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    Armc9 armadillo repeat containing 9 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 301579, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Armc9provided by RGD
    Official Full Name
    armadillo repeat containing 9provided by RGD
    Primary source
    RGD:1305615
    See related
    EnsemblRapid:ENSRNOG00000025418 AllianceGenome:RGD:1305615
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1305615
    Summary
    Predicted to be involved in cilium assembly and positive regulation of smoothened signaling pathway. Predicted to be located in cilium. Predicted to be active in centriole; ciliary basal body; and 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
    Biased expression in Testes (RPKM 66.5), Brain (RPKM 52.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Armc9 in Genome Data Viewer
    Location:
    9q35
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (94250492..94376589)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (86802791..86928611)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (93172718..93299119)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134480602 Neighboring gene proteasome 26S subunit, non-ATPase 1 Neighboring gene 5-hydroxytryptamine receptor 2B Neighboring gene uncharacterized LOC102548542 Neighboring gene transfer RNA proline (anticodon AGG) 49 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Mutations in ARMC9, which Encodes a Basal Body Protein, Cause Joubert Syndrome in Humans and Ciliopathy Phenotypes in Zebrafish. Van De Weghe JC, et al. Am J Hum Genet, 2017 Jul 6. PMID 28625504, Free PMC Article
    2. 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
    3. Large-scale proteomics and phosphoproteomics of urinary exosomes. Gonzales PA, et al. J Am Soc Nephrol, 2009 Feb. PMID 19056867, Free PMC Article
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cilium assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cilium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of smoothened signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of smoothened signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in centriole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centriole IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in ciliary tip ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in ciliary tip ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cilium ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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_001109663.2 → NP_001103133.1  lisH domain-containing protein ARMC9 isoform 1

      See identical proteins and their annotated locations for NP_001103133.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/TrEMBL
      A0A8I6GK98, A6JWG3

    2. NM_001398574.1 → NP_001385503.1  lisH domain-containing protein ARMC9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/TrEMBL
      A0A8I6AFM3
      Related
      ENSRNOP00000075022.3, ENSRNOT00000088525.3
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    3. NM_001398575.1 → NP_001385504.1  lisH domain-containing protein ARMC9 isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      Related
      ENSRNOP00000093331.2, ENSRNOT00000117592.2

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086027.1 Reference GRCr8

      Range
      94250492..94376589
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039083408.2 → XP_038939336.1  lisH domain-containing protein ARMC9 isoform X1

      UniProtKB/TrEMBL
      A0A8I6GK98
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    2. XM_039083409.2 → XP_038939337.1  lisH domain-containing protein ARMC9 isoform X2

      UniProtKB/TrEMBL
      A0A8I6GK98
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    3. XM_039083412.2 → XP_038939340.1  lisH domain-containing protein ARMC9 isoform X6

      UniProtKB/Swiss-Prot
      A1A5P5
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    4. XM_063267030.1 → XP_063123100.1  lisH domain-containing protein ARMC9 isoform X7

    5. XM_063267031.1 → XP_063123101.1  lisH domain-containing protein ARMC9 isoform X9

      Related
      ENSRNOP00000059344.5, ENSRNOT00000066934.5

    6. XM_063267032.1 → XP_063123102.1  lisH domain-containing protein ARMC9 isoform X10

      UniProtKB/TrEMBL
      A0A0G2K9J8
      Related
      ENSRNOP00000110386.1, ENSRNOT00000173600.1

    7. XM_039083411.2 → XP_038939339.1  lisH domain-containing protein ARMC9 isoform X3

      UniProtKB/TrEMBL
      F1M3U9
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    8. XM_039083415.2 → XP_038939343.1  lisH domain-containing protein ARMC9 isoform X11

      UniProtKB/TrEMBL
      F1M3U9
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    9. XM_063267028.1 → XP_063123098.1  lisH domain-containing protein ARMC9 isoform X4

    10. XM_063267033.1 → XP_063123103.1  lisH domain-containing protein ARMC9 isoform X12

    11. XM_063267035.1 → XP_063123105.1  lisH domain-containing protein ARMC9 isoform X14

    12. XM_063267029.1 → XP_063123099.1  lisH domain-containing protein ARMC9 isoform X5

      Related
      ENSRNOP00000100795.1, ENSRNOT00000146096.1

    13. XM_039083416.2 → XP_038939344.1  lisH domain-containing protein ARMC9 isoform X15

      UniProtKB/TrEMBL
      F1M3U9
      Related
      ENSRNOP00000093397.1, ENSRNOT00000105720.2
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    14. XM_039083417.2 → XP_038939345.1  lisH domain-containing protein ARMC9 isoform X16

      UniProtKB/TrEMBL
      A6JWG5
      Conserved Domains (1) summary
      smart00667
      Location:7 → 38
      LisH; Lissencephaly type-1-like homology motif

    15. XM_063267037.1 → XP_063123107.1  lisH domain-containing protein ARMC9 isoform X17

    16. XM_039083414.2 → XP_038939342.1  lisH domain-containing protein ARMC9 isoform X8

      UniProtKB/TrEMBL
      A0A8I6GK98

    17. XM_063267034.1 → XP_063123104.1  lisH domain-containing protein ARMC9 isoform X13

    18. XM_039083418.2 → XP_038939346.1  lisH domain-containing protein ARMC9 isoform X18

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A1A5P5.1 GenPept UniProtKB/Swiss-Prot:A1A5P5

    Gene LinkOut

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