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NIN ninein [ Homo sapiens (human) ]

Gene ID: 51199, updated on 2-Nov-2024

Summary

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Official Symbol
NINprovided by HGNC
Official Full Name
nineinprovided by HGNC
Primary source
HGNC:HGNC:14906
See related
Ensembl:ENSG00000100503 MIM:608684; AllianceGenome:HGNC:14906
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SCKL7
Summary
This gene encodes one of the proteins important for centrosomal function. This protein is important for positioning and anchoring the microtubules minus-ends in epithelial cells. Localization of this protein to the centrosome requires three leucine zippers in the central coiled-coil domain. Multiple alternatively spliced transcript variants that encode different isoforms have been reported. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in lymph node (RPKM 13.5), appendix (RPKM 9.8) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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See NIN in Genome Data Viewer
Location:
14q22.1
Exon count:
35
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (50719763..50831503, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (44925893..45037887, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (51186481..51297880, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 452, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:51123951-51124450 Neighboring gene salvador family WW domain containing protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8361 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5725 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5726 Neighboring gene ZFP64 zinc finger protein pseudogene 1 Neighboring gene uncharacterized LOC124903313 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:51210620-51211819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8365 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5727 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8368 Neighboring gene uncharacterized LOC105370489 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5732 Neighboring gene small nucleolar RNA U83B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5733 Neighboring gene abhydrolase domain containing 12B Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:51359698-51360520 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:51362989-51363812

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Ninein promotes F-actin cup formation and inward phagosome movement during phagocytosis in macrophages. Omer S, et al. Mol Biol Cell, 2024 Mar 1. PMID 38117588, Free PMC Article
  2. Identification of a Ninein (NIN) mutation in a family with spondyloepimetaphyseal dysplasia with joint laxity (leptodactylic type)-like phenotype. Grosch M, et al. Matrix Biol, 2013 Oct-Nov. PMID 23665482
  3. Differential expression of centrosome-associated proteins in human brain tumors: a possible role of hNinein isoform 6 in cell differentiation. Loh JK, et al. Biofactors, 2012 Nov-Dec. PMID 23047184
  4. Genomic organization and molecular characterization of the human ninein gene. Hong YR, et al. Biochem Biophys Res Commun, 2000 Dec 29. PMID 11162463
  5. Positive selection on NIN, a gene involved in neurogenesis, and primate brain evolution. Montgomery SH, et al. Genes Brain Behav, 2012 Nov. PMID 22937743

See all (81) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Ninein promotes F-actin cup formation and inward phagosome movement during phagocytosis in macrophages.
    Title: Ninein promotes F-actin cup formation and inward phagosome movement during phagocytosis in macrophages.
  2. beta3-Endonexin interacts with ninein in vascular endothelial cells to promote angiogenesis.
    Title: β3-Endonexin interacts with ninein in vascular endothelial cells to promote angiogenesis.
  3. Genetic susceptibility of common polymorphisms in NIN and SIGLEC5 to chronic periodontitis.
    Title: Genetic susceptibility of common polymorphisms in NIN and SIGLEC5 to chronic periodontitis.
  4. Our analyses suggest a relationship with prenatal neurogenesis and identify the human data point as an outlier, possibly explained by postnatal changes in development on the human lineage.
    Title: Positive selection on NIN, a gene involved in neurogenesis, and primate brain evolution.
  5. Ninein influences the rate of axonal growth and branching by affecting microtubule stability and dynamics.
    Title: Sip1 downstream Effector ninein controls neocortical axonal growth, ipsilateral branching, and microtubule growth and stability.
  6. JAK2 Tyrosine Kinase phosphorylates centrosomal protein ninein, which negatively regulates it
    Title: JAK2 tyrosine kinase phosphorylates and is negatively regulated by centrosomal protein Ninein.
  7. A Ninein (NIN) missense mutation identified in a family with spondyloepimetaphyseal dysplasia with joint laxity (leptodactylic type)-like phenotype.
    Title: Identification of a Ninein (NIN) mutation in a family with spondyloepimetaphyseal dysplasia with joint laxity (leptodactylic type)-like phenotype.
  8. The role of hNinein isoform 6 expression in cell differentiation was assessed in BrdU-treated IMR-32 cells
    Title: Differential expression of centrosome-associated proteins in human brain tumors: a possible role of hNinein isoform 6 in cell differentiation.
  9. The prevalence of hNinein autoreactivity and its specificity in 22 rheumatoid arthritis and 32 systemic lupus erythematosus autoimmune disease sera.
    Title: Autoimmunity against hNinein, a human centrosomal protein, in patients with rheumatoid arthritis and systemic lupus erythematosus.
  10. Trichoplein controls microtubule anchoring at the centrosome by binding to Odf2 and ninein.
    Title: Trichoplein controls microtubule anchoring at the centrosome by binding to Odf2 and ninein.
Submit: New GeneRIF Correction See all GeneRIFs (23)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Seckel syndrome 7
MedGen: C3553870 OMIM: 614851 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Common genetic variation and performance on standardized cognitive tests.
EBI GWAS Catalog
Genome-wide association study of periodontal health measured by probing depth in adults ages 18-49 years.
EBI GWAS Catalog
Lupus nephritis susceptibility Loci in women with systemic lupus erythematosus.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1565

Gene Ontology Provided by GOA

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 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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in centrosome localization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in centrosome localization TAS
Traceable Author Statement
more info
 PubMed 
involved_in centrosome-templated microtubule nucleation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in collateral sprouting IEA
Inferred from Electronic Annotation
more info
  
involved_in corpus callosum morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in corticospinal tract morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in microtubule anchoring at centrosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in microtubule anchoring at centrosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of axonogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in protein localization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in apical part of cell IEA
Inferred from Electronic Annotation
more info
  
located_in axonal growth cone IEA
Inferred from Electronic Annotation
more info
  
part_of centriolar subdistal appendage 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 
is_active_in centrosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of ciliary transition fiber IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasmic microtubule IEA
Inferred from Electronic Annotation
more info
  
located_in dendrite IEA
Inferred from Electronic Annotation
more info
  
located_in mitotic spindle IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in mitotic spindle pole IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in pericentriolar material IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in pericentriolar material IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in spindle pole IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
ninein
Names
glycogen synthase kinase 3 beta-interacting protein
hNinein
ninein (GSK3B interacting protein)
ninein centrosomal protein

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.

Genomic

  1. NG_032968.2 RefSeqGene

    Range
    5341..116740
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_016350.5 → NP_057434.4  ninein isoform 6

    See identical proteins and their annotated locations for NP_057434.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks an alternate in-frame exon in the central coding region and uses a distinct 3' coding region and 3' UTR, compared to variant 2. The resulting isoform (6) lacks an internal segment and has a shorter and distinct C-terminus, compared to isoform 2.
    Source sequence(s)
    AF302773, AL133485, BC090932
    Consensus CDS
    CCDS32078.2
    UniProtKB/TrEMBL
    A0A0B4J215
    Related
    ENSP00000324210.10, ENST00000324330.13
    Conserved Domains (2) summary
    pfam05262
    Location:304 → 515
    Borrelia_P83; Borrelia P83/100 protein
    cl25732
    Location:425 → 1247
    SMC_N; RecF/RecN/SMC N terminal domain

  2. NM_020921.4 → NP_065972.4  ninein isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) is the longest transcript and it encodes the longest isoform (2).
    Source sequence(s)
    AL133485, AL606834
    Consensus CDS
    CCDS91876.1
    UniProtKB/TrEMBL
    A0A6F7YPF6
    Related
    ENSP00000436092.2, ENST00000530997.7
    Conserved Domains (3) summary
    COG1196
    Location:920 → 1648
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    TIGR02168
    Location:407 → 825
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    NF033454
    Location:764 → 922
    BREX_5_MTaseX; BREX-5 system adenine-specific DNA-methyltransferase PglX

  3. NM_182944.3 → NP_891989.3  ninein isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) contains a different 3' coding region and 3' UTR when compared to variant 2. The resulting isoform (1) has a distinct and shorter C-terminus, as compared to isoform 2.
    Source sequence(s)
    AL133485, AL606834
    Consensus CDS
    CCDS45103.1
    UniProtKB/TrEMBL
    A0A6F7YPF6, C9J066
    Related
    ENSP00000412391.1, ENST00000453196.6
    Conserved Domains (4) summary
    COG1196
    Location:920 → 1648
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    TIGR02168
    Location:407 → 825
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    TIGR04523
    Location:1508 → 1957
    Mplasa_alph_rch; helix-rich Mycoplasma protein
    NF033454
    Location:764 → 922
    BREX_5_MTaseX; BREX-5 system adenine-specific DNA-methyltransferase PglX

  4. NM_182946.2 → NP_891991.2  ninein isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has multiple differences in the coding region and 3' UTR when compared to variant 2. The resulting isoform (5) has a distinct and shorter C-terminus as compared to isoform 2. Isoform 5 has also been referred to as hNinein-Lm.
    Source sequence(s)
    AL133485, AL606834
    Consensus CDS
    CCDS32079.1
    UniProtKB/Swiss-Prot
    A6NDB8, B7WPA3, C9JSB6, C9JSG2, C9JXL2, Q5BKU3, Q6P0P6, Q8N4C6, Q9BWU6, Q9C012, Q9C013, Q9C014, Q9H5I6, Q9HAT7, Q9HBY5, Q9HCK7, Q9UH61
    UniProtKB/TrEMBL
    A0A6F7YPF6
    Related
    ENSP00000371472.3, ENST00000382041.7
    Conserved Domains (3) summary
    COG1196
    Location:920 → 1648
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    TIGR02168
    Location:407 → 825
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    NF033454
    Location:764 → 922
    BREX_5_MTaseX; BREX-5 system adenine-specific DNA-methyltransferase PglX

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    50719763..50831503 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047431452.1 → XP_047287408.1  ninein isoform X25

  2. XM_047431439.1 → XP_047287395.1  ninein isoform X11

  3. XM_047431453.1 → XP_047287409.1  ninein isoform X23

  4. XM_047431438.1 → XP_047287394.1  ninein isoform X10

    Related
    ENSP00000374519.3, ENST00000389869.7

  5. XM_047431450.1 → XP_047287406.1  ninein isoform X23

  6. XM_047431442.1 → XP_047287398.1  ninein isoform X15

  7. XM_047431432.1 → XP_047287388.1  ninein isoform X3

  8. XM_047431445.1 → XP_047287401.1  ninein isoform X18

  9. XM_047431440.1 → XP_047287396.1  ninein isoform X13

    Related
    ENSP00000516509.1, ENST00000706706.1

  10. XM_047431434.1 → XP_047287390.1  ninein isoform X6

  11. XM_047431441.1 → XP_047287397.1  ninein isoform X14

  12. XM_047431431.1 → XP_047287387.1  ninein isoform X2

  13. XM_047431443.1 → XP_047287399.1  ninein isoform X16

  14. XM_011536822.3 → XP_011535124.1  ninein isoform X12

    UniProtKB/TrEMBL
    A0A0B4J215
    Conserved Domains (5) summary
    COG1196
    Location:455 → 1277
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    cd16269
    Location:821 → 832
    GBP_C; coiled coil [structural motif]
    cl19219
    Location:505 → 597
    DUF342; Protein of unknown function (DUF342)
    cl20817
    Location:734 → 850
    GBP_C; Guanylate-binding protein, C-terminal domain
    cl23750
    Location:441 → 534
    vATP-synt_E; ATP synthase (E/31 kDa) subunit

  15. XM_047431433.1 → XP_047287389.1  ninein isoform X4

  16. XM_024449622.2 → XP_024305390.1  ninein isoform X1

    UniProtKB/TrEMBL
    A0A6F7YPF6
    Conserved Domains (3) summary
    pfam04111
    Location:859 → 1003
    APG6; Autophagy protein Apg6
    cl25732
    Location:437 → 855
    SMC_N; RecF/RecN/SMC N terminal domain
    cl28159
    Location:335 → 455
    Aminotran_5; Aminotransferase class-V

  17. XM_047431449.1 → XP_047287405.1  ninein isoform X22

  18. XM_047431451.1 → XP_047287407.1  ninein isoform X24

  19. XM_047431446.1 → XP_047287402.1  ninein isoform X19

  20. XM_047431447.1 → XP_047287403.1  ninein isoform X20

  21. XM_047431435.1 → XP_047287391.1  ninein isoform X7

  22. XM_047431444.1 → XP_047287400.1  ninein isoform X17

  23. XM_011536819.4 → XP_011535121.1  ninein isoform X5

    UniProtKB/TrEMBL
    A0A6F7YPF6
    Conserved Domains (5) summary
    COG1196
    Location:950 → 1678
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    cd16269
    Location:821 → 832
    GBP_C; coiled coil [structural motif]
    cl19219
    Location:505 → 597
    DUF342; Protein of unknown function (DUF342)
    cl20817
    Location:734 → 850
    GBP_C; Guanylate-binding protein, C-terminal domain
    cl23750
    Location:441 → 534
    vATP-synt_E; ATP synthase (E/31 kDa) subunit

  24. XM_047431437.1 → XP_047287393.1  ninein isoform X9

    UniProtKB/TrEMBL
    E9PN67
    Related
    ENSP00000432924.1, ENST00000476352.5

  25. XM_047431448.1 → XP_047287404.1  ninein isoform X21

  26. XM_047431436.1 → XP_047287392.1  ninein isoform X8

  27. XM_047431454.1 → XP_047287410.1  ninein isoform X26

    Related
    ENSP00000431485.2, ENST00000485005.2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    44925893..45037887 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054376195.1 → XP_054232170.1  ninein isoform X25

  2. XM_054376181.1 → XP_054232156.1  ninein isoform X11

  3. XM_054376196.1 → XP_054232171.1  ninein isoform X23

  4. XM_054376180.1 → XP_054232155.1  ninein isoform X10

  5. XM_054376193.1 → XP_054232168.1  ninein isoform X23

  6. XM_054376185.1 → XP_054232160.1  ninein isoform X15

  7. XM_054376173.1 → XP_054232148.1  ninein isoform X3

  8. XM_054376188.1 → XP_054232163.1  ninein isoform X18

  9. XM_054376183.1 → XP_054232158.1  ninein isoform X13

  10. XM_054376176.1 → XP_054232151.1  ninein isoform X6

  11. XM_054376184.1 → XP_054232159.1  ninein isoform X14

  12. XM_054376172.1 → XP_054232147.1  ninein isoform X2

  13. XM_054376182.1 → XP_054232157.1  ninein isoform X12

  14. XM_054376171.1 → XP_054232146.1  ninein isoform X1

  15. XM_054376174.1 → XP_054232149.1  ninein isoform X4

  16. XM_054376186.1 → XP_054232161.1  ninein isoform X16

  17. XM_054376189.1 → XP_054232164.1  ninein isoform X19

  18. XM_054376177.1 → XP_054232152.1  ninein isoform X7

  19. XM_054376175.1 → XP_054232150.1  ninein isoform X5

  20. XM_054376190.1 → XP_054232165.1  ninein isoform X20

  21. XM_054376187.1 → XP_054232162.1  ninein isoform X17

  22. XM_054376192.1 → XP_054232167.1  ninein isoform X22

  23. XM_054376194.1 → XP_054232169.1  ninein isoform X24

  24. XM_054376179.1 → XP_054232154.1  ninein isoform X9

  25. XM_054376178.1 → XP_054232153.1  ninein isoform X8

  26. XM_054376191.1 → XP_054232166.1  ninein isoform X21

  27. XM_054376197.1 → XP_054232172.1  ninein isoform X26

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_182945.1: Suppressed sequence

    Description
    NM_182945.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N4C6.4 GenPept UniProtKB/Swiss-Prot:Q8N4C6

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