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Aliases for NIP7 Gene

Aliases for NIP7 Gene

  • NIP7, Nucleolar Pre-RRNA Processing Protein 2 3 5
  • KD93 3 4
  • 60S Ribosome Subunit Biogenesis Protein NIP7 Homolog 3
  • Nuclear Import 7 Homolog (S. Cerevisiae) 2
  • Nuclear Import 7 Homolog 3
  • HSPC031 3
  • CGI-37 3

External Ids for NIP7 Gene

Previous GeneCards Identifiers for NIP7 Gene

  • GC16P067932
  • GC16P055252

Summaries for NIP7 Gene

GeneCards Summary for NIP7 Gene

NIP7 (NIP7, Nucleolar Pre-RRNA Processing Protein) is a Protein Coding gene. Diseases associated with NIP7 include Shwachman-Diamond Syndrome 1. Gene Ontology (GO) annotations related to this gene include RNA binding.

UniProtKB/Swiss-Prot for NIP7 Gene

  • Required for proper 34S pre-rRNA processing and 60S ribosome subunit assembly.

Gene Wiki entry for NIP7 Gene

Additional gene information for NIP7 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NIP7 Gene

Genomics for NIP7 Gene

GeneHancer (GH) Regulatory Elements for NIP7 Gene

Promoters and enhancers for NIP7 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J069338 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 672.3 +0.4 359 3.2 DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF416 ZNF143 SP3 SSRP1 ZNF610 NIP7 COG8 ENSG00000272617 PIR44456 LOC400541 CHTF8 SNTB2 PDPR PDXDC2P-NPIPB14P NONOP1
GH16J069721 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 21.3 +385.8 385822 7.2 CLOCK MLX DMAP1 SLC30A9 ZNF143 SP3 NFYC SSRP1 GLIS1 RCOR2 NQO1 ENSG00000262136 SF3B3 SNTB2 NONOP1 CHTF8 NFAT5 DDX19B PDPR NPIPB14P
GH16J069070 Enhancer 1.3 Ensembl ENCODE dbSUPER 21.1 -266.7 -266725 3.6 SIN3A ETS1 GTF3C2 GLIS2 FOS MCM3 REST NFIL3 ZSCAN16 GLIS1 PRMT7 NFAT5 NONOP1 CHTF8 SNTB2 PDXDC2P-NPIPB14P ZFP90 COG8 NIP7 ENSG00000259797
GH16J069328 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 12.8 -9.5 -9470 3.3 HDGF PKNOX1 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 PDF PIR46379 PDPR SNTB2 UTP4 LOC400541 DDX19B NIP7 TMED6 PIR53878
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NIP7 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NIP7 gene promoter:
  • p53
  • CUTL1
  • HEN1
  • AML1a
  • NF-AT
  • CP1A
  • CBF-B
  • CBF-A
  • CBF(2)

Genomic Locations for NIP7 Gene

Genomic Locations for NIP7 Gene
3,682 bases
Plus strand
3,682 bases
Plus strand

Genomic View for NIP7 Gene

Genes around NIP7 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NIP7 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NIP7 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NIP7 Gene

Proteins for NIP7 Gene

  • Protein details for NIP7 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    60S ribosome subunit biogenesis protein NIP7 homolog
    Protein Accession:
    Secondary Accessions:
    • B2RD04
    • Q9NZZ0

    Protein attributes for NIP7 Gene

    180 amino acids
    Molecular mass:
    20463 Da
    Quaternary structure:
    • Monomer. Interacts with pre-ribosome complex. May bind to RNA (By similarity). Interacts with NOL8. May interact with SBDS. Interacts with FTSJ3.

    Three dimensional structures from OCA and Proteopedia for NIP7 Gene

    Alternative splice isoforms for NIP7 Gene


neXtProt entry for NIP7 Gene

Post-translational modifications for NIP7 Gene

  • Ubiquitination at isoforms=2155, isoforms=115, isoforms=94, and isoforms=250
  • Modification sites at PhosphoSitePlus

Other Protein References for NIP7 Gene

No data available for DME Specific Peptides for NIP7 Gene

Domains & Families for NIP7 Gene

Gene Families for NIP7 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for NIP7 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the NIP7 family.
  • Belongs to the NIP7 family.
genes like me logo Genes that share domains with NIP7: view

Function for NIP7 Gene

Molecular function for NIP7 Gene

UniProtKB/Swiss-Prot Function:
Required for proper 34S pre-rRNA processing and 60S ribosome subunit assembly.

Phenotypes From GWAS Catalog for NIP7 Gene

Gene Ontology (GO) - Molecular Function for NIP7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI 14660641
genes like me logo Genes that share ontologies with NIP7: view
genes like me logo Genes that share phenotypes with NIP7: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NIP7 Gene

Localization for NIP7 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NIP7 Gene

Nucleus, nucleolus.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NIP7 gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NIP7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005730 nucleolus IBA,IDA --
GO:0005829 cytosol IDA --
GO:0030687 preribosome, large subunit precursor IBA --
genes like me logo Genes that share ontologies with NIP7: view

Pathways & Interactions for NIP7 Gene

No Data Available

Gene Ontology (GO) - Biological Process for NIP7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042254 ribosome biogenesis IEA --
GO:0042255 ribosome assembly IEA --
GO:0042273 ribosomal large subunit biogenesis IBA --
genes like me logo Genes that share ontologies with NIP7: view

No data available for Pathways by source and SIGNOR curated interactions for NIP7 Gene

Drugs & Compounds for NIP7 Gene

(1) Drugs for NIP7 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Radezolid Investigational Pharma Target 2
genes like me logo Genes that share compounds with NIP7: view

Transcripts for NIP7 Gene

mRNA/cDNA for NIP7 Gene

Unigene Clusters for NIP7 Gene

NIP7, nucleolar pre-rRNA processing protein:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NIP7 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c
SP1: - -
SP2: - - - -
SP3: -
SP4: -
SP5: - - -
SP6: - - -

Relevant External Links for NIP7 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NIP7 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NIP7 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for NIP7 Gene

This gene is overexpressed in Monocytes (21.1), Lung (9.1), Pancreas (7.5), and CD8 Tcells (7.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NIP7 Gene

Protein tissue co-expression partners for NIP7 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NIP7 Gene:


SOURCE GeneReport for Unigene cluster for NIP7 Gene:


mRNA Expression by UniProt/SwissProt for NIP7 Gene:

Tissue specificity: Expressed in hematopoietic stem/progenitor cells.

Evidence on tissue expression from TISSUES for NIP7 Gene

  • Skin(4.2)
  • Blood(4.1)
genes like me logo Genes that share expression patterns with NIP7: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NIP7 Gene

Orthologs for NIP7 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for NIP7 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NIP7 34 33
  • 100 (n)
(Canis familiaris)
Mammalia NIP7 34 33
  • 91.48 (n)
(Bos Taurus)
Mammalia NIP7 34 33
  • 90.74 (n)
(Ornithorhynchus anatinus)
Mammalia NIP7 34
  • 90 (a)
(Rattus norvegicus)
Mammalia Nip7 33
  • 88.15 (n)
(Monodelphis domestica)
Mammalia NIP7 34
  • 88 (a)
(Mus musculus)
Mammalia Nip7 16 34 33
  • 87.04 (n)
(Gallus gallus)
Aves NIP7 34 33
  • 77.96 (n)
(Anolis carolinensis)
Reptilia NIP7 34
  • 84 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nip7 33
  • 77.41 (n)
Str.10336 33
(Danio rerio)
Actinopterygii nip7 34 33
  • 73.52 (n)
Dr.16108 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6718 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002330 33
  • 64.43 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG7006 34 33
  • 63.5 (n)
(Caenorhabditis elegans)
Secernentea C43E11.9 34 33
  • 59.22 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFL104W 33
  • 60.15 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B02266g 33
  • 59.22 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NIP7 36 34 33
  • 56.98 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G15770 33
  • 61.64 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.383 33
(Oryza sativa)
Liliopsida Os07g0670600 33
  • 55.87 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5575 34
  • 74 (a)
Cin.6681 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPCC320.11c 33
  • 64.06 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU00105 33
  • 53.45 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6681 33
Species where no ortholog for NIP7 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NIP7 Gene

Gene Tree for NIP7 (if available)
Gene Tree for NIP7 (if available)
Evolutionary constrained regions (ECRs) for NIP7: view image

Paralogs for NIP7 Gene Pseudogenes for NIP7 Gene

genes like me logo Genes that share paralogs with NIP7: view

No data available for Paralogs for NIP7 Gene

Variants for NIP7 Gene

Sequence variations from dbSNP and Humsavar for NIP7 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs11542583 benign, likely-benign, not specified, Congenital disorder of glycosylation 69,339,511(+) T/A/C/G upstream_transcript_variant
rs144030835 uncertain-significance, Congenital disorder of glycosylation 69,339,304(+) G/A/C upstream_transcript_variant
rs756986120 likely-benign, Congenital disorder of glycosylation type 2H 69,339,541(+) C/A/T 5_prime_UTR_variant
VAR_036488 A breast cancer sample p.Glu171Gln
rs1057521994 likely-benign, not specified 69,339,402(+) G/A/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for NIP7 Gene

Variant ID Type Subtype PubMed ID
nsv827715 CNV loss 20364138

Variation tolerance for NIP7 Gene

Residual Variation Intolerance Score: 34.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.58; 12.58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NIP7 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NIP7 Gene

Disorders for NIP7 Gene

MalaCards: The human disease database

(1) MalaCards diseases for NIP7 Gene - From: DISEASES

Disorder Aliases PubMed IDs
shwachman-diamond syndrome 1
  • sds1
- elite association - COSMIC cancer census association via MalaCards
Search NIP7 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NIP7

genes like me logo Genes that share disorders with NIP7: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NIP7 Gene

Publications for NIP7 Gene

  1. The human nucleolar protein FTSJ3 associates with NIP7 and functions in pre-rRNA processing. (PMID: 22195017) Morello LG … Zanchin NI (PloS one 2011) 2 3 4 58
  2. Crystal structure of KD93, a novel protein expressed in human hematopoietic stem/progenitor cells. (PMID: 15522784) Liu JF … Liang DC (Journal of structural biology 2004) 3 4 22 58
  3. A novel human nucleolar protein, Nop132, binds to the G proteins, RRAG A/C/D. (PMID: 14660641) Sekiguchi T … Nishimoto T (The Journal of biological chemistry 2004) 2 3 4 58
  4. The NIP7 protein is required for accurate pre-rRNA processing in human cells. (PMID: 20798176) Morello LG … Zanchin NI (Nucleic acids research 2011) 2 3 58
  5. The Shwachman-Bodian-Diamond syndrome associated protein interacts with HsNip7 and its down-regulation affects gene expression at the transcriptional and translational levels. (PMID: 17643419) Hesling C … Zanchin NI (Experimental cell research 2007) 3 4 58

Products for NIP7 Gene

Sources for NIP7 Gene

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