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    Armc9 armadillo repeat containing 9 [ Mus musculus (house mouse) ]

    Gene ID: 78795, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Armc9provided by MGI
    Official Full Name
    armadillo repeat containing 9provided by MGI
    Primary source
    MGI:MGI:1926045
    See related
    Ensembl:ENSMUSG00000062590 AllianceGenome:MGI:1926045
    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
    3830422A13Rik; 4831423D23Rik; 4930438O05Rik; 5730415N24Rik
    Summary
    Involved in positive regulation of smoothened signaling pathway. Located in ciliary tip. Human ortholog(s) of this gene implicated in Joubert syndrome 30. Orthologous to human ARMC9 (armadillo repeat containing 9). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis adult (RPKM 4.8), frontal lobe adult (RPKM 2.3) and 24 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Armc9 in Genome Data Viewer
    Location:
    1 C5; 1 43.94 cM
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (86082436..86207491)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (86154729..86278284)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene proteasome (prosome, macropain) 26S subunit, non-ATPase, 1 Neighboring gene predicted gene, 22786 Neighboring gene predicted gene, 53570 Neighboring gene 5-hydroxytryptamine (serotonin) receptor 2B Neighboring gene STARR-seq mESC enhancer starr_01562 Neighboring gene STARR-seq mESC enhancer starr_01563 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:88051083-88051236 Neighboring gene STARR-positive B cell enhancer ABC_E4330 Neighboring gene STARR-seq mESC enhancer starr_01567 Neighboring gene STARR-positive B cell enhancer mm9_chr1:88110756-88111056 Neighboring gene STARR-positive B cell enhancer mm9_chr1:88125353-88125654 Neighboring gene STARR-seq mESC enhancer starr_01568 Neighboring gene STARR-positive B cell enhancer mm9_chr1:88154834-88155134 Neighboring gene predicted gene, 46098 Neighboring gene predicted gene 16341 Neighboring gene predicted gene 28626 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. A CRISPR-based screen for Hedgehog signaling provides insights into ciliary function and ciliopathies. Breslow DK, et al. Nat Genet, 2018 Mar. PMID 29459677, Free PMC Article
    2. Fancd2 in vivo interaction network reveals a non-canonical role in mitochondrial function. Zhang T, et al. Sci Rep, 2017 Apr 5. PMID 28378742, Free PMC Article
    3. EUCOMM--the European conditional mouse mutagenesis program. Friedel RH, et al. Brief Funct Genomic Proteomic, 2007 Sep. PMID 17967808
    4. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Stryke D, et al. Nucleic Acids Res, 2003 Jan 1. PMID 12520002, Free PMC Article
    5. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Watahiki A, et al. Nat Methods, 2004 Dec. PMID 15782199

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cilium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of smoothened signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in centriole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centriole ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in centriole ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in ciliary basal body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ciliary basal body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in ciliary basal body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in ciliary tip IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ciliary tip IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cilium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lisH domain-containing protein ARMC9

    NCBI Reference Sequences (RefSeq)

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    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_001310702.2 → NP_001297631.1  lisH domain-containing protein ARMC9 isoform 3

      See identical proteins and their annotated locations for NP_001297631.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
      Source sequence(s)
      AC104896, AC157768
      Consensus CDS
      CCDS78642.1
      UniProtKB/Swiss-Prot
      Q9D2I5
      Related
      ENSMUSP00000108934.3, ENSMUST00000113309.9
      Conserved Domains (2) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif
      cd00020
      Location:337 → 440
      ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...

    2. NM_027456.3 → NP_081732.1  lisH domain-containing protein ARMC9 isoform 2

      See identical proteins and their annotated locations for NP_081732.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks several exons and its 3' terminal exon extends past a splice site that is used in variant 3. The resulting isoform (2) is shorter at the C-terminus compared to isoform 3.
      Source sequence(s)
      AC157768
      Consensus CDS
      CCDS48303.1
      UniProtKB/Swiss-Prot
      Q9D2I5
      Related
      ENSMUSP00000117267.2, ENSMUST00000131412.8

    3. NM_030184.3 → NP_084460.1  lisH domain-containing protein ARMC9 isoform 1

      See identical proteins and their annotated locations for NP_084460.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) uses an alternate in-frame splice junction in the 3' end compared to variant 3. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 3.
      Source sequence(s)
      AC104896, AC157768
      Consensus CDS
      CCDS15118.1
      UniProtKB/Swiss-Prot
      Q8BQQ3, Q8BR45, Q8BSX7, Q8C6A6, Q8C889, Q8CA23, Q8CBG2, Q8K112, Q9CYL1, Q9D2I5, Q9D2L3
      Related
      ENSMUSP00000027434.9, ENSMUST00000027434.15
      Conserved Domains (2) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif
      cd00020
      Location:337 → 440
      ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...

    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_000067.7 Reference GRCm39 C57BL/6J

      Range
      86082436..86207491
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006529952.5 → XP_006530015.1  lisH domain-containing protein ARMC9 isoform X1

      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    2. XM_006529958.5 → XP_006530021.1  lisH domain-containing protein ARMC9 isoform X6

      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    3. XM_006529954.4 → XP_006530017.1  lisH domain-containing protein ARMC9 isoform X3

      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    4. XM_006529953.5 → XP_006530016.1  lisH domain-containing protein ARMC9 isoform X2

      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    5. XM_006529957.5 → XP_006530020.1  lisH domain-containing protein ARMC9 isoform X5

      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    6. XM_006529956.5 → XP_006530019.1  lisH domain-containing protein ARMC9 isoform X4

      UniProtKB/Swiss-Prot
      Q9D2I5
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    7. XM_006529959.4 → XP_006530022.1  lisH domain-containing protein ARMC9 isoform X7

      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    8. XM_036154435.1 → XP_036010328.1  lisH domain-containing protein ARMC9 isoform X8

      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    9. XM_006529960.4 → XP_006530023.1  lisH domain-containing protein ARMC9 isoform X9

      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    10. XM_011248111.4 → XP_011246413.1  lisH domain-containing protein ARMC9 isoform X10

      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    11. XM_011248112.4 → XP_011246414.1  lisH domain-containing protein ARMC9 isoform X11

      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    RNA

    1. XR_387199.5 RNA Sequence

    2. XR_004935067.1 RNA Sequence

    3. XR_001778466.3 RNA Sequence

    4. XR_387200.5 RNA Sequence

    5. XR_003947323.2 RNA Sequence

    6. XR_387202.4 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9D2I5.1 GenPept UniProtKB/Swiss-Prot:Q9D2I5

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