NBPF16: Difference between revisions

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{{Infobox gene}}
{{Infobox gene}}
'''Neuroblastoma Breakpoint Family, Member 16''', also known as '''NBPF16''', is a [[protein]] which in humans is encoded by the ''NBPF16'' [[gene]].<ref name="entrez">{{cite web | title = Entrez Gene: NBPF16 neuroblastoma breakpoint family, member 16| url = https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=retrieve&dopt=full_report&list_uids=728936&log$=databasead&logdbfrom=protein| accessdate = 13 May 2009}}</ref> The gene is 18762 bp long, with [[mRNA]] that is 3837 bp long.  The gene is located on chromosome 1q21.1.  Its sub-cellular location is predicted to be in the [[Cell nucleus|nucleus]] and [[cytoplasm]].<ref name="urlSDSC Biology Workbench">{{cite web | url = http://workbench.sdsc.edu/ | title = SDSC Biology Workbench | author = | date = | work = | publisher = San Diego Supercomputer Center | pages = | archiveurl = | archivedate = | accessdate = 13 May 2009}}</ref> It contains what is known as the NBPF repeat, which is a two exon stretch of sequence that is characteristic of all 21 members of the NBPF gene family.  The repeat is considered the ancestral exons, and the NBPF family has been linked to primate evolution.<ref name="Vande">{{cite journal | vauthors = Vandepoele K, Van Roy N, Staes K, Speleman F, van Roy F | title = A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution | journal = Molecular Biology and Evolution | volume = 22 | issue = 11 | pages = 2265–2274 |date=August 2005 | pmid = 16079250 | doi = 10.1093/molbev/msi222  | url =  }}</ref>
'''Neuroblastoma Breakpoint Family, Member 16''', also known as '''NBPF16''', is a [[protein]] which in humans is encoded by the ''NBPF16'' [[gene]].<ref name="entrez">{{cite web | title = Entrez Gene: NBPF16 neuroblastoma breakpoint family, member 16| url = https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=retrieve&dopt=full_report&list_uids=728936&log$=databasead&logdbfrom=protein| accessdate = 13 May 2009}}</ref> The gene is 18762 bp long, with [[mRNA]] that is 3837 bp long.  The gene is located on chromosome 1q21.1.  Its sub-cellular location is predicted to be in the [[Cell nucleus|nucleus]] and [[cytoplasm]].<ref name="urlSDSC Biology Workbench">{{cite web | url = http://workbench.sdsc.edu/ | title = SDSC Biology Workbench | author = | date = | work = | publisher = San Diego Supercomputer Center | pages = | accessdate = 13 May 2009}}</ref> It contains what is known as the NBPF repeat, which is a two exon stretch of sequence that is characteristic of all 21 members of the NBPF gene family.  The repeat is considered the ancestral exons, and the NBPF family has been linked to primate evolution.<ref name="Vande">{{cite journal | vauthors = Vandepoele K, Van Roy N, Staes K, Speleman F, van Roy F | title = A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution | journal = Molecular Biology and Evolution | volume = 22 | issue = 11 | pages = 2265–2274 |date=August 2005 | pmid = 16079250 | doi = 10.1093/molbev/msi222  | url =  }}</ref>


== Function ==
== Function ==
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Properties of NBPF16 that were predicted using [[Bioinformatics]] tools:
Properties of NBPF16 that were predicted using [[Bioinformatics]] tools:
* Molecular Weight: 76 kD<ref name="SAPS">{{cite journal | vauthors = Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S | title = Methods and algorithms for statistical analysis of protein sequences | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 89 | issue = 6 | pages = 2002–6 |date=March 1992 | pmid = 1549558 | pmc = 48584 | doi = 10.1073/pnas.89.6.2002| url =  }}</ref>
* Molecular Weight: 76 kD<ref name="SAPS">{{cite journal | vauthors = Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S | title = Methods and algorithms for statistical analysis of protein sequences | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 89 | issue = 6 | pages = 2002–6 |date=March 1992 | pmid = 1549558 | pmc = 48584 | doi = 10.1073/pnas.89.6.2002| url =  }}</ref>
* [[Isoelectric point]]: 4.43<ref name=PI>{{cite web |title= PI Program (Isoelectric Point Prediction) |url=http://www.embl-heidelberg.de/cgi/pi-wrapper.pl}}</ref>
* [[Isoelectric point]]: 4.43<ref name=PI>{{cite web |title= PI Program (Isoelectric Point Prediction) |url= http://www.embl-heidelberg.de/cgi/pi-wrapper.pl |deadurl= yes |archiveurl= https://web.archive.org/web/20081026062821/http://www.embl-heidelberg.de/cgi/pi-wrapper.pl |archivedate= 26 October 2008 |df= dmy-all }}</ref>
* [[Posttranslational modification|Post-translational modification]]: None predicted.
* [[Posttranslational modification|Post-translational modification]]: None predicted.
* No predicted [[Signal peptide|Signal Peptide]] or signal peptide cleavage site.<ref name="SignalP">{{cite journal | vauthors = Bendtsen JD, Nielsen H, von Heijne G, Brunak S | title = Improved prediction of signal peptides: SignalP 3.0 | journal = Journal of Molecular Biology | volume = 340 | issue = 4 | pages = 783–95 |date=July 2004 | pmid = 15223320 | doi = 10.1016/j.jmb.2004.05.028 | url =  }}</ref>
* No predicted [[Signal peptide|Signal Peptide]] or signal peptide cleavage site.<ref name="SignalP">{{cite journal | vauthors = Bendtsen JD, Nielsen H, von Heijne G, Brunak S | title = Improved prediction of signal peptides: SignalP 3.0 | journal = Journal of Molecular Biology | volume = 340 | issue = 4 | pages = 783–95 |date=July 2004 | pmid = 15223320 | doi = 10.1016/j.jmb.2004.05.028 | url =  }}</ref>

Latest revision as of 19:55, 1 March 2018

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Identifiers
Aliases
External IDsGeneCards: [1]
Orthologs
SpeciesHumanMouse
Entrez

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Ensembl

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UniProt

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RefSeq (mRNA)

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RefSeq (protein)

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Location (UCSC)n/an/a
PubMed searchn/an/a
Wikidata
View/Edit Human

Neuroblastoma Breakpoint Family, Member 16, also known as NBPF16, is a protein which in humans is encoded by the NBPF16 gene.[1] The gene is 18762 bp long, with mRNA that is 3837 bp long. The gene is located on chromosome 1q21.1. Its sub-cellular location is predicted to be in the nucleus and cytoplasm.[2] It contains what is known as the NBPF repeat, which is a two exon stretch of sequence that is characteristic of all 21 members of the NBPF gene family. The repeat is considered the ancestral exons, and the NBPF family has been linked to primate evolution.[3]

Function

The function of NBPF16 is not fully understood. It is a member of the NBPF family of proteins, which have been linked to possible roles in oncogenesis and tumor suppressor genes.[3]

Protein

The protein is composed of 670 amino acids. The gene contains five domains of unknown function, called DUF1220. DUF1220 domains are found in all members of the NBPF gene family, although the number differs between each member. Repetitive structure with high intergenic and intragenic sequence conservation, both in coding and noncoding regions. Makes it possible for homologous recombination to occur easily between different alleles. The repetitiveness of it, and the other members of the NBPF gene family is thought to have arisen from segmental duplications on chromosome 1.[3]

Predicted properties

Properties of NBPF16 that were predicted using Bioinformatics tools:

Expression

There is little to no expression data available for the gene, but most indications point to it being ubiquitously expressed throughout the body.

Homology

Orthologs

There exists no great orthologs outside of primates. These orthologs were gathered from BLAT.[7] and BLAST searches[8]

Species Organism common name Sequence identity Sequence similarity Length (AAs)
Homo sapiens Human 100% 100% 670
Pan troglodytes Chimpanzee 90% 92% 509
Macaca mulatta Rhesus macaque 57% 68% 620
Gallus gallus Chicken 36% 54% 1394
Rattus norvegicus Norway rat 34% 67% 2324
Bos taurus Cattle 34% 50% 816
Xenopus laevis African clawed frog 33% 52% 728
Mus musculus House mouse 32% 55% 2446

Paralogs

Due to there being 21 other members of the NBPF gene family, there are 21 paralogs of NBPF16. They all show high conservation and repetitive structures.

References

  1. ↑ "Entrez Gene: NBPF16 neuroblastoma breakpoint family, member 16". Retrieved 13 May 2009.
  2. ↑ "SDSC Biology Workbench". San Diego Supercomputer Center. Retrieved 13 May 2009.
  3. ↑ 3.0 3.1 3.2 Vandepoele K, Van Roy N, Staes K, Speleman F, van Roy F (August 2005). "A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution". Molecular Biology and Evolution. 22 (11): 2265–2274. doi:10.1093/molbev/msi222. PMID 16079250.
  4. ↑ Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S (March 1992). "Methods and algorithms for statistical analysis of protein sequences". Proceedings of the National Academy of Sciences of the United States of America. 89 (6): 2002–6. doi:10.1073/pnas.89.6.2002. PMC 48584. PMID 1549558.
  5. ↑ "PI Program (Isoelectric Point Prediction)". Archived from the original on 26 October 2008.
  6. ↑ Bendtsen JD, Nielsen H, von Heijne G, Brunak S (July 2004). "Improved prediction of signal peptides: SignalP 3.0". Journal of Molecular Biology. 340 (4): 783–95. doi:10.1016/j.jmb.2004.05.028. PMID 15223320.
  7. ↑ "BLAT Search Genome". Retrieved 13 May 2009.
  8. ↑ "BLAST". Retrieved 13 May 2009.


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