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

Gene ID: 78795, updated on 2-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 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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