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    NIN ninein [ Homo sapiens (human) ]

    Gene ID: 51199, updated on 28-Oct-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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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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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    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.

    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

    Gene LinkOut

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

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