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    NIP7 nucleolar pre-rRNA processing protein NIP7 [ Homo sapiens (human) ]

    Gene ID: 51388, updated on 5-Mar-2024

    Summary

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    Official Symbol
    NIP7provided by HGNC
    Official Full Name
    nucleolar pre-rRNA processing protein NIP7provided by HGNC
    Primary source
    HGNC:HGNC:24328
    See related
    Ensembl:ENSG00000132603 MIM:619204; AllianceGenome:HGNC:24328
    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
    KD93; CGI-37; HSPC031
    Summary
    Enables RNA binding activity. Predicted to be involved in ribosomal large subunit biogenesis. Located in cytosol; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in lymph node (RPKM 9.5), appendix (RPKM 8.7) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See NIP7 in Genome Data Viewer
    Location:
    16q22.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (69339772..69343106)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (75141466..75144800)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (69373675..69377009)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene syntrophin beta 2 Neighboring gene zinc finger CCHC-type and RNA binding motif containing 1 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:69344125-69345075 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:69345076-69346025 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:69349279-69350478 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:69363857-69364504 Neighboring gene vacuolar protein sorting 4 homolog A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7657 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:69365153-69365800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11036 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11037 Neighboring gene component of oligomeric golgi complex 8 Neighboring gene peptide deformylase, mitochondrial Neighboring gene MPRA-validated peak2627 silencer Neighboring gene transmembrane p24 trafficking protein 6 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:69405429-69405928 Neighboring gene telomeric repeat binding factor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7660

    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. The NIP7 protein is required for accurate pre-rRNA processing in human cells. Morello LG, et al. Nucleic Acids Res, 2011 Jan. PMID 20798176, Free PMC Article
    2. Crystal structure of KD93, a novel protein expressed in human hematopoietic stem/progenitor cells. Liu JF, et al. J Struct Biol, 2004 Dec. PMID 15522784
    3. The human nucleolar protein FTSJ3 associates with NIP7 and functions in pre-rRNA processing. Morello LG, et al. PLoS One, 2011. PMID 22195017, Free PMC Article
    4. Comprehensive Bioinformatic Analysis Genes Associated to the Prognosis of Liposarcoma. Liu J, et al. Med Sci Monit, 2018 Oct 14. PMID 30317246, Free PMC Article
    5. The Shwachman-Bodian-Diamond syndrome associated protein interacts with HsNip7 and its down-regulation affects gene expression at the transcriptional and translational levels. Hesling C, et al. Exp Cell Res, 2007 Dec 10. PMID 17643419

    See all (73) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Cox regression model revealed that only NIP7, RPL10L, and MCM2 exhibited significant correlation with distant recurrence-free survival in liposarcoma in the GSE30929 dataset, and the regression coefficients were -0.676, -0.703, and 0.868, respectively
      Title: Comprehensive Bioinformatic Analysis Genes Associated to the Prognosis of Liposarcoma.
    2. The results presented in this work indicate a close functional interaction between NIP7 and FTSJ3 during pre-rRNA processing and show that FTSJ3 participates in ribosome synthesis in human cells.
      Title: The human nucleolar protein FTSJ3 associates with NIP7 and functions in pre-rRNA processing.
    3. Downregulation of NIP7 affects pre-rRNA processing, causing an imbalance of the 40S/60S subunit ratio.
      Title: The NIP7 protein is required for accurate pre-rRNA processing in human cells.
    4. SBDS is found in complexes containing the human Nip7 ortholog.
      Title: The Shwachman-Bodian-Diamond syndrome associated protein interacts with HsNip7 and its down-regulation affects gene expression at the transcriptional and translational levels.
    5. KD93 is a novel protein expressed in human hematopoietic stem/progenitor cells
      Title: Crystal structure of KD93, a novel protein expressed in human hematopoietic stem/progenitor cells.
    Submit: New GeneRIF Correction

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Expression of HIV-1 Tat upregulates the abundance of nuclear import 7 homolog (NIP7) in the nucleoli of Jurkat T-cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ10296

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in ribosomal large subunit biogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ribosome assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleolus 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
    		  
    part_of preribosome, large subunit precursor IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    60S ribosome subunit biogenesis protein NIP7 homolog
    Names
    NIP7, nucleolar pre-rRNA processing protein
    nuclear import 7 homolog

    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_001199434.2 → NP_001186363.1  60S ribosome subunit biogenesis protein NIP7 homolog isoform 2

      See identical proteins and their annotated locations for NP_001186363.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AF161528, AW001672, BC015941, DB453898, DR423435
      Consensus CDS
      CCDS56003.1
      UniProtKB/TrEMBL
      B3KM49
      Related
      ENSP00000254941.6, ENST00000254941.6
      Conserved Domains (1) summary
      cl00607
      Location:1 → 129
      PUA; PUA domain

    2. NM_016101.5 → NP_057185.1  60S ribosome subunit biogenesis protein NIP7 homolog isoform 1

      See identical proteins and their annotated locations for NP_057185.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AW001672, BC015941, DB453898, DR423435
      Consensus CDS
      CCDS10877.1
      UniProtKB/Swiss-Prot
      B2RD04, Q9NZZ0, Q9Y221
      Related
      ENSP00000254940.5, ENST00000254940.10
      Conserved Domains (1) summary
      COG1374
      Location:1 → 176
      NIP7; Rbosome biogenesis protein Nip4, contains PUA domain [Translation, ribosomal structure and biogenesis]

    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
      69339772..69343106
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      75141466..75144800
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y221.1 GenPept UniProtKB/Swiss-Prot:Q9Y221

    Gene LinkOut

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

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