U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Nin ninein [ Mus musculus (house mouse) ]

Gene ID: 18080, updated on 8-Apr-2026
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 axonogenesis; microtubule cytoskeleton organization; and positive regulation of axonogenesis. Located in several cellular components, including axonal growth cone; dendrite; and microtubule cytoskeleton. Part of ciliary transition fiber. Is expressed in several structures, including alimentary system; brain; genitourinary system; immune system; and sensory organ. Human ortholog(s) of this gene implicated in Seckel syndrome 7. Orthologous to human NIN (ninein). [provided by Alliance of Genome Resources, Jul 2025]
Expression
Ubiquitous expression in CNS E18 (RPKM 5.4), CNS E14 (RPKM 4.0) and 23 other tissues See more
Orthologs
all
Try the new Gene page
Try the new Transcripts and proteins table
See Nin in Genome Data Viewer
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

Go to nucleotide: Graphics FASTA GenBank

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Loss of ninein interferes with osteoclast formation and causes premature ossification.
    Title: Loss of ninein interferes with osteoclast formation and causes premature ossification.
  2. 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.
  3. 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.
  4. 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

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Chemically induced (ENU) (1) 
  • Endonuclease-mediated (4) 
  • Spontaneous (1)  1 citation
  • Targeted (4)  1 citation
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC169413

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables microtubule minus-end binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
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
  
involved_in microtubule anchoring at centrosome ISS
Inferred from Sequence or Structural Similarity
more info
  
acts_upstream_of_or_within mitotic spindle organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within negative regulation of protein localization to centrosome EXP
Inferred from Experiment
more info
 PubMed 
acts_upstream_of_or_within positive regulation of axonogenesis IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within positive regulation of neuron differentiation EXP
Inferred from Experiment
more info
 PubMed 
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 
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 IEA
Inferred from Electronic Annotation
more info
  
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 IEA
Inferred from Electronic Annotation
more info
  
located_in centrosome ISO
Inferred from Sequence Orthology
more info
  
located_in centrosome ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in ciliary basal body 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 cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in dendrite IDA
Inferred from Direct Assay
more info
 PubMed 
located_in desmosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in desmosome IEA
Inferred from Electronic Annotation
more info
  
located_in microtubule IDA
Inferred from Direct Assay
more info
 PubMed 
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 
Preferred Names
ninein

NEW Try the new Transcript table

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
    UniProtKB/TrEMBL
    A0A1Y7VNC5

  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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools