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    NINL ninein like [ Homo sapiens (human) ]

    Gene ID: 22981, updated on 5-Mar-2024

    Summary

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    Official Symbol
    NINLprovided by HGNC
    Official Full Name
    ninein likeprovided by HGNC
    Primary source
    HGNC:HGNC:29163
    See related
    Ensembl:ENSG00000101004 MIM:609580; AllianceGenome:HGNC:29163
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NLP
    Summary
    Predicted to enable calcium ion binding activity. Predicted to be involved in microtubule anchoring at centrosome. Located in cytosol; intercellular bridge; and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in kidney (RPKM 4.4), ovary (RPKM 3.4) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    20p11.21
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (25452697..25585531, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (25517773..25650553, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (25433333..25566167, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene abhydrolase domain containing 12, lysophospholipase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12751 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12752 Neighboring gene uncharacterized LOC105372581 Neighboring gene peptidylprolyl isomerase A pseudogene 2 Neighboring gene MPRA-validated peak4176 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17669 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:25388698-25389455 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25418017-25418688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25418689-25419360 Neighboring gene GINS complex subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25457461-25457961 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25483989-25484500 Neighboring gene Sharpr-MPRA regulatory region 10548 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25506669-25507224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25507225-25507779 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25513199-25514199 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25529495-25530318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25541385-25541914 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:25545021-25545520 Neighboring gene Sharpr-MPRA regulatory region 10614 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12753 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:25582716-25583915 Neighboring gene RNA, U6atac small nuclear 17, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:25603923-25604598 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17671 Neighboring gene N-acetylneuraminic acid phosphatase

    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
    • 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. Overexpression of centrosomal protein Nlp confers breast carcinoma resistance to paclitaxel. Zhao W, et al. Cancer Biol Ther, 2012 Feb 1. PMID 22353935
    2. The role of centrosomal Nlp in the control of mitotic progression and tumourigenesis. Li J, et al. Br J Cancer, 2011 May 10. PMID 21505454, Free PMC Article
    3. Ninein-like protein is overexpressed in head and neck squamous cell carcinoma and contributes to cancer growth and resistance to apoptosis. Yu L, et al. Oncol Rep, 2009 Oct. PMID 19724857
    4. Usher syndrome and Leber congenital amaurosis are molecularly linked via a novel isoform of the centrosomal ninein-like protein. van Wijk E, et al. Hum Mol Genet, 2009 Jan 1. PMID 18826961, Free PMC Article
    5. Increased expression of Nlp, a potential oncogene in ovarian cancer, and its implication in carcinogenesis. Qu D, et al. Gynecol Oncol, 2008 Aug. PMID 18538832

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Upon UVC radiation, Nlp interacts with XPA and ERCC1, and enhances their association
      Title: Mitotic regulator Nlp interacts with XPA/ERCC1 complexes and regulates nucleotide excision repair (NER) in response to UV radiation.
    2. these data support a model where CC2D2A associates with NINL to provide a docking point for cilia-directed cargo vesicles, suggesting a mechanism by which transition zone proteins can control the protein content of the ciliary compartment.
      Title: The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking.
    3. Overexpression of ninein and the ninein-like protein NIP induces fragmentation of the Golgi and causes lysosomes to disperse toward the cell periphery.
      Title: Phosphorylation of Nlp by Plk1 negatively regulates its dynein-dynactin-dependent targeting to the centrosome.
    4. Breast cancer patients with high expression of Nlp were likely resistant to the treatment of paclitaxel.
      Title: Overexpression of centrosomal protein Nlp confers breast carcinoma resistance to paclitaxel.
    5. This review summarises our current knowledge of physiological roles of Nlp, with an emphasis on its potentials in tumourigenesis.
      Title: The role of centrosomal Nlp in the control of mitotic progression and tumourigenesis.
    6. findings demonstrate that Cdc2/cyclin B1 is a key regulator in maintaining appropriate degradation and subcellular localization of Nlp, providing novel insights into understanding on the role of Cdc2/cyclin B1 in mitotic progression
      Title: Cdc2/cyclin B1 regulates centrosomal Nlp proteolysis and subcellular localization.
    7. regulation of Nlp by Aurora B is critical for the completion of cytokinesis, providing novel insights into understanding the machinery of cell cycle progression.
      Title: Aurora B interaction of centrosomal Nlp regulates cytokinesis.
    8. Nlp abnormalities may contribute to genomic instability and tumorigenesis and might serve as a potential biomarker for clinical diagnosis and as a therapeutic target.
      Title: Centrosomal Nlp is an oncogenic protein that is gene-amplified in human tumors and causes spontaneous tumorigenesis in transgenic mice.
    9. Nlp overexpression might contribute to the development of head and neck squamous cell carcinoma
      Title: Ninein-like protein is overexpressed in head and neck squamous cell carcinoma and contributes to cancer growth and resistance to apoptosis.
    10. BRCA1 interaction of Nlp might be required for the successful mitotic progression, and abnormalities of Nlp lead to genomic instability.
      Title: BRCA1 interaction of centrosomal protein Nlp is required for successful mitotic progression.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11792, KIAA0980, dJ691N24.1

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion 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 microtubule anchoring at centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    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 cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in microtubule IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ninein-like 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.

    mRNA and Protein(s)

    1. NM_001318226.2 → NP_001305155.1  ninein-like protein isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      BC036380, DA448124, DA871028, EU718622
      Consensus CDS
      CCDS82605.1
      UniProtKB/Swiss-Prot
      Q9Y2I6
      Conserved Domains (6) summary
      cd00051
      Location:212 → 259
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      TIGR02168
      Location:341 → 1014
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam13499
      Location:201 → 259
      EF-hand_7; EF-hand domain pair
      cd16269
      Location:989 → 1000
      GBP_C; coiled coil [structural motif]
      cl19219
      Location:607 → 699
      DUF342; Protein of unknown function (DUF342)
      cl20817
      Location:930 → 1019
      GBP_C; Guanylate-binding protein, C-terminal domain

    2. NM_025176.6 → NP_079452.3  ninein-like protein isoform 1

      See identical proteins and their annotated locations for NP_079452.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB023197, BC036380, DA448124, DA871028
      Consensus CDS
      CCDS33452.1
      UniProtKB/Swiss-Prot
      A6NJN0, B3V9H6, B7Z1V8, Q5JYP0, Q8NE38, Q9NQE3, Q9Y2I6
      Related
      ENSP00000278886.6, ENST00000278886.11
      Conserved Domains (5) summary
      cd00051
      Location:212 → 259
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam13499
      Location:201 → 259
      EF-hand_7; EF-hand domain pair
      cd16269
      Location:1338 → 1349
      GBP_C; coiled coil [structural motif]
      cl19219
      Location:607 → 699
      DUF342; Protein of unknown function (DUF342)
      cl20817
      Location:1279 → 1368
      GBP_C; Guanylate-binding protein, C-terminal domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      25452697..25585531 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047440021.1 → XP_047295977.1  ninein-like protein isoform X6

    2. XM_047440033.1 → XP_047295989.1  ninein-like protein isoform X20

    3. XM_047440027.1 → XP_047295983.1  ninein-like protein isoform X12

    4. XM_011529188.1 → XP_011527490.1  ninein-like protein isoform X5

      See identical proteins and their annotated locations for XP_011527490.1

      Conserved Domains (3) summary
      COG1196
      Location:1118 → 1443
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02169
      Location:398 → 706
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
      pfam13499
      Location:198 → 259
      EF-hand_7; EF-hand domain pair

    5. XM_047440022.1 → XP_047295978.1  ninein-like protein isoform X7

    6. XM_047440026.1 → XP_047295982.1  ninein-like protein isoform X11

    7. XM_047440020.1 → XP_047295976.1  ninein-like protein isoform X4

    8. XM_047440025.1 → XP_047295981.1  ninein-like protein isoform X10

    9. XM_047440019.1 → XP_047295975.1  ninein-like protein isoform X3

    10. XM_047440023.1 → XP_047295979.1  ninein-like protein isoform X8

    11. XM_011529189.2 → XP_011527491.1  ninein-like protein isoform X5

      See identical proteins and their annotated locations for XP_011527491.1

      Conserved Domains (3) summary
      COG1196
      Location:1118 → 1443
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02169
      Location:398 → 706
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
      pfam13499
      Location:198 → 259
      EF-hand_7; EF-hand domain pair

    12. XM_047440032.1 → XP_047295988.1  ninein-like protein isoform X19

    13. XM_047440024.1 → XP_047295980.1  ninein-like protein isoform X9

    14. XM_011529187.3 → XP_011527489.1  ninein-like protein isoform X2

      Conserved Domains (6) summary
      cd00051
      Location:228 → 275
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam00261
      Location:1186 → 1408
      Tropomyosin; Tropomyosin
      pfam13499
      Location:217 → 275
      EF-hand_7; EF-hand domain pair
      cd16269
      Location:1421 → 1432
      GBP_C; coiled coil [structural motif]
      cl19219
      Location:623 → 715
      DUF342; Protein of unknown function (DUF342)
      cl20817
      Location:1362 → 1451
      GBP_C; Guanylate-binding protein, C-terminal domain

    15. XM_011529186.3 → XP_011527488.1  ninein-like protein isoform X1

      Conserved Domains (6) summary
      cd00051
      Location:228 → 275
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam00261
      Location:1191 → 1413
      Tropomyosin; Tropomyosin
      pfam13499
      Location:217 → 275
      EF-hand_7; EF-hand domain pair
      cd16269
      Location:1426 → 1437
      GBP_C; coiled coil [structural motif]
      cl19219
      Location:628 → 720
      DUF342; Protein of unknown function (DUF342)
      cl20817
      Location:1367 → 1456
      GBP_C; Guanylate-binding protein, C-terminal domain

    16. XM_011529191.1 → XP_011527493.1  ninein-like protein isoform X13

      Conserved Domains (5) summary
      cd00051
      Location:53 → 100
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam13499
      Location:42 → 100
      EF-hand_7; EF-hand domain pair
      cd16269
      Location:1251 → 1262
      GBP_C; coiled coil [structural motif]
      cl19219
      Location:453 → 545
      DUF342; Protein of unknown function (DUF342)
      cl20817
      Location:1192 → 1281
      GBP_C; Guanylate-binding protein, C-terminal domain

    17. XM_047440029.1 → XP_047295985.1  ninein-like protein isoform X15

    18. XM_047440028.1 → XP_047295984.1  ninein-like protein isoform X14

    19. XM_047440031.1 → XP_047295987.1  ninein-like protein isoform X18

    20. XM_047440030.1 → XP_047295986.1  ninein-like protein isoform X16

    21. XM_011529192.3 → XP_011527494.1  ninein-like protein isoform X17

      Conserved Domains (3) summary
      cd16269
      Location:1038 → 1049
      GBP_C; coiled coil [structural motif]
      cl19219
      Location:240 → 332
      DUF342; Protein of unknown function (DUF342)
      cl20817
      Location:979 → 1068
      GBP_C; Guanylate-binding protein, C-terminal domain

    22. XM_047440034.1 → XP_047295990.1  ninein-like protein isoform X23

    23. XM_011529194.3 → XP_011527496.1  ninein-like protein isoform X21

      Conserved Domains (3) summary
      cd16269
      Location:976 → 987
      GBP_C; coiled coil [structural motif]
      cl19219
      Location:178 → 270
      DUF342; Protein of unknown function (DUF342)
      cl20817
      Location:917 → 1006
      GBP_C; Guanylate-binding protein, C-terminal domain

    24. XM_047440035.1 → XP_047295991.1  ninein-like protein isoform X24

    25. XM_011529195.3 → XP_011527497.1  ninein-like protein isoform X22

      Conserved Domains (3) summary
      cd16269
      Location:919 → 930
      GBP_C; coiled coil [structural motif]
      cl19219
      Location:121 → 213
      DUF342; Protein of unknown function (DUF342)
      cl20817
      Location:860 → 949
      GBP_C; Guanylate-binding protein, C-terminal domain

    26. XM_017027735.2 → XP_016883224.1  ninein-like protein isoform X25

      Conserved Domains (2) summary
      cd16269
      Location:785 → 796
      GBP_C; coiled coil [structural motif]
      cl20817
      Location:726 → 815
      GBP_C; Guanylate-binding protein, C-terminal domain

    27. XM_011529198.1 → XP_011527500.1  ninein-like protein isoform X26

      Conserved Domains (2) summary
      cd16269
      Location:767 → 778
      GBP_C; coiled coil [structural motif]
      cl20817
      Location:708 → 797
      GBP_C; Guanylate-binding protein, C-terminal domain

    RNA

    1. XR_007067446.1 RNA Sequence

    2. XR_007067445.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      25517773..25650553 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323213.1 → XP_054179188.1  ninein-like protein isoform X6

    2. XM_054323225.1 → XP_054179200.1  ninein-like protein isoform X20

    3. XM_054323218.1 → XP_054179193.1  ninein-like protein isoform X12

    4. XM_054323211.1 → XP_054179186.1  ninein-like protein isoform X5

    5. XM_054323210.1 → XP_054179185.1  ninein-like protein isoform X4

    6. XM_054323214.1 → XP_054179189.1  ninein-like protein isoform X7

    7. XM_054323217.1 → XP_054179192.1  ninein-like protein isoform X11

    8. XM_054323216.1 → XP_054179191.1  ninein-like protein isoform X10

    9. XM_054323215.1 → XP_054179190.1  ninein-like protein isoform X8

    10. XM_054323212.1 → XP_054179187.1  ninein-like protein isoform X5

    11. XM_054323219.1 → XP_054179194.1  ninein-like protein isoform X13

    12. XM_054323221.1 → XP_054179196.1  ninein-like protein isoform X15

    13. XM_054323220.1 → XP_054179195.1  ninein-like protein isoform X14

    14. XM_054323224.1 → XP_054179199.1  ninein-like protein isoform X18

    15. XM_054323222.1 → XP_054179197.1  ninein-like protein isoform X16

    16. XM_054323223.1 → XP_054179198.1  ninein-like protein isoform X17

    17. XM_054323226.1 → XP_054179201.1  ninein-like protein isoform X21

    18. XM_054323228.1 → XP_054179203.1  ninein-like protein isoform X23

    19. XM_054323229.1 → XP_054179204.1  ninein-like protein isoform X24

    20. XM_054323227.1 → XP_054179202.1  ninein-like protein isoform X22

    21. XM_054323230.1 → XP_054179205.1  ninein-like protein isoform X25

    22. XM_054323231.1 → XP_054179206.1  ninein-like protein isoform X26

    RNA

    1. XR_008485246.1 RNA Sequence

    2. XR_008485245.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y2I6.2 GenPept UniProtKB/Swiss-Prot:Q9Y2I6

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