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Aliases NBPF3, AE2, neuroblastoma breakpoint family member 3, NBPF member 3
External IDs HomoloGene: 88936 GeneCards: NBPF3
RNA expression pattern
PBB GE NBPF3 201103 x at fs.png

PBB GE NBPF3 212854 x at fs.png

PBB GE NBPF3 213612 x at fs.png
More reference expression data
Species Human Mouse
RefSeq (mRNA)



RefSeq (protein)



Location (UCSC) Chr 1: 21.44 – 21.49 Mb n/a
PubMed search [1] n/a
View/Edit Human

Neuroblastoma breakpoint family, member 3, also known as NBPF3, is a human gene of the neuroblastoma breakpoint family, which resides on chromosome 1 of the human genome. NBPF3 is located at 1p36.12, immediately upstream of genes ALPL and RAP1GAP.[2]

Protein sequence[edit]

The NBPF3 gene is 633 amino acids long and contains five DUF1220 domains, which are highlighted in the image below. DUF1220 domains are found in all other members of the neuroblastoma breakpoint family. The protein has a very repetitive structure, since, along with the remaining members of its protein family, it likely arose form segmental duplications on chromosome 1.

634 × 172 px

The domains are located at residues 236-298, 322-385, 394-460, 469-535, and 544-610.

The protein sequence is rich in three amino acids that are polar and negatively charged at physiological pH: glutamic acid, aspartic acid and glutamine. The isoelectric point of the protein is 4.21, the acidity of which may be attributed to the abundance of these amino acids.

Isoforms and sequence characteristics[edit]

There are four known isoforms of the NPBF3 gene. While isoform 1 is the dominant form of the gene, each other isoform has unique changes to the protein sequence that may affect the structure, expression or function of the gene product:[3]

Isoform Sequence Omissions Sequence Additions Length
1 - - 633
2 1-56 - 577
4 1-358 - 275

These isoforms are represented in the following schematic, along with additional sequence characteristics which include Poly-Glu compositional biases and a potential coiled coil.

676 × 620 px


The function of the neuroblastoma breakpoint family proteins, including NPBF3, is not yet understood by the scientific community. Because of the repetitive composition of this family of genes as well as their amplification in primates, it has been suggested that the family is involved in cognitive development and the evolution of primates.

It has also been suggested that there is a connection between the neuroblastoma breakpoint family and oncogenesis. Due to the up-regulation of NBPF genes in some tumor tissues, proteins of this family have been hypothesized to be oncogenes. It has also been suggested that members of the neuroblastoma breakpoint family are tumor suppressor genes, due to a loss of heterozygosity in tumor tissue in the region of chromosome 1 where NBPF3 and other NBPF proteins are located.[4]


Orthologs of NBPF3 are found primarily in primate species, though orthologous sequences can be found in cow, horse, and dog species. There is no mouse ortholog of NPBF3.

Species Organism common name NCBI accession Sequence identity Sequence similarity Length (AAs) Number of DUF1220 domains
Homo sapiens Human CAB66824 100% 100% 633 5
Pan troglodytes Chimpanzee XP_001163311.1 96% 98% 633 5
Macaca mulatta Rhesus macaque XP_001114167.1 55% 65% 620 4
Pongo albelii Orangutan NP_001127345.1 89% 93% 202 3
Bos taurus Cow XP_611707.4 33% 49% 816 4
Equus caballus Horse XP_001916030.1 37% 55% 1037 0
Canis lupus familiaris Dog XP_540269.2 40% 59% 176 0

NPBF3 has many human paralogs because it is a member of a gene family.

Species Gene name NCBI accession Sequence identity Sequence similarity Length (AAs)
Homo sapiens NBPF3 CAB66824 100% 100% 633
Homo sapiens NBPF10 NP_001034792.2 77% 83% 867
Homo sapiens NBPF1 NP_060410.2 75% 83% 1214
Homo sapiens NBPF20 NP_001032764.1 75% 84% 942
Homo sapiens NBPF8 XP_001726998.1 75% 84% 3815
Homo sapiens NBPF16 NP_001096133.1 75% 84% 670
Homo sapiens NBPF15 NP_775909.1 75% 84% 670
Homo sapiens NBPF11 NP_899228.3 75% 83% 790
Homo sapiens NBPF14 NP_056198.1 74% 83% 921
Homo sapiens NBPF9 XP_001717450.1 80% 88% 687
Homo sapiens NBPF7 NP_001041445.1 69% 79% 421
Homo sapiens NBPF6 NP_001137459.1 54% 68% 667
Homo sapiens NBPF4 NP_001137461.1 53% 67% 638
Homo sapiens NBPF12 XP_001715862.1 55% 63% 427
Homo sapiens NBPF5 XP_001714524.1 60% 73% 428

Both orthologs and paralogs of NBPF3 were found using the databases BLAT.[5] and BLAST [6]

Protein interactions[edit]

NPBF3 interacts with three other proteins: C1orf19, Ankyrin-1 (ANK1) and Ewing Sarcoma Breakpoint region 1 (EWSR1).[7] It is not known how these proteins interact or what the product of these interactions may be.

703 × 475 px


  1. ^ "Human PubMed Reference:". 
  2. ^ "Entrez Gene: NBPF3 neuroblastoma breakpoint family, member 3". 
  3. ^ "UniProt". Retrieved 14 May 2009. 
  4. ^ Vandepoele K, Van Roy N, Staes K, et al. (2006). "A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution.". Mol. Biol. Evol. 22 (11): 2265–74. doi:10.1093/molbev/msi222. PMID 16079250. 
  5. ^ "BLAT Search Genome". Retrieved 4 May 2009. 
  6. ^ "BLAST". Retrieved 4 May 2009. 
  7. ^ "STRING: Known and Predicted Protein-Protein Interactions". 

Further reading[edit]