The protein encoded by this gene, along with IMP3 and MPP10, is part of the 60-80S U3 small nucleolar ribonucleoprotein (U3 snoRNP) complex. This complex is necessary for the early cleavage steps of pre-18S ribosomal RNA processing. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016] See more...

Aliases for IMP4 Gene

Aliases for IMP4 Gene

  • IMP U3 Small Nucleolar Ribonucleoprotein 4 2 3 5
  • BXDC4 2 3 4
  • U3 Small Nucleolar Ribonucleoprotein Protein IMP4 3 4
  • Brix Domain-Containing Protein 4 3 4
  • U3 SnoRNP Protein IMP4 3 4
  • IMP4, U3 Small Nucleolar Ribonucleoprotein, Homolog (Yeast) 2
  • IMP4, U3 Small Nucleolar Ribonucleoprotein, Homolog 3
  • IMP4 Homolog, U3 Small Nucleolar Ribonucleoprotein 3
  • U3 SnoRNP Protein 4 Homolog 3
  • MGC19606 2
  • IMP4 5

External Ids for IMP4 Gene

Previous GeneCards Identifiers for IMP4 Gene

  • GC02P131004
  • GC02P131193
  • GC02P130816
  • GC02P131099
  • GC02P123390

Summaries for IMP4 Gene

Entrez Gene Summary for IMP4 Gene

  • The protein encoded by this gene, along with IMP3 and MPP10, is part of the 60-80S U3 small nucleolar ribonucleoprotein (U3 snoRNP) complex. This complex is necessary for the early cleavage steps of pre-18S ribosomal RNA processing. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

GeneCards Summary for IMP4 Gene

IMP4 (IMP U3 Small Nucleolar Ribonucleoprotein 4) is a Protein Coding gene. Among its related pathways are rRNA processing in the nucleus and cytosol and Ribosome biogenesis in eukaryotes. Gene Ontology (GO) annotations related to this gene include snoRNA binding and rRNA primary transcript binding. An important paralog of this gene is RPF1.

UniProtKB/Swiss-Prot Summary for IMP4 Gene

  • Component of the 60-80S U3 small nucleolar ribonucleoprotein (U3 snoRNP). Required for the early cleavages during pre-18S ribosomal RNA processing.

Gene Wiki entry for IMP4 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for IMP4 Gene

Genomics for IMP4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for IMP4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J130341 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.3 258 4.2 BCLAF1 SP1 ZNF207 MYC ZNF600 IKZF1 SIX5 ZNF580 KLF9 POLR2A CCDC115 HSALNG0018800 IMP4 lnc-PTPN18-2 lnc-POTEI-3 piR-37496 SMPD4 PTPN18
GH02J130327 Enhancer 0.5 ENCODE 5.1 -13.6 -13610 1.8 GABPB1 FOSL2 NRF1 CBX2 BHLHE40 ELF1 CTCF ENSG00000224352 PTPN18 KLF2P1 IMP4 TUBA3E TEKT4P3 lnc-CCDC115-1
GH02J131016 Enhancer 0.6 ENCODE 4.2 +675.4 675403 2.3 CEBPB ZNF189 HNF4A NFIB GLIS1 ZNF398 EGR2 ZFHX2 PRDM1 SP1 MZT2A IMP4 piR-34990 piR-34822-182 SMIM39 ARHGEF4
GH02J130315 Enhancer 0.2 Ensembl 6.7 -26.3 -26341 1 lnc-CCDC115-1 TEKT4P3 TUBA3E IMP4 PTPN18 ENSG00000224352
GH02J130336 Promoter/Enhancer 1.5 ENCODE CraniofacialAtlas 0.7 -3.9 -3875 3.4 BCLAF1 ZNF207 IKZF1 ZNF600 SSRP1 JUND ZNF580 ZNF592 CEBPA ATF3 TRE-TTC1-1 SMPD4 PTPN18 RAB6C-AS1 CCDC115 IMP4 lnc-POTEI-3 TUBA3E
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around IMP4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for IMP4

Top Transcription factor binding sites by QIAGEN in the IMP4 gene promoter:
  • ATF6
  • CREB
  • deltaCREB
  • MIF-1
  • MyoD
  • Pax-4a
  • PPAR-alpha
  • SRF
  • SRF (504 AA)
  • YY1

Genomic Locations for IMP4 Gene

Latest Assembly
chr2:130,342,242-130,347,967
(GRCh38/hg38)
Size:
5,726 bases
Orientation:
Plus strand

Previous Assembly
chr2:131,100,470-131,105,540
(GRCh37/hg19 by Entrez Gene)
Size:
5,071 bases
Orientation:
Plus strand

chr2:131,099,798-131,105,383
(GRCh37/hg19 by Ensembl)
Size:
5,586 bases
Orientation:
Plus strand

Genomic View for IMP4 Gene

Genes around IMP4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
IMP4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for IMP4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for IMP4 Gene

Proteins for IMP4 Gene

  • Protein details for IMP4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96G21-IMP4_HUMAN
    Recommended name:
    U3 small nucleolar ribonucleoprotein protein IMP4
    Protein Accession:
    Q96G21
    Secondary Accessions:
    • Q3ZTT3

    Protein attributes for IMP4 Gene

    Size:
    291 amino acids
    Molecular mass:
    33757 Da
    Quaternary structure:
    • Component of a heterotrimeric complex containing IMP3, IMP4 and MPHOSPH10. Interacts with MPHOSPH10.

neXtProt entry for IMP4 Gene

Post-translational modifications for IMP4 Gene

  • Ubiquitination at Lys183
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for IMP4 Gene

Domains & Families for IMP4 Gene

Gene Families for IMP4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for IMP4 Gene

InterPro:
Blocks:
  • Brix domain

Suggested Antigen Peptide Sequences for IMP4 Gene

GenScript: Design optimal peptide antigens:
  • Brix domain-containing protein 4 (IMP4_HUMAN)
  • cDNA, FLJ93237, Homo sapiens U3 snoRNP protein 4 homolog (IMP4), mRNA (Q3ZTT3_HUMAN)
genes like me logo Genes that share domains with IMP4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for IMP4 Gene

Function for IMP4 Gene

Molecular function for IMP4 Gene

UniProtKB/Swiss-Prot Function:
Component of the 60-80S U3 small nucleolar ribonucleoprotein (U3 snoRNP). Required for the early cleavages during pre-18S ribosomal RNA processing.

Phenotypes From GWAS Catalog for IMP4 Gene

Gene Ontology (GO) - Molecular Function for IMP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12655004
GO:0030515 snoRNA binding IBA 21873635
genes like me logo Genes that share ontologies with IMP4: view
genes like me logo Genes that share phenotypes with IMP4: view

miRNA for IMP4 Gene

miRTarBase miRNAs that target IMP4

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for IMP4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for IMP4 Gene

Localization for IMP4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for IMP4 Gene

Nucleus, nucleolus.

Subcellular locations from

COMPARTMENTS
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 IMP4 gene
Compartment Confidence
nucleus 5
mitochondrion 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for IMP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IEA,IDA 12655004
GO:0030684 preribosome IDA 12655004
genes like me logo Genes that share ontologies with IMP4: view

Pathways & Interactions for IMP4 Gene

genes like me logo Genes that share pathways with IMP4: view

SIGNOR curated interactions for IMP4 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for IMP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006364 rRNA processing NAS,TAS --
GO:0042254 ribosome biogenesis IEA --
genes like me logo Genes that share ontologies with IMP4: view

Drugs & Compounds for IMP4 Gene

No Compound Related Data Available

Transcripts for IMP4 Gene

mRNA/cDNA for IMP4 Gene

16 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
17 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for IMP4

Alternative Splicing Database (ASD) splice patterns (SP) for IMP4 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b · 8c ^ 9a · 9b ^ 10a · 10b
SP1: - - - - - -
SP2: - - - - - - -
SP3: - - - -
SP4: - - - - -
SP5: - - - -
SP6: - - - - - - -
SP7: - - - -
SP8: - - - - -
SP9: - - -
SP10:
SP11:
SP12:

Relevant External Links for IMP4 Gene

GeneLoc Exon Structure for
IMP4

Expression for IMP4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for IMP4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Tonsil (Hematopoietic System)

Protein differential expression in normal tissues from HIPED for IMP4 Gene

This gene is overexpressed in Plasma (26.6), Cervix (21.6), and Lung (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for IMP4 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for IMP4

SOURCE GeneReport for Unigene cluster for IMP4 Gene:

Hs.91579

Evidence on tissue expression from TISSUES for IMP4 Gene

  • Nervous system(4.9)
genes like me logo Genes that share expression patterns with IMP4: view

Primer products for research

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for IMP4 Gene

Orthologs for IMP4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for IMP4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia IMP4 29 30
  • 98.74 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia IMP4 29 30
  • 87.74 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia IMP4 29 30
  • 87.64 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Imp4 29 16 30
  • 87.62 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Imp4 29
  • 86.31 (n)
Oppossum
(Monodelphis domestica)
Mammalia IMP4 30
  • 86 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia IMP4 30
  • 80 (a)
OneToOne
Chicken
(Gallus gallus)
Aves IMP4 29 30
  • 63.9 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia IMP4 30
  • 85 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia imp4 29
  • 74.17 (n)
Str.1165 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.6114 29
Zebrafish
(Danio rerio)
Actinopterygii imp4 29 30
  • 67.38 (n)
OneToOne
Dr.19345 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2996 29
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003890 29
  • 58.9 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG11920 29 30
  • 56.2 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea ZK795.3 30
  • 59 (a)
OneToOne
CELE_ZK795.3 29
  • 56 (n)
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AER430W 29
  • 55.43 (n)
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E07833g 29
  • 49.51 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes IMP4 29 30 32
  • 49.15 (n)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons IMP4 29
  • 53.38 (n)
Rice
(Oryza sativa)
Liliopsida Os08g0155000 29
  • 56.7 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.6162 30
  • 63 (a)
OneToOne
Bread mold
(Neurospora crassa)
Ascomycetes NCU04243 29
  • 51.59 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC19A8.07c 29
  • 50.69 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.8068 29
Species where no ortholog for IMP4 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • 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 IMP4 Gene

ENSEMBL:
Gene Tree for IMP4 (if available)
TreeFam:
Gene Tree for IMP4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for IMP4: view image
Alliance of Genome Resources:
Additional Orthologs for IMP4

Paralogs for IMP4 Gene

Paralogs for IMP4 Gene

(1) SIMAP similar genes for IMP4 Gene using alignment to 6 proteins:

  • IMP4_HUMAN
  • B8ZZ47_HUMAN
  • B9A008_HUMAN
  • E7ENR5_HUMAN
  • F8WCN0_HUMAN
  • H0Y714_HUMAN
genes like me logo Genes that share paralogs with IMP4: view

Variants for IMP4 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for IMP4 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for IMP4 Gene

Variant ID Type Subtype PubMed ID
dgv2032n106 OTHER inversion 24896259
dgv4073n100 CNV gain 25217958
dgv475n27 CNV gain 19166990
dgv7079n54 CNV loss 21841781
dgv7080n54 CNV gain 21841781
dgv7083n54 CNV loss 21841781
esv2751826 CNV gain 17911159
esv2759092 CNV gain+loss 17122850
esv2760631 CNV gain+loss 21179565
esv2763387 CNV loss 21179565
esv3584065 CNV loss 25503493
esv3592450 CNV loss 21293372
esv3592451 CNV gain 21293372
esv3893326 CNV gain 25118596
nsv1001073 CNV gain 25217958
nsv1005664 CNV loss 25217958
nsv1147463 OTHER inversion 26484159
nsv428403 CNV loss 18775914
nsv459274 CNV loss 19166990
nsv459341 CNV loss 19166990
nsv470485 CNV gain 18288195
nsv520559 CNV gain+loss 19592680
nsv583046 CNV loss 21841781
nsv583113 CNV gain 21841781
nsv583132 CNV gain 21841781
nsv583133 CNV loss 21841781
nsv7327 OTHER inversion 18451855
nsv818080 CNV gain 17921354
nsv998333 CNV gain+loss 25217958

Variation tolerance for IMP4 Gene

Residual Variation Intolerance Score: 43.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.55; 72.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for IMP4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
IMP4
Leiden Open Variation Database (LOVD)
IMP4

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for IMP4 Gene

Disorders for IMP4 Gene

Additional Disease Information for IMP4

No disorders were found for IMP4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for IMP4 Gene

Publications for IMP4 Gene

  1. The human Imp3 and Imp4 proteins form a ternary complex with hMpp10, which only interacts with the U3 snoRNA in 60-80S ribonucleoprotein complexes. (PMID: 12655004) Granneman S … Pruijn GJ (Nucleic acids research 2003) 2 3 4
  2. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  4. Large-scale concatenation cDNA sequencing. (PMID: 9110174) Yu W … Gibbs RA (Genome research 1997) 2 3
  5. A "double adaptor" method for improved shotgun library construction. (PMID: 8619474) Andersson B … Gibbs RA (Analytical biochemistry 1996) 2 3

Products for IMP4 Gene

Sources for IMP4 Gene