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

Summary

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: mouse all
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Genomic context

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_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH102445 (e-PCR)
- UniSTS:96779

RH94251 (e-PCR)
- UniSTS:92443

RH92410 (e-PCR)
- UniSTS:83628

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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)

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
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]