neighboring gene RIKEN cDNA 6430590A10 gene Neighboring gene STARR-seq mESC enhancer starr_27752 Neighboring gene solute carrier family 6 (neurotransmitter transporter), member 15

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    acts_upstream_of_or_within anterior/posterior pattern specification IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within embryonic limb morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in embryonic skeletal system morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within embryonic skeletal system morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within mesenchymal cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within neural tube closure IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of epithelial to mesenchymal transition ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of epithelial to mesenchymal transition ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within roof of mouth development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within stem cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    part_of transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    ALX homeobox protein 1
    Names
    cartilage homeoprotein 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001421474.1NP_001408403.1  ALX homeobox protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC167468
      UniProtKB/TrEMBL
      A0A1W2P8B9
      Related
      ENSMUSP00000152017.2, ENSMUST00000217946.2
    2. NM_001421475.1NP_001408404.1  ALX homeobox protein 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC167468
      UniProtKB/Swiss-Prot
      Q8C370, Q8C8B0
      Related
      ENSMUSP00000152018.2, ENSMUST00000219194.2
    3. NM_001421476.1NP_001408405.1  ALX homeobox protein 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC167468
      UniProtKB/Swiss-Prot
      Q8C370, Q8C8B0
      Related
      ENSMUSP00000129230.2, ENSMUST00000167156.9
    4. NM_172553.4NP_766141.1  ALX homeobox protein 1 isoform 1

      See identical proteins and their annotated locations for NP_766141.1

      Status: VALIDATED

      Source sequence(s)
      AC167468
      Consensus CDS
      CCDS24155.1
      UniProtKB/Swiss-Prot
      Q8C370, Q8C8B0
      Related
      ENSMUSP00000042512.6, ENSMUST00000040859.6
      Conserved Domains (2) summary
      pfam00046
      Location:135189
      Homeobox; Homeobox domain
      pfam03826
      Location:302320
      OAR; OAR domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000076.7 Reference GRCm39 C57BL/6J

      Range
      102834564..102865501 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006513529.4XP_006513592.1  ALX homeobox protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006513592.1

      UniProtKB/Swiss-Prot
      Q8C370, Q8C8B0
      Related
      ENSMUSP00000151776.2, ENSMUST00000218282.2
      Conserved Domains (2) summary
      pfam00046
      Location:135189
      Homeobox; Homeobox domain
      pfam03826
      Location:302320
      OAR; OAR domain