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    Nin ninein [ Mus musculus (house mouse) ]

    Gene ID: 18080, updated on 3-Apr-2024

    Summary

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    Official Symbol
    Ninprovided by MGI
    Official Full Name
    nineinprovided by MGI
    Primary source
    MGI:MGI:105108
    See related
    Ensembl:ENSMUSG00000021068 AllianceGenome:MGI:105108
    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
    mKIAA1565; 3110068G20Rik
    Summary
    Enables microtubule minus-end binding activity. Acts upstream of or within several processes, including generation of neurons; microtubule cytoskeleton organization; and negative regulation of protein localization to centrosome. Located in several cellular components, including axonal growth cone; dendrite; and microtubule cytoskeleton. Part of ciliary transition fiber. Is expressed in several structures, including brain; genitourinary system; gut; limb; and respiratory system. Human ortholog(s) of this gene implicated in Seckel syndrome 7. Orthologous to human NIN (ninein). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E18 (RPKM 5.4), CNS E14 (RPKM 4.0) and 23 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    12 C2; 12 28.94 cM
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (70058209..70160575, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (70011435..70113811, complement)

    Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene salvador family WW domain containing 1 Neighboring gene predicted gene, 53725 Neighboring gene predicted gene, 23579 Neighboring gene STARR-seq mESC enhancer starr_32383 Neighboring gene predicted gene 9997 Neighboring gene STARR-seq mESC enhancer starr_32384 Neighboring gene STARR-positive B cell enhancer ABC_E10757 Neighboring gene STARR-positive B cell enhancer mm9_chr12:71246077-71246378 Neighboring gene predicted gene, 53726 Neighboring gene abhydrolase domain containing 12B

    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. Relocalization of a microtubule-anchoring protein, ninein, from the centrosome to dendrites during differentiation of mouse neurons. Ohama Y, et al. Histochem Cell Biol, 2009 Nov. PMID 19690882
    2. An RNA Switch of a Large Exon of Ninein Is Regulated by the Neural Stem Cell Specific-RNA Binding Protein, Qki5. Hayakawa-Yano Y, et al. Int J Mol Sci, 2019 Feb 26. PMID 30813567, Free PMC Article
    3. Asymmetric centrosome inheritance maintains neural progenitors in the neocortex. Wang X, et al. Nature, 2009 Oct 15. PMID 19829375, Free PMC Article
    4. Microtubule minus-end anchorage at centrosomal and non-centrosomal sites: the role of ninein. Mogensen MM, et al. J Cell Sci, 2000 Sep. PMID 10934040
    5. Cloning and characterization of a novel human ninein protein that interacts with the glycogen synthase kinase 3beta. Hong YR, et al. Biochim Biophys Acta, 2000 Jul 24. PMID 11004522

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Ninein is involved in the development of an intact epidermis, by at least two cellular mechanisms: by contributing to spindle orientation during the division of progenitor cells and by organizing a keratinocyte-specific cortical microtubule network.
      Title: Epidermal development requires ninein for spindle orientation and cortical microtubule organization.
    2. the mRNA coding for the Ninein protein is listed as one of Qki protein-dependent alternative splicing targets.
      Title: An RNA Switch of a Large Exon of Ninein Is Regulated by the Neural Stem Cell Specific-RNA Binding Protein, Qki5.
    3. ninein is localized at the centrosome in undifferentiated neural precursors; but ninein was barely detected in migrating neurons, such as those in the intermediate layer of the cerebral cortex and the internal granular layer of the cerebellar cortex
      Title: Relocalization of a microtubule-anchoring protein, ninein, from the centrosome to dendrites during differentiation of mouse neurons.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (4)  1 citation
    • Endonuclease-mediated (4) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC169413

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables GTP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables kinase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables microtubule minus-end binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in centriole-centriole cohesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in centrosome localization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within centrosome localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in centrosome-templated microtubule nucleation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within centrosome-templated microtubule nucleation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within collateral sprouting IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within corpus callosum morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within corticospinal tract morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in microtubule anchoring at centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within microtubule anchoring at centrosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in microtubule anchoring at centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of axonogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in protein localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in apical part of cell IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in axon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in axonal growth cone IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of centriolar subdistal appendage ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in centriole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centriole IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in centriole ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of ciliary transition fiber IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of ciliary transition fiber IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasmic microtubule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in dendrite IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in microtubule IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitotic spindle ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in mitotic spindle pole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitotic spindle pole IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in pericentriolar material IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in pericentriolar material ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in spindle pole ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ninein

    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_001081453.1 → NP_001074922.1  ninein isoform 1

      See identical proteins and their annotated locations for NP_001074922.1

      Status: VALIDATED

      Source sequence(s)
      AC116574, AK134860, AK147187, AY515727, CN535148
      Consensus CDS
      CCDS36468.1
      UniProtKB/Swiss-Prot
      A0A1Y7VJL5, B2RQ73, B7ZMZ9, E9Q488, E9Q4S3, Q61043, Q674R4, Q6ZPM7
      UniProtKB/TrEMBL
      A0A1Y7VNC5
      Related
      ENSMUSP00000082422.4, ENSMUST00000085314.11
      Conserved Domains (2) summary
      COG1196
      Location:1424 → 2096
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:869 → 1735
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    2. NM_001286079.2 → NP_001273008.1  ninein isoform 2

      See identical proteins and their annotated locations for NP_001273008.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an internal exon in the 5' UTR, compared to variant 2. Variants 2 and 3 encode the same isoform 2.
      Source sequence(s)
      AK141891, AK147187, BY739065, CJ089455, CN535148, U40342
      Consensus CDS
      CCDS36469.1
      UniProtKB/TrEMBL
      A0A1Y7VNC5
      Related
      ENSMUSP00000129648.2, ENSMUST00000169074.2
      Conserved Domains (5) summary
      TIGR02168
      Location:869 → 1735
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam03528
      Location:1544 → 1929
      Rabaptin; Rabaptin
      pfam09798
      Location:1474 → 1561
      LCD1; DNA damage checkpoint protein
      cl19219
      Location:475 → 567
      DUF342; Protein of unknown function (DUF342)
      cl23887
      Location:625 → 728
      DUF4349; Domain of unknown function (DUF4349)

    3. NM_001286080.2 → NP_001273009.1  ninein isoform 3

      Status: VALIDATED

      Source sequence(s)
      AK147187, AK162150, AY515727, BY739065, CN695964, U40342
      UniProtKB/TrEMBL
      A0A1Y7VNC5
      Conserved Domains (4) summary
      TIGR02168
      Location:869 → 1735
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam09798
      Location:1474 → 1561
      LCD1; DNA damage checkpoint protein
      cl19219
      Location:475 → 567
      DUF342; Protein of unknown function (DUF342)
      cl23887
      Location:625 → 728
      DUF4349; Domain of unknown function (DUF4349)

    4. NM_001403832.1 → NP_001390761.1  ninein isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC112146, AC116574

    5. NM_008697.4 → NP_032723.2  ninein isoform 2

      See identical proteins and their annotated locations for NP_032723.2

      Status: VALIDATED

      Source sequence(s)
      AK147187, AK162150, AY515727, BY739065, CN535148
      Consensus CDS
      CCDS36469.1
      UniProtKB/TrEMBL
      A0A1Y7VNC5
      Related
      ENSMUSP00000021468.8, ENSMUST00000021468.14
      Conserved Domains (5) summary
      TIGR02168
      Location:869 → 1735
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam03528
      Location:1544 → 1929
      Rabaptin; Rabaptin
      pfam09798
      Location:1474 → 1561
      LCD1; DNA damage checkpoint protein
      cl19219
      Location:475 → 567
      DUF342; Protein of unknown function (DUF342)
      cl23887
      Location:625 → 728
      DUF4349; Domain of unknown function (DUF4349)

    RNA

    1. NR_104397.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AK134860, AK147187, AK162150, AY515727, BY739065, CN535148
      Related
      ENSMUST00000223257.2

    2. NR_104398.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AK134860, AY515727
      Related
      ENSMUST00000220689.2

    3. NR_175597.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC112146, AC116574

    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_000078.7 Reference GRCm39 C57BL/6J

      Range
      70058209..70160575 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036157228.1 → XP_036013121.1  ninein isoform X5

      Conserved Domains (1) summary
      TIGR02168
      Location:354 → 1093
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    2. XM_006515532.3 → XP_006515595.1  ninein isoform X4

      Conserved Domains (2) summary
      COG1196
      Location:825 → 1403
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:354 → 1093
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    3. XM_011244009.3 → XP_011242311.1  ninein isoform X2

      See identical proteins and their annotated locations for XP_011242311.1

      UniProtKB/Swiss-Prot
      A0A1Y7VJL5, B2RQ73, B7ZMZ9, E9Q488, E9Q4S3, Q61043, Q674R4, Q6ZPM7
      UniProtKB/TrEMBL
      A0A1Y7VNC5
      Conserved Domains (2) summary
      COG1196
      Location:1424 → 2096
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:869 → 1735
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    4. XM_036157227.1 → XP_036013120.1  ninein isoform X3

      UniProtKB/TrEMBL
      A0A1Y7VNC5
      Conserved Domains (2) summary
      COG1196
      Location:1422 → 1805
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:697 → 1607
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    5. XM_006515530.4 → XP_006515593.1  ninein isoform X1

      See identical proteins and their annotated locations for XP_006515593.1

      UniProtKB/TrEMBL
      A0A1Y7VNC5
      Conserved Domains (1) summary
      TIGR02168
      Location:869 → 1735
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    6. XM_006515528.4 → XP_006515591.1  ninein isoform X1

      See identical proteins and their annotated locations for XP_006515591.1

      UniProtKB/TrEMBL
      A0A1Y7VNC5
      Conserved Domains (1) summary
      TIGR02168
      Location:869 → 1735
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    7. XM_030246599.2 → XP_030102459.1  ninein isoform X1

      UniProtKB/TrEMBL
      A0A1Y7VNC5
      Conserved Domains (1) summary
      TIGR02168
      Location:869 → 1735
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    RNA

    1. XR_003949997.2 RNA Sequence

    2. XR_004937416.1 RNA Sequence

    3. XR_001780420.3 RNA Sequence

    4. XR_872709.3 RNA Sequence

    5. XR_003949996.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q61043.4 GenPept UniProtKB/Swiss-Prot:Q61043

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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