User:Sophie.Ann.O/sandbox: Difference between revisions - Wikipedia

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== ”’NBPF8”’ ==

NBPF8 (transcript variant 1 in Homo sapiens), a member of the ”’neuroblastoma breakpoint family (NBPF)”’ ”'(link to Wikipedia page)”’, is located on human chromosome 1 and spans 7,256 base pairs; its coding sequence, however, spans 2,828 base pairs. On the first chromosome, its specific region to which it belongs can be noted as 1p11.2<ref>{{Cite web |title=NBPF8 NBPF member 8 [Homo sapiens (human)] – Gene – NCBI |url=https://www.ncbi.nlm.nih.gov/gene/728841/ |access-date=2025-09-29 |website=www.ncbi.nlm.nih.gov}}</ref>, its accession number is NM_001037501, and it is located on the + strand<ref>{{Cite web |url=https://genome.ucsc.edu/cgi-bin/hgc?hgsid=3187065910_8YIbycv0vnJa3qanaG5pud2a2Hjq&g=htcGetDna2&table=&i=mixed&o=120415034&l=120415034&r=120469676&getDnaPos=chr1:120,415,035-120,469,676&db=hg38&hgSeq.cdsExon=1&hgSeq.padding5=400&hgSeq.padding3=400&hgSeq.casing=lower&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=Get+DNA |access-date=2025-09-29 |website=genome.ucsc.edu}}</ref>. Additionally, this gene has a molecular weight of ~109 kDa<ref>{{Cite web |last=GeneCards Human Gene Database |title=NBPF8 Gene – GeneCards {{!}} NBPF8 Protein {{!}} NBPF8 Antibody |url=https://www.genecards.org/cgi-bin/carddisp.pl?gene=NBPF8 |archive-url=http://web.archive.org/web/20250815101623/https://www.genecards.org/cgi-bin/carddisp.pl?gene=NBPF8 |archive-date=2025-08-15 |access-date=2025-09-29 |website=www.genecards.org |language=en}}</ref>.

==== Transcription ====

Within the NCBI Build 37.2, a single genomic continuum on the assembly of the gene; one of the open reading frames is NBPF8. This gene contains, within the first coding exon, there are deletion a deletion of two nucleotides therefore causing a frameshift mutation<ref>{{Citation |last=Andries |first=Vanessa |title=The NBPF Gene Family |date=2012-02-08 |work=Neuroblastoma – Present and Future |url=https://doi.org/10.5772/28470 |access-date=2025-09-29 |publisher=InTech |isbn=978-953-307-016-2 |last2=Vandepoele |first2=Karl |last3=van |first3=Frans}}</ref>. As far as variety, there are only two isoforms other than NBPF8 transcript variant 1 and those are transcript variants X1 and X<ref>{{Cite web |title=NBPF8 NBPF member 8 [Homo sapiens (human)] – Gene – NCBI |url=https://www.ncbi.nlm.nih.gov/gene/728841/ |access-date=2025-09-29 |website=www.ncbi.nlm.nih.gov}}</ref>.

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==== Clinical Significance ====

Where most ”’Olduvai domains”’ ”'(link to Wikipedia page)”’ are located, in 1q21.1, gene copy number variations in this region of the chromosome have been identified in certain diseases, both developmental and neurogenetic, consisting of micro- and macrocephaly, autism, schizophrenia, cognitive disability, congenital heart disease, neuroblastoma, and congenital kidney and urinary tract anomalies, as well as some types of cancer<ref>{{Cite web |title=NBPF8 NBPF member 8 [Homo sapiens (human)] – Gene – NCBI |url=https://www.ncbi.nlm.nih.gov/gene/728841/ |access-date=2025-09-29 |website=www.ncbi.nlm.nih.gov}}</ref>. The expression of the NBPF8 gene has been detected in the skin, the lymph node, and about 25 other tissues as well.

==== Relational Information Regarding Orthologs and Paralogs ====

The NBPF8 gene is a part of a gene family, the neuroblastoma breakpoint family, and therefore has many paralogs within this family. Outside of genes within the neuroblastoma breakpoint family, and excluding uncharacterized proteins, there is only one paralog associated with NBPF8 which is myomegalin; myomegalin isoform 16 has the highest percent identity of 32.94%. Something notable is that myomegalin has orthologs in sharks and rays (bony fish) which extends further back evolutionarily than NBPF8’s orthologs; as a note, the neuroblastoma breakpoint family as a whole does not extend further evolutionarily than NBPF8 individually.

There are only eight direct orthologs of NBPF8; evolutionary speaking, the furthest species from humans (”Homo sapiens”) these orthologs of NBPF8 are found in, are birds. The following will depict what each of the orthologs is and what its three letter code followed by “_NBPF8” represents as these codes will to be used to depict which protein sequence is which in a more concise manner:

* Cni_NBPF8: the NBPF8 protein found in ”Caloenas nicobarica” (the Nicobar pigeon)

* Cci_NBPF8: the NBPF8 protein found in ”Cinclus cinclus” (the White-throated dipper)

* Hru_NBPF8: the NBPF8 protein found in ”Hirundo rustica” (the Barn swallow)

* Pat_NBPF8: the NBPF8 protein found in ”Poecile atricapillus” (the Black-capped chickadee)

* Ana_NBPF8: the NBPF8 protein found in ”Aotus nancymaae” (the Ma’s night monkey)

* Ppa_NBPF8: the NBPF8 protein found in ”Pan paniscus” (the Pygmy chimpanzee)

* Hsa_NBPF8: the NBPF8 protein found in ”Homo sapiens” (the Human)

* Ggo_NBPF8: the NBPF8 protein found in ”Gorilla gorilla gorilla” (the Western lowland gorilla)

Table 1. Paralogs of NBPF8

{| class=”wikitable”

!Paralog’s Name

!Accession Number

!Query Cover

!Percent Identity

!E-Value

!NBPF8

!NP_001032590.2

!100%

!0.0

!NBPF9 (Isoform 2)

!NP_001032764.2

!100%

!96.71%

!0.0

!NBPF15 (Isoform 1)

!NP_001164226.1

!99%

!96.13%

!0.0

!NBPF26 (Isoform 3 precursor)

!NP_001382566.1

!100%

!94.45%

!0.0

!NBPF10 (Isoform A)

!NP_001289300.1

!100%

!94.34%

!0.0

!NBPF14 (Isoform 2)

!NP_001382560.1

!100%

!94.34%

!0.0

!NBPF19

!NP_001338294.1

!99%

!93.83%

!0.0

!NBPF1 (Isoform 12)

!NP_001392630.1

!99%

!93.60%

!0.0

!NBPF20 (Isoform 1)

!NP_001384140.1

!99%

!93.52%

!0.0

!NBPF12

!NP_001265070.1

!100%

!92.17%

!0.0

!NBPF7

!NP_001392671.1

!100%

!91.52%

!0.0

!NBPF11 (Isoform B)

!NP_001095133.3

!98%

!89.95%

!0.0

!NBPF3 (Isoform 1)

!NP_115640.1

!100%

!75.62%

!0.0

|”’NBPF6 (Isoform X1)”’

|”’XP_011540314.1”’

|”’97%”’

|”’56.36%”’

|”’2e-142”’

|”’NBPF4 (Isoform X5)”’

|”’XP_054190561.1”’

|”’97%”’

|”’56.36%”’

|”’2e-142”’

|”’Myomegalin (Isoform 16)”’

|”’NP_001382226.1”’

|”’17%”’

|”’32.94%”’

|”’5e-10”’

Table 2. Orthologs of NBPF8

{| class=”wikitable”

|Genus and Species

|Common Name

|Taxonomic Group

|Date of Divergence from the Human Lineage (units of millions of years ago: MYA)

|Accession Number

|Sequence Length (units of amino acids (aa))

|Sequence Identity to Human Protein

|Sequence Similarity to Human Protein

|”Homo sapiens”

|Human

|NP_001032590.2

|942

|100%

|”Aotus nancymaae”

|Ma’s night monkey

|Primates

|43

|XP_021529833.2

|276

|”Gorilla gorilla gorilla”

|Western lowland gorilla

|Primates

|8.6

|XP_063552414.1

|1458

|”Pan paniscus”

|Pygmy chimpanzee

|Primates

|6.4

|XP_054958518.2

|2628

|”Hirundo rustica”

|Barn swallow

|Aves

|319

|XP_039929560.1

|2245

|”Poecile atricapillus”

|Black-capped chickadee

|Aves

|319

|XP_058698605.1

|2285

|”Caloenas nicobarica”

|Nicobar pigeon

|Aves

|319

|XP_065505110.1

|2326

|”Cinclus cinclus”

|White-throated dipper

|Aves

|319

|XP_062353720.1

|2312

[[File:Phylogenetic Tree of NBPF8.png|thumb|289x289px|Figure 1: as to contextualize this figure, this is a phylogenetic tree of the NBPF8 gene in Humans, depicted as “Hsa” on the tree (representative of ”Homo sapiens”), and its 7 orthologs in other species. “Ana” stands for ”Aotus nancymaae” (the Ma’s night monkey); “Ggo” represents ”Gorilla gorilla gorilla” (the Western lowland gorilla); “Ppa” stands for ”Pan paniscus” (the Pygmy chimpanzee); “Hru” stands for ”Hirundo rustica” (the Barn swallow); “Pat” is indicative of ”Poecile atricapillus” (the Black-capped chickadee); “Cni” is representative of ”Caloenas nicobarica” (the Nicobar pigeon); and lastly, “Cci” stands for ”Cinclus cinclus” (the White-throated dipper).]]

==== Evolutionary Context ====

NBPF8 first appeared in birds, and all of the members of the neuroblastoma breakpoint family also have orthologs that only extend as far back in the evolutionary tree as NBPF8; there are no members of the family that extend further back than aves. In fact, NBPF8 is the only gene within the neuroblastoma breakpoint family (of which contains 22 genes total) that has orthologs further back evolutionarily than mammals.

NBPF8

NBPF8 (transcript variant 1 in Homo sapiens), a member of the neuroblastoma breakpoint family (NBPF) (link to Wikipedia page), is located on human chromosome 1 and spans 7,256 base pairs; its coding sequence, however, spans 2,828 base pairs. On the first chromosome, its specific region to which it belongs can be noted as 1p11.2^[1], its accession number is NM_001037501, and it is located on the + strand^[2]. Additionally, this gene has a molecular weight of ~109 kDa^[3].

Transcription

Protein

The NBPF8 protein spans 942 amino acids and its accession number is NP_001032590. The NBPF family is identified via repeated copies of DUF1220 protein domains, also known as Olduvai domains^[6]. These domains are an incredibly important factor in determining what this gene codes for/what its function really is.

Clinical Significance

Where most Olduvai domains (link to Wikipedia page) are located, in 1q21.1, gene copy number variations in this region of the chromosome have been identified in certain diseases, both developmental and neurogenetic, consisting of micro- and macrocephaly, autism, schizophrenia, cognitive disability, congenital heart disease, neuroblastoma, and congenital kidney and urinary tract anomalies, as well as some types of cancer^[7]. The expression of the NBPF8 gene has been detected in the skin, the lymph node, and about 25 other tissues as well.

Relational Information Regarding Orthologs and Paralogs

There are only eight direct orthologs of NBPF8; evolutionary speaking, the furthest species from humans (Homo sapiens) these orthologs of NBPF8 are found in, are birds. The following will depict what each of the orthologs is and what its three letter code followed by “_NBPF8” represents as these codes will to be used to depict which protein sequence is which in a more concise manner:

Cni_NBPF8: the NBPF8 protein found in Caloenas nicobarica (the Nicobar pigeon)
Cci_NBPF8: the NBPF8 protein found in Cinclus cinclus (the White-throated dipper)
Hru_NBPF8: the NBPF8 protein found in Hirundo rustica (the Barn swallow)
Pat_NBPF8: the NBPF8 protein found in Poecile atricapillus (the Black-capped chickadee)
Ana_NBPF8: the NBPF8 protein found in Aotus nancymaae (the Ma’s night monkey)
Ppa_NBPF8: the NBPF8 protein found in Pan paniscus (the Pygmy chimpanzee)
Hsa_NBPF8: the NBPF8 protein found in Homo sapiens (the Human)

Ggo_NBPF8: the NBPF8 protein found in Gorilla gorilla gorilla (the Western lowland gorilla)

Table 1. Paralogs of NBPF8

Paralog’s Name	Accession Number	Query Cover	Percent Identity	E-Value
NBPF8	NP_001032590.2	100%	100%	0.0
NBPF9 (Isoform 2)	NP_001032764.2	100%	96.71%	0.0
NBPF15 (Isoform 1)	NP_001164226.1	99%	96.13%	0.0
NBPF26 (Isoform 3 precursor)	NP_001382566.1	100%	94.45%	0.0
NBPF10 (Isoform A)	NP_001289300.1	100%	94.34%	0.0
NBPF14 (Isoform 2)	NP_001382560.1	100%	94.34%	0.0
NBPF19	NP_001338294.1	99%	93.83%	0.0
NBPF1 (Isoform 12)	NP_001392630.1	99%	93.60%	0.0
NBPF20 (Isoform 1)	NP_001384140.1	99%	93.52%	0.0
NBPF12	NP_001265070.1	100%	92.17%	0.0
NBPF7	NP_001392671.1	100%	91.52%	0.0
NBPF11 (Isoform B)	NP_001095133.3	98%	89.95%	0.0
NBPF3 (Isoform 1)	NP_115640.1	100%	75.62%	0.0
NBPF6 (Isoform X1)	XP_011540314.1	97%	56.36%	2e-142
NBPF4 (Isoform X5)	XP_054190561.1	97%	56.36%	2e-142
Myomegalin (Isoform 16)	NP_001382226.1	17%	32.94%	5e-10

Table 2. Orthologs of NBPF8

Genus and Species	Common Name	Taxonomic Group	Date of Divergence from the Human Lineage (units of millions of years ago: MYA)	Accession Number	Sequence Length (units of amino acids (aa))	Sequence Identity to Human Protein	Sequence Similarity to Human Protein
Homo sapiens	Human		0	NP_001032590.2	942	100%	100%
Aotus nancymaae	Ma’s night monkey	Primates	43	XP_021529833.2	276
Gorilla gorilla gorilla	Western lowland gorilla	Primates	8.6	XP_063552414.1	1458
Pan paniscus	Pygmy chimpanzee	Primates	6.4	XP_054958518.2	2628
Hirundo rustica	Barn swallow	Aves	319	XP_039929560.1	2245
Poecile atricapillus	Black-capped chickadee	Aves	319	XP_058698605.1	2285
Caloenas nicobarica	Nicobar pigeon	Aves	319	XP_065505110.1	2326
Cinclus cinclus	White-throated dipper	Aves	319	XP_062353720.1	2312

Evolutionary Context

^ “NBPF8 NBPF member 8 [Homo sapiens (human)] – Gene – NCBI”. www.ncbi.nlm.nih.gov. Retrieved 2025-09-29.
^ genome.ucsc.edu https://genome.ucsc.edu/cgi-bin/hgc?hgsid=3187065910_8YIbycv0vnJa3qanaG5pud2a2Hjq&g=htcGetDna2&table=&i=mixed&o=120415034&l=120415034&r=120469676&getDnaPos=chr1:120,415,035-120,469,676&db=hg38&hgSeq.cdsExon=1&hgSeq.padding5=400&hgSeq.padding3=400&hgSeq.casing=lower&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=Get+DNA. Retrieved 2025-09-29.
^ GeneCards Human Gene Database. “NBPF8 Gene – GeneCards | NBPF8 Protein | NBPF8 Antibody”. www.genecards.org. Archived from the original on 2025-08-15. Retrieved 2025-09-29.
^ Andries, Vanessa; Vandepoele, Karl; van, Frans (2012-02-08), “The NBPF Gene Family”, Neuroblastoma – Present and Future, InTech, ISBN 978-953-307-016-2, retrieved 2025-09-29
^ “NBPF8 NBPF member 8 [Homo sapiens (human)] – Gene – NCBI”. www.ncbi.nlm.nih.gov. Retrieved 2025-09-29.
^ “NBPF8 NBPF member 8 [Homo sapiens (human)] – Gene – NCBI”. www.ncbi.nlm.nih.gov. Retrieved 2025-09-29.
^ “NBPF8 NBPF member 8 [Homo sapiens (human)] – Gene – NCBI”. www.ncbi.nlm.nih.gov. Retrieved 2025-09-29.

User:Sophie.Ann.O/sandbox: Difference between revisions – Wikipedia