Nin ninein [Mus musculus (house mouse)] - Gene

Summary

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, Nov 2024]
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

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_000078.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Loss of ninein interferes with osteoclast formation and causes premature ossification.
Title: Loss of ninein interferes with osteoclast formation and causes premature ossification.
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.
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.
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.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (4)
Targeted (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH144501 (e-PCR)
- UniSTS:233746

NoName (e-PCR)
- UniSTS:236864

D12Dcr5 (e-PCR), detects polymorphism
- UniSTS:507488

AI385615 (e-PCR)
- UniSTS:180405

D12Mit114 (e-PCR), detects polymorphism
- UniSTS:126664

AU024711 (e-PCR)
- UniSTS:160216

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 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 centriole-centriole cohesion	IEA Inferred from Electronic Annotation 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
involved_in microtubule anchoring at centrosome	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within positive regulation of axonogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in protein localization	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation 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
located_in centrosome	ISS Inferred from Sequence or Structural Similarity 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 cytoplasmic microtubule	IDA Inferred from Direct Assay more info	PubMed
located_in dendrite	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	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation 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)

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

Status: VALIDATED

Source sequence(s)

AC112146, AC116574
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

NR_104397.2 RNA Sequence

Status: VALIDATED

Source sequence(s)

AK134860, AK147187, AK162150, AY515727, BY739065, CN535148

Related

ENSMUST00000223257.2
NR_104398.2 RNA Sequence

Status: VALIDATED

Source sequence(s)

AK134860, AY515727

Related

ENSMUST00000220689.2
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

NC_000078.7 Reference GRCm39 C57BL/6J

Range

70058209..70160575 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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
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