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CENPN centromere protein N [ Homo sapiens (human) ]

Gene ID: 55839, updated on 3-Apr-2024

Summary

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Official Symbol
CENPNprovided by HGNC
Official Full Name
centromere protein Nprovided by HGNC
Primary source
HGNC:HGNC:30873
See related
Ensembl:ENSG00000166451 MIM:611509; AllianceGenome:HGNC:30873
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
BM039; CENP-N; ICEN32; C16orf60
Summary
The protein encoded by this gene forms part of the nucleosome-associated complex and is important for kinetochore assembly. It is bound to kinetochores during S phase and G2 and recruits other proteins to the centromere. Pseudogenes of this gene are located on chromosome 2. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Jul 2012]
Expression
Ubiquitous expression in prostate (RPKM 4.4), bone marrow (RPKM 3.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
16q23.2
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (81007214..81033107)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (87068448..87094631)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (81040819..81066712)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene androgen receptor regulated long noncoding RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11172 Neighboring gene Sharpr-MPRA regulatory region 7727 Neighboring gene C-X9-C motif containing 2 Neighboring gene NANOG hESC enhancer GRCh37_chr16:81032399-81032965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7748 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11175 Neighboring gene CENPN antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7750 Neighboring gene ATM interactor Neighboring gene chromosome 16 open reading frame 46 Neighboring gene uncharacterized LOC105371361

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. CENP-N promotes the compaction of centromeric chromatin. Zhou K, et al. Nat Struct Mol Biol, 2022 Apr. PMID 35422519, Free PMC Article
  2. Centromere protein N promotes lung adenocarcinoma progression by activating PI3K/AKT signaling pathway. Zheng Y, et al. Genes Genomics, 2022 Sep. PMID 35150399
  3. Structural mechanisms of centromeric nucleosome recognition by the kinetochore protein CENP-N. Chittori S, et al. Science, 2018 Jan 19. PMID 29269420, Free PMC Article
  4. Dynamics of CENP-N kinetochore binding during the cell cycle. Hellwig D, et al. J Cell Sci, 2011 Nov 15. PMID 22100916, Free PMC Article
  5. The CENP-L-N Complex Forms a Critical Node in an Integrated Meshwork of Interactions at the Centromere-Kinetochore Interface. McKinley KL, et al. Mol Cell, 2015 Dec 17. PMID 26698661, Free PMC Article

See all (31) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Dynamic phosphorylation of CENP-N by CDK1 guides accurate chromosome segregation in mitosis.
    Title: Dynamic phosphorylation of CENP-N by CDK1 guides accurate chromosome segregation in mitosis.
  2. Clinical implications and immune features of CENPN in breast cancer.
    Title: Clinical implications and immune features of CENPN in breast cancer.
  3. Knockdown of CENPN Inhibits Glucose Metabolism and Induces G1 Arrest in Esophageal Cancer Cells by Regulating PI3K/AKT Signaling Pathway.
    Title: Knockdown of CENPN Inhibits Glucose Metabolism and Induces G1 Arrest in Esophageal Cancer Cells by Regulating PI3K/AKT Signaling Pathway.
  4. Centromere protein N promotes lung adenocarcinoma progression by activating PI3K/AKT signaling pathway.
    Title: Centromere protein N promotes lung adenocarcinoma progression by activating PI3K/AKT signaling pathway.
  5. CENP-N promotes the compaction of centromeric chromatin.
    Title: CENP-N promotes the compaction of centromeric chromatin.
  6. The Elusive Structure of Centro-Chromatin: Molecular Order or Dynamic Heterogenetity?
    Title: The Elusive Structure of Centro-Chromatin: Molecular Order or Dynamic Heterogenetity?
  7. CENP-N stabilizes CENP-A nucleosomes alone and additively with CENP-C in vitro. However, removal of CENP-C and CENP-N from cells, or mutating CENP-A so that it no longer interacts with CENP-C or CENP-N, had no effect on centromeric CENP-A stability in vivo. Thus, the stability of CENP-A nucleosomes in chromatin does not arise solely from its interactions with CENP-C or CENP-N.
    Title: Constitutive centromere-associated network contacts confer differential stability on CENP-A nucleosomes in vitro and in the cell.
  8. Collectively, these studies clarify how CENP-N and CENP-C decode and stabilize the non-canonical CENP-A nucleosome to enforce epigenetic centromere specification and kinetochore assembly.
    Title: Decoding the centromeric nucleosome through CENP-N.
  9. this study reports cryo-electron microscopy (cryo-EM), biophysical, biochemical, and cell biological studies of the interaction between the CENP-A nucleosome and CENP-N.
    Title: Structural mechanisms of centromeric nucleosome recognition by the kinetochore protein CENP-N.
  10. Study demonstrate that the CENP-L-N complex plays a crucial role at the core of the 16-subunit Constitutive Centromere-Associated Network through interactions with CENP-C and CENP-H-I-KM.
    Title: The CENP-L-N Complex Forms a Critical Node in an Integrated Meshwork of Interactions at the Centromere-Kinetochore Interface.
Submit: New GeneRIF Correction See all GeneRIFs (12)

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

  • FLJ13607, FLJ22660

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in CENP-A containing chromatin assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in chromosome segregation NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  
part_of inner kinetochore IPI
Inferred from Physical Interaction
more info
 PubMed 
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
centromere protein N
Names
interphase centromere complex protein 32

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_001100624.3 → NP_001094094.2  centromere protein N isoform 2

    See identical proteins and their annotated locations for NP_001094094.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate 3' terminal exon compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC092718, AK023669, BC039021, HY167728
    Consensus CDS
    CCDS42200.1
    UniProtKB/Swiss-Prot
    A8MZE6, B3KN53, B4DJD1, B4DPY7, C9JJM5, D3DUK8, E7ES30, E7ETS3, Q96H22, Q9NZ83
    Related
    ENSP00000305608.5, ENST00000305850.10
    Conserved Domains (1) summary
    pfam05238
    Location:3 → 339
    CENP-N; Kinetochore protein CHL4 like

  2. NM_001100625.3 → NP_001094095.2  centromere protein N isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK023669, AK026313, HY374758
    Consensus CDS
    CCDS42199.1
    UniProtKB/Swiss-Prot
    Q96H22
    Related
    ENSP00000377007.3, ENST00000393335.7
    Conserved Domains (1) summary
    pfam05238
    Location:3 → 315
    CENP-N; Kinetochore protein CHL4 like

  3. NM_001270473.2 → NP_001257402.1  centromere protein N isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an exon in the coding region and uses an alternate 3' terminal exon compared to variant 1. The resulting protein (isoform 4) is shorter than isoform 1.
    Source sequence(s)
    AC092718, AK023669, AK296024, BC039021
    Consensus CDS
    CCDS58483.1
    UniProtKB/Swiss-Prot
    Q96H22
    Related
    ENSP00000395235.3, ENST00000439957.7
    Conserved Domains (1) summary
    pfam05238
    Location:3 → 319
    CENP-N; Kinetochore protein CHL4 like

  4. NM_001270474.2 → NP_001257403.1  centromere protein N isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an exon in the coding region and uses an alternate 3' terminal exon compared to variant 1. The resulting protein (isoform 5) is shorter than isoform 1.
    Source sequence(s)
    AC092718, AK023669, AK298554, BC039021, HY363272
    Consensus CDS
    CCDS58482.1
    UniProtKB/Swiss-Prot
    Q96H22
    Related
    ENSP00000393991.2, ENST00000428963.6
    Conserved Domains (1) summary
    pfam05238
    Location:3 → 305
    CENP-N; Kinetochore protein CHL4 like

  5. NM_018455.6 → NP_060925.2  centromere protein N isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks several exons in the 3' coding region and uses an alternate 3' terminal exon, compared to variant 1. The resulting protein (isoform 3) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC007334, BQ013821, HY167728
    Consensus CDS
    CCDS10931.1
    UniProtKB/TrEMBL
    H3BMC7
    Related
    ENSP00000299572.5, ENST00000299572.9
    Conserved Domains (1) summary
    pfam05238
    Location:3 → 165
    CENP-N; Kinetochore protein CHL4 like

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    81007214..81033107
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006721236.5 → XP_006721299.1  centromere protein N isoform X1

    See identical proteins and their annotated locations for XP_006721299.1

    UniProtKB/Swiss-Prot
    A8MZE6, B3KN53, B4DJD1, B4DPY7, C9JJM5, D3DUK8, E7ES30, E7ETS3, Q96H22, Q9NZ83
    Conserved Domains (1) summary
    pfam05238
    Location:3 → 339
    CENP-N; Kinetochore protein CHL4 like

  2. XM_047434366.1 → XP_047290322.1  centromere protein N isoform X2

  3. XM_017023456.3 → XP_016878945.1  centromere protein N isoform X3

    UniProtKB/TrEMBL
    H3BMC7
    Related
    ENSP00000454327.1, ENST00000564669.5
    Conserved Domains (1) summary
    pfam05238
    Location:3 → 165
    CENP-N; Kinetochore protein CHL4 like

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791800.1 Reference GRCh38.p14 PATCHES

    Range
    55152..81346
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333194.1 → XP_054189169.1  centromere protein N isoform X1

    UniProtKB/Swiss-Prot
    A8MZE6, B3KN53, B4DJD1, B4DPY7, C9JJM5, D3DUK8, E7ES30, E7ETS3, Q96H22, Q9NZ83

  2. XM_054333196.1 → XP_054189171.1  centromere protein N isoform X3

  3. XM_054333195.1 → XP_054189170.1  centromere protein N isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    87068448..87094631
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054313490.1 → XP_054169465.1  centromere protein N isoform X1

  2. XM_054313492.1 → XP_054169467.1  centromere protein N isoform X3

  3. XM_054313491.1 → XP_054169466.1  centromere protein N isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96H22.2 GenPept UniProtKB/Swiss-Prot:Q96H22

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