NBPF3

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.[3]

NBPF3
Identifiers
AliasesNBPF3, AE2, neuroblastoma breakpoint family member 3, NBPF member 3
External IDsOMIM: 612992 HomoloGene: 88936 GeneCards: NBPF3
Gene location (Human)
Chr.Chromosome 1 (human)[1]
Band1p36.12Start21,440,128 bp[1]
End21,485,005 bp[1]
RNA expression pattern




More reference expression data
Orthologs
SpeciesHumanMouse
Entrez

84224

n/a

Ensembl

ENSG00000142794

n/a

UniProt

Q9H094

n/a

RefSeq (mRNA)

n/a

RefSeq (protein)

n/a

Location (UCSC)Chr 1: 21.44 – 21.49 Mbn/a
PubMed search[2]n/a
Wikidata
View/Edit Human

Protein sequence

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.

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

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:[4]

Isoform Sequence Omissions Sequence Additions Length
1--633
21-56-577
3350-386331 R→RSSGRFCCLISVGYIFCHPCPAWLIR621
41-358-275

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

Function

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.[5]

Homology

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 sapiensHumanCAB66824100%100%6335
Pan troglodytesChimpanzeeXP_001163311.196%98%6335
Macaca mulattaRhesus macaqueXP_001114167.155%65%6204
Pongo albeliiOrangutanNP_001127345.189%93%2023
Bos taurusCowXP_611707.433%49%8164
Equus caballusHorseXP_001916030.137%55%10370
Canis lupus familiarisDogXP_540269.240%59%1760

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 sapiensNBPF3CAB66824100%100%633
Homo sapiensNBPF10NP_001034792.277%83%867
Homo sapiensNBPF1NP_060410.275%83%1214
Homo sapiensNBPF20NP_001032764.175%84%942
Homo sapiensNBPF8XP_001726998.175%84%3815
Homo sapiensNBPF16NP_001096133.175%84%670
Homo sapiensNBPF15NP_775909.175%84%670
Homo sapiensNBPF11NP_899228.375%83%790
Homo sapiensNBPF14NP_056198.174%83%921
Homo sapiensNBPF9XP_001717450.180%88%687
Homo sapiensNBPF7NP_001041445.169%79%421
Homo sapiensNBPF6NP_001137459.154%68%667
Homo sapiensNBPF4NP_001137461.153%67%638
Homo sapiensNBPF12XP_001715862.155%63%427
Homo sapiensNBPF5XP_001714524.160%73%428

Both orthologs and paralogs of NBPF3 were found using the databases BLAT.[6] and BLAST [7]

Protein interactions

NPBF3 interacts with three other proteins: C1orf19, ankyrin-1 (ANK1) and Ewing sarcoma breakpoint region 1 (EWSR1).[8] It is not known how these proteins interact or what the product of these interactions may be.



References
  1. GRCh38: Ensembl release 89: ENSG00000142794 - Ensembl, May 2017
  2. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  3. "Entrez Gene: NBPF3 neuroblastoma breakpoint family, member 3".
  4. "UniProt". Retrieved 14 May 2009.
  5. 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.
  6. "BLAT Search Genome". Retrieved 4 May 2009.
  7. "BLAST". Retrieved 4 May 2009.
  8. "STRING: Known and Predicted Protein-Protein Interactions".

Further reading
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