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

Gene ID: 51388, updated on 3-Nov-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, Nov 2024]
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_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (69339772..69343106)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (75141466..75144800)
RS_2024_09 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 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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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)

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_2024_08

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

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Chemical Information
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