This gene is a member of the neuroblastoma breakpoint family (NBPF) which consists of dozens of recently duplicated genes primarily located in segmental duplications on human chromosome 1. This gene family has experienced its greatest expansion within the human lineage and has expanded, to a lesser extent, among primates in general. Members of this gene family are characterized... See more...

Aliases for NBPF4 Gene

Aliases for NBPF4 Gene

  • NBPF Member 4 2 3 5
  • Neuroblastoma Breakpoint Family Member 4 3 4
  • Neuroblastoma Breakpoint Family, Member 4 2
  • FLJ32833 2
  • NBPF4 5

External Ids for NBPF4 Gene

Previous GeneCards Identifiers for NBPF4 Gene

  • GC01M108478
  • GC01M108765
  • GC01M106711

Summaries for NBPF4 Gene

Entrez Gene Summary for NBPF4 Gene

  • This gene is a member of the neuroblastoma breakpoint family (NBPF) which consists of dozens of recently duplicated genes primarily located in segmental duplications on human chromosome 1. This gene family has experienced its greatest expansion within the human lineage and has expanded, to a lesser extent, among primates in general. Members of this gene family are characterized by tandemly repeated copies of DUF1220 protein domains. Gene copy number variations in the human chromosomal region 1q21.1, where most DUF1220 domains are located, have been implicated in a number of developmental and neurogenetic diseases such as microcephaly, macrocephaly, autism, schizophrenia, cognitive disability, congenital heart disease, neuroblastoma, and congenital kidney and urinary tract anomalies. Altered expression of some gene family members is associated with several types of cancer. This gene family contains numerous pseudogenes. [provided by RefSeq, Mar 2013]

GeneCards Summary for NBPF4 Gene

NBPF4 (NBPF Member 4) is a Protein Coding gene. Diseases associated with NBPF4 include Autosomal Recessive Nonsyndromic Deafness 32 and Hydrolethalus Syndrome 1. An important paralog of this gene is NBPF6.

Additional gene information for NBPF4 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NBPF4 Gene

Genomics for NBPF4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NBPF4 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
GH01J108217 Enhancer 0.9 Ensembl ENCODE 0.3 +27.1 27096 2.4 CREB1 PRDM10 PKNOX1 DPF2 CTBP1 CEBPB ZNF217 JUND FOSL1 NFIC SLC25A24 piR-56883-008 piR-41881-001 NBPF4
GH01J108208 Enhancer 0.8 Ensembl CraniofacialAtlas 0.3 +34.8 34754 1.1 CEBPG GTF2F1 GATAD2B ZNF316 NCOR1 ELF1 ZFHX2 IKZF1 DPF2 EBF1 piR-56883-008 SLC25A24 piR-41881-001 NBPF4
GH01J108235 Enhancer 0.3 Ensembl 0.4 +8.7 8680 0.4 ARID1B piR-36760-001 piR-41881-001 NBPF4 SLC25A24
GH01J108211 Enhancer 0.4 Ensembl 0.3 +32.6 32617 0.3 USF2 SREBF1 CREB1 SLC25A24 piR-56883-008 piR-41881-001 NBPF4
GH01J108247 Enhancer 0.2 Ensembl 0.7 -3.4 -3420 0.6 piR-55736-001 NBPF4 piR-37599-001 NBPF6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NBPF4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NBPF4

Top Transcription factor binding sites by QIAGEN in the NBPF4 gene promoter:
  • AP-4

Genomic Locations for NBPF4 Gene

Genomic Locations for NBPF4 Gene
chr1:108,222,464-108,244,081
(GRCh38/hg38)
Size:
21,618 bases
Orientation:
Minus strand
chr1:108,765,963-108,786,703
(GRCh37/hg19)
Size:
20,741 bases
Orientation:
Minus strand

Genomic View for NBPF4 Gene

Genes around NBPF4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NBPF4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NBPF4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NBPF4 Gene

Proteins for NBPF4 Gene

  • Protein details for NBPF4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96M43-NBPF4_HUMAN
    Recommended name:
    Neuroblastoma breakpoint family member 4
    Protein Accession:
    Q96M43
    Secondary Accessions:
    • Q5T483

    Protein attributes for NBPF4 Gene

    Size:
    638 amino acids
    Molecular mass:
    72053 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB71469.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305};
    Miscellaneous:
    • Encoded by one of the numerous copies of NBPF genes clustered in the p36, p12 and q21 region of the chromosome 1.

neXtProt entry for NBPF4 Gene

Post-translational modifications for NBPF4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NBPF4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NBPF4 Gene

Domains & Families for NBPF4 Gene

Gene Families for NBPF4 Gene

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

Protein Domains for NBPF4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NBPF4 Gene

GenScript: Design optimal peptide antigens:
  • NBPF4 protein (A4QN26_HUMAN)
  • Neuroblastoma breakpoint family member 4 (NBPF4_HUMAN)
  • cDNA FLJ50291, weakly similar to Homo sapiens phosphodiesterase 4D interacting protein, transcript variant 1, mRNA (Q5T483_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96M43

UniProtKB/Swiss-Prot:

NBPF4_HUMAN :
  • Belongs to the NBPF family.
Family:
  • Belongs to the NBPF family.
genes like me logo Genes that share domains with NBPF4: view

Function for NBPF4 Gene

genes like me logo Genes that share phenotypes with NBPF4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NBPF4

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for NBPF4 Gene

Localization for NBPF4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NBPF4 Gene

Cytoplasm.

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 NBPF4 gene
Compartment Confidence
nucleus 2
extracellular 1
cytosol 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NBPF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with NBPF4: view

Pathways & Interactions for NBPF4 Gene

PathCards logo

SuperPathways for NBPF4 Gene

No Data Available

Interacting Proteins for NBPF4 Gene

Gene Ontology (GO) - Biological Process for NBPF4 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for NBPF4 Gene

Drugs & Compounds for NBPF4 Gene

No Compound Related Data Available

Transcripts for NBPF4 Gene

mRNA/cDNA for NBPF4 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NBPF4

Alternative Splicing Database (ASD) splice patterns (SP) for NBPF4 Gene

No ASD Table

Relevant External Links for NBPF4 Gene

GeneLoc Exon Structure for
NBPF4

Expression for NBPF4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NBPF4 Gene

mRNA differential expression in normal tissues according to GTEx for NBPF4 Gene

This gene is overexpressed in Testis (x22.0), Brain - Putamen (basal ganglia) (x5.5), and Small Intestine - Terminal Ileum (x5.0).

Protein differential expression in normal tissues from HIPED for NBPF4 Gene

This gene is overexpressed in Plasma (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for NBPF4 Gene



Protein tissue co-expression partners for NBPF4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NBPF4

SOURCE GeneReport for Unigene cluster for NBPF4 Gene:

Hs.511849

mRNA Expression by UniProt/SwissProt for NBPF4 Gene:

Q96M43-NBPF4_HUMAN
Tissue specificity: Expressed in testis.
genes like me logo Genes that share expression patterns with NBPF4: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for NBPF4 Gene

Orthologs for NBPF4 Gene

This gene was present in the common ancestor of mammals.

Orthologs for NBPF4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LOC740049 30
  • 97.91 (n)
-- 31
  • 94 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia LOC101903302 30
  • 64.66 (n)
-- 31
  • 40 (a)
ManyToMany
-- 31
  • 35 (a)
ManyToMany
Dog
(Canis familiaris)
Mammalia -- 31
  • 40 (a)
OneToMany
Species where no ortholog for NBPF4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Mouse (Mus musculus)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for NBPF4 Gene

ENSEMBL:
Gene Tree for NBPF4 (if available)
TreeFam:
Gene Tree for NBPF4 (if available)

Paralogs for NBPF4 Gene

(17) SIMAP similar genes for NBPF4 Gene using alignment to 2 proteins:

  • NBPF4_HUMAN
  • A4QN26_HUMAN

Pseudogenes.org Pseudogenes for NBPF4 Gene

genes like me logo Genes that share paralogs with NBPF4: view

Variants for NBPF4 Gene

Additional dbSNP identifiers (rs#s) for NBPF4 Gene

Structural Variations from Database of Genomic Variants (DGV) for NBPF4 Gene

Variant ID Type Subtype PubMed ID
dgv248n100 CNV gain 25217958
dgv469n54 CNV gain 21841781
dgv481n54 CNV loss 21841781
dgv74e212 CNV loss 25503493
dgv75e212 CNV gain 25503493
esv23343 CNV gain+loss 19812545
esv2758958 CNV gain+loss 17122850
esv2763802 CNV loss 21179565
esv3578071 CNV loss 25503493
nsv1004890 CNV loss 25217958
nsv10550 CNV loss 18304495
nsv1124570 CNV duplication 24896259
nsv1149603 CNV duplication 26484159
nsv428179 CNV gain 18775914
nsv526757 CNV loss 19592680
nsv821352 CNV deletion 20802225
nsv946119 CNV duplication 23825009

Variation tolerance for NBPF4 Gene

Gene Damage Index Score: 0.94; 19.46% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NBPF4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NBPF4

SNP Genotyping and Copy Number Assay Products

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 NBPF4 Gene

Disorders for NBPF4 Gene

MalaCards: The human disease database

(5) MalaCards diseases for NBPF4 Gene - From: DISEASES and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search NBPF4 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with NBPF4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NBPF4 Gene

Publications for NBPF4 Gene

  1. A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution. (PMID: 16079250) Vandepoele K … van Roy F (Molecular biology and evolution 2005) 2 3 4
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 4
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 3

Products for NBPF4 Gene

Sources for NBPF4 Gene