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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

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