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NEK3 NIMA related kinase 3 [ Homo sapiens (human) ]

Gene ID: 4752, updated on 10-Dec-2024

Summary

Official Symbol
NEK3provided by HGNC
Official Full Name
NIMA related kinase 3provided by HGNC
Primary source
HGNC:HGNC:7746
See related
Ensembl:ENSG00000136098 MIM:604044; AllianceGenome:HGNC:7746
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
HSPK36
Summary
This gene encodes a member of the NimA (never in mitosis A) family of serine/threonine protein kinases. The encoded protein differs from other NimA family members in that it is not cell cycle regulated and is found primarily in the cytoplasm. The kinase is activated by prolactin stimulation, leading to phosphorylation of VAV2 guanine nucleotide exchange factor, paxillin, and activation of the RAC1 GTPase. Two functional alleles for this gene have been identified in humans. The reference genome assembly (GRCh38) represents a functional allele that is associated with the inclusion of an additional coding exon in protein-coding transcripts, compared to an alternate functional allele that lacks the exon. [provided by RefSeq, Sep 2019]
Annotation information
Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
Note: Available sequence data supports two haplotypes in the human population that differ by a 1 nt indel (rs3837575) at the end of exon 10. Both haplotypes appear to encode functional proteins via alternative splicing of exon 11. The GRCh38 reference assembly includes the extra nt and expresses a full-length protein that includes exon 11, whereas haplotypes that lack the extra nt express a full-length protein lacking exon 11. [30 Sep 2019]
Expression
Broad expression in testis (RPKM 10.8), placenta (RPKM 6.5) and 24 other tissues See more
Orthologs
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Genomic context

See NEK3 in Genome Data Viewer
Location:
13q14.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (52132647..52159860, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (51347480..51374691, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (52706783..52733995, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ALG11 alpha-1,2-mannosyltransferase Neighboring gene UTP14C small subunit processome component Neighboring gene NIMA related kinase 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:52653033-52653791 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:52653792-52654549 Neighboring gene Sharpr-MPRA regulatory region 10224 Neighboring gene Sharpr-MPRA regulatory region 2352 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:52696487-52696693 Neighboring gene uncharacterized LOC101929657 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:52706487-52707686 Neighboring gene uncharacterized LOC124903176 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5381 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5382 Neighboring gene Sharpr-MPRA regulatory region 2809 Neighboring gene mitochondrial ribosomal protein S31 pseudogene 5 Neighboring gene thrombospondin type 1 domain containing 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:52764223-52764724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7788 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7789 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:52796837-52797005 Neighboring gene TPTE2 pseudogene 2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

General gene information

Clone Names

  • MGC29949

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3-phosphoinositide-dependent protein kinase activity  
enables AMP-activated protein kinase activity  
enables ATP binding  
enables DNA-dependent protein kinase activity  
enables Rho-dependent protein serine/threonine kinase activity  
enables eukaryotic translation initiation factor 2alpha kinase activity  
enables histone H2AS1 kinase activity  
enables histone H2AS121 kinase activity  
enables histone H2AT120 kinase activity  
enables histone H2AXS139 kinase activity  
enables histone H2BS14 kinase activity  
enables histone H2BS36 kinase activity  
enables histone H3S10 kinase activity  
enables histone H3S28 kinase activity  
enables histone H3S57 kinase activity  
enables histone H3T11 kinase activity  
enables histone H3T3 kinase activity  
enables histone H3T45 kinase activity  
enables histone H3T6 kinase activity  
enables histone H4S1 kinase activity  
enables metal ion binding  
enables protein binding PubMed 
enables protein serine kinase activity  
enables protein serine/threonine kinase activity PubMed 
enables ribosomal protein S6 kinase activity  
Process Evidence Code Pubs
involved_in cell division  
involved_in chromatin remodeling  
involved_in establishment of cell polarity  
involved_in mitotic cell cycle PubMed 
involved_in neuron projection morphogenesis  
involved_in protein phosphorylation  
involved_in regulation of tubulin deacetylation  
Component Evidence Code Pubs
located_in axon  
located_in cytoplasm  
located_in nucleus PubMed 

General protein information

Preferred Names
serine/threonine-protein kinase Nek3
Names
HSPK 36
NIMA (never in mitosis gene a)-related kinase 3
glycogen synthase A kinase
hydroxyalkyl-protein kinase
never in mitosis A-related kinase 3
nimA-related protein kinase 3
phosphorylase B kinase kinase
NP_001139571.1
NP_001411183.1
NP_001411184.1
NP_001411186.1
NP_001411188.1
NP_001411193.1
NP_001411194.1
NP_001411195.1
NP_001411197.1
NP_001411198.1
NP_001411199.1
NP_001411200.1
NP_002489.1
NP_689933.1

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)

  1. NM_001146099.2NP_001139571.1  serine/threonine-protein kinase Nek3 isoform b

    See identical proteins and their annotated locations for NP_001139571.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the splice pattern of variant 5 but without the extra 'A' found in the GRCh38 haplotype.
    Source sequence(s)
    CP068265
    UniProtKB/TrEMBL
    Q6ZN64
    Conserved Domains (1) summary
    cd08219
    Location:3257
    STKc_Nek3; Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 3
  2. NM_001424254.1NP_001411183.1  serine/threonine-protein kinase Nek3 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) represents the splice pattern of variant 19 but with the extra 'A' found in the GRCh38 haplotype.
    Source sequence(s)
    AL139082, KF459684
    UniProtKB/TrEMBL
    Q5JPB0
  3. NM_001424255.1NP_001411184.1  serine/threonine-protein kinase Nek3 isoform d

    Status: REVIEWED

    Source sequence(s)
    AL139082, KF459684
    UniProtKB/TrEMBL
    Q5JPB0
  4. NM_001424257.1NP_001411186.1  serine/threonine-protein kinase Nek3 isoform d

    Status: REVIEWED

    Source sequence(s)
    AL139082, KF459684
    UniProtKB/TrEMBL
    Q5JPB0
  5. NM_001424259.1NP_001411188.1  serine/threonine-protein kinase Nek3 isoform e

    Status: REVIEWED

    Source sequence(s)
    AL139082, KF459684
  6. NM_001424264.1NP_001411193.1  serine/threonine-protein kinase Nek3 isoform f

    Status: REVIEWED

    Source sequence(s)
    AL139082, KF459684
    UniProtKB/TrEMBL
    Q5JPB0
  7. NM_001424265.1NP_001411194.1  serine/threonine-protein kinase Nek3 isoform a

    Status: REVIEWED

    Source sequence(s)
    AL139082, KF459684
    UniProtKB/Swiss-Prot
    A8K2J4, P51956, Q5TAP2, Q8J023, Q8WUN5
    UniProtKB/TrEMBL
    Q5JPB0
  8. NM_001424266.1NP_001411195.1  serine/threonine-protein kinase Nek3 isoform a

    Status: REVIEWED

    Source sequence(s)
    AL139082, KF459684
    UniProtKB/Swiss-Prot
    A8K2J4, P51956, Q5TAP2, Q8J023, Q8WUN5
    UniProtKB/TrEMBL
    Q5JPB0
  9. NM_001424268.1NP_001411197.1  serine/threonine-protein kinase Nek3 isoform b

    Status: REVIEWED

    Source sequence(s)
    CP068265
    UniProtKB/TrEMBL
    Q6ZN64
  10. NM_001424269.1NP_001411198.1  serine/threonine-protein kinase Nek3 isoform b

    Status: REVIEWED

    Source sequence(s)
    CP068265
    UniProtKB/TrEMBL
    Q6ZN64
  11. NM_001424270.1NP_001411199.1  serine/threonine-protein kinase Nek3 isoform g

    Status: REVIEWED

    Source sequence(s)
    CP068265
    UniProtKB/TrEMBL
    Q6ZN64
  12. NM_001424271.1NP_001411200.1  serine/threonine-protein kinase Nek3 isoform h

    Status: REVIEWED

    Source sequence(s)
    CP068265
    UniProtKB/TrEMBL
    Q6ZN64
  13. NM_002498.3NP_002489.1  serine/threonine-protein kinase Nek3 isoform a

    See identical proteins and their annotated locations for NP_002489.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the splice pattern of variant 4 but with the extra 'A' found in the GRCh38 haplotype.
    Source sequence(s)
    AL139082, BC019916
    Consensus CDS
    CCDS73576.1
    UniProtKB/Swiss-Prot
    A8K2J4, P51956, Q5TAP2, Q8J023, Q8WUN5
    UniProtKB/TrEMBL
    Q5JPB0
    Related
    ENSP00000480328.1, ENST00000610828.5
    Conserved Domains (1) summary
    cd08219
    Location:3257
    STKc_Nek3; Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 3
  14. NM_152720.3NP_689933.1  serine/threonine-protein kinase Nek3 isoform a

    See identical proteins and their annotated locations for NP_689933.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the splice pattern of variant 6 but with the extra 'A' found in the GRCh38 haplotype.
    Source sequence(s)
    AI209040, AK131359, AK290259, AL139082, H15146
    Consensus CDS
    CCDS73576.1
    UniProtKB/Swiss-Prot
    A8K2J4, P51956, Q5TAP2, Q8J023, Q8WUN5
    UniProtKB/TrEMBL
    Q5JPB0
    Related
    ENSP00000484443.1, ENST00000618534.4
    Conserved Domains (1) summary
    cd08219
    Location:3257
    STKc_Nek3; Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 3

RNA

  1. NR_027415.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) represents the splice pattern of variant 1 but without the extra 'A' found in the GRCh38 haplotype. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    CP068265
  2. NR_164641.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) represents the splice pattern of variant 3 but with the extra 'A' found in the GRCh38 haplotype. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL139082, KF459684
  3. NR_172104.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) represents the splice pattern of variant 2 but without the extra 'A' found in the GRCh38 haplotype. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL139082, KF459684
  4. NR_188248.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (19) represents the splice pattern of variant 7 but without the extra 'A' found in the GRCh38 haplotype. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    CP068265

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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    52132647..52159860 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    51347480..51374691 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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