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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
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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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