User:Ljroth7/sandbox/knop1

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Lysine-rich nucleolar protein 1 (KNOP1) Is a protein encoding gene that encodes KNOP1. The known aliases for KNOP1 are TSG118, C16orf88, and FAM191A[1]. It is located at 16p12.3.[2]

Gene

KNOP1 is located on the [negative DNA strand] of chromosome 16 at 16p12.3. It covers 15.21 kb, from 19729556 to 19714347 and has 6

5' UTR and coding sequence. The result is shorter at the N-terminus
. Isoform B and C do not contain exon 1 shifting the start codon to exon 2. Isoform C does not contain exon 4 which contains the DUF5595 domain.

Human_chromosome_16_ideogram_from_GHR

Gene Neighborhood

The genes surrounding KNOP1 are

obsessive-compulsive disorder in a genome-wide association study[4]. The VPS35L encodes the protein VPS35L that acts as a component of the retriever complex which[5]
.

Gene Expression

KNOP1 expression in Human tissues[6]

KNOP1 is shown to have high levels of expression superior cervical ganglion[7], testis, placenta, and in early stages of hear and lung development[8]. KNOP1 showed low levels of expression in the liver and pancreas.


Species distribution

There are many orthologs of KNOP1 in many different species of animals but not in the other kingdoms. No paralogs of KNOP1 were found. Table 1 lists select KNOP1 orthologs.

Table 1: KNOP1 Orthologs
Genus, Species Divergence from Homo sapiens (MYA)[9] NCBI accession number Sequence Length (AA) Sequence Similarity to Homo sapien KNOP1[10]
Homo sapiens -- NP_001335456.1 518 100%
Pan paniscus 6 XP_034795825.1 604 85.1%
Mus musculus 89 NP_075686.2 532 65.8%
Lagenorhynchus obliquidens 94 XP_026953897.1 454 72.6%
Galemys pyrenaicus 94 KAG8513613.1 534 67.1%
Phyllostomus discolor 94 KAF6125017.1 434 64.3%
Monodelphis domestica 160 XP_016279153.1 601 47.1%
Ornithorhynchus anatinus 180 XP_028910011.1 544 47.2%
Tyto alba 318 XP_042654773.1 627 42.1%
Gallus gallus 318 XP_004945520.2 548 32.4%
Bufo bufo 352 XP_040296565.1 513 37.7%
Danio rerio 433 XP_687135.1 475 40.4%
Branchiostoma floridae 637 XP_035694713.1 666 34.2%
[Owenia fusiformis] 787 CAC9610945.1 553 34.7%

Protein

The exact function of KNOP1 is not yet understood it is hypothesized to mimic nucleostemin, a nucleolar protein linked to the proliferation potential of stem cells[11]. The protein is 518 amino acids long[12], Isoform B is 458 amino acids[13], and Isoform C is 435 amino acids[14] . It has a molecular weight of 58 kdal and an isoelectric point of 9.92 [15] The protein is rich in lysine[16] and has a lysine-rich region from amino acid 123-355[17]. There is a region of the protein that interacts with the protein ZNF106[18]. Some papers have associated it with the surface of the condensed chromosomes[19].

Domains

Domains of KNOP1:The green box is domain DUF5595:The blue box is domain SMAP:The green line is region of interaction for ZNF106[20]

KNOP1 has two domains Duf5595 (Not found in isoform C) and SMAP located at the end of the protein[21]. DUF5595 is found in Nude C 80 (Ndc80) proteins which can be found in species such as Homo sapiens. Ndc80 protein complexes are a core component of the end-on attachment sites for kinetochore microtubules[22]. SMAP (Small acidic protein family) is found in eukaryotes, and is approximately 70 amino acids in length. There is a single completely conserved residue G that may be functionally important at G441 [23].

KNOP1 Conceptual Translation

Interacting protein

KNOP1 has been shown to interact with ZNF106[24] and has been confirmed by Grasberger, H., & Bell, G. I.[25]. This study concluded that the rapid downregulation of KNOP1 expression during in vitro terminal differentiation coincides with a loss of nucleolar ZFP106.

References

  1. ^ GeneCards (https://www.genecards.org/cgi-bin/carddisp.pl?gene=KNOP1)
  2. ^ U.S. National Library of Medicine. (n.d.). ACEVIEW: Gene:c16orf88, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView. National Center for Biotechnology Information. Retrieved October 4, 2021, from https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&term=C16orf88&submit=Go
  3. ^ (NCBI Gene (https://www.ncbi.nlm.nih.gov/gene/400506#genomic-context)
  4. ^ U.S. National Library of Medicine. (n.d.). IQCK IQ motif containing K [homo sapiens (human)] - gene - NCBI. National Center for Biotechnology Information. Retrieved December 18, 2021, from https://www.ncbi.nlm.nih.gov/gene/124152
  5. ^ McNally, K. E., Faulkner, R., Steinberg, F., Gallon, M., Ghai, R., Pim, D., Langton, P., Pearson, N., Danson, C. M., Nägele, H., Morris, L. L., Singla, A., Overlee, B. L., Heesom, K. J., Sessions, R., Banks, L., Collins, B. M., Berger, I., Billadeau, D. D., Burstein, E., … Cullen, P. J. (2017). Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling. Nature cell biology, 19(10), 1214–1225. https://doi.org/10.1038/ncb3610
  6. ^ NCBI GEO (https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS596:213235_at)
  7. ^ NCBI GEO (https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS596:213235_at)
  8. ^ NCBI RNA-seq data (https://www.ncbi.nlm.nih.gov/gene/400506#genomic-context)
  9. ^ TimeTree (http://www.timetree.org/)
  10. ^ NCBI BLAST
  11. ^ Grasberger, H., & Bell, G. I. (2005). Subcellular recruitment by TSG118 and TSPYL implicates a role for zinc finger protein 106 in a novel Developmental pathway. The International Journal of Biochemistry & Cell Biology, 37(7), 1421–1437. https://doi.org/10.1016/j.biocel.2005.01.013
  12. ^ NCBI Protein (https://www.ncbi.nlm.nih.gov/protein/1143077058)
  13. ^ NCBI KNOP1 Isoform B (https://www.ncbi.nlm.nih.gov/protein/1142736531)
  14. ^ NCBI KNOP1 Isoform C (https://www.ncbi.nlm.nih.gov/protein/NP_001335461.1)
  15. ^ Expasy-Compute pI/Mw (https://web.expasy.org/compute_pi/)
  16. ^ Statistical Analysis of Protein Sequences (https://www.ebi.ac.uk/Tools/seqstats/saps/)
  17. ^ Motif Scan (https://myhits.sib.swiss/cgi-bin/motif_scan)
  18. ^ UniProt (https://www.uniprot.org/uniprot/Q1ED39)
  19. ^ Larsson, M., Brundell, E., Jörgensen, P. M., Ståhl, S., & Höög, C. (1999). Characterization of a novel nucleolar protein that transiently associates with the condensed chromosomes in mitotic cells. European journal of cell biology, 78(6), 382-390.
  20. ^ ProSite (https://prosite.expasy.org/cgi-bin/prosite/mydomains/)
  21. ^ MOTIF Search (https://www.genome.jp/tools/motif/)
  22. ^ DUF5595 (https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam18077)
  23. ^ SMAP (https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam15477)
  24. ^ String Protein-Protein Interaction Networks(https://string-db.org/cgi/network?taskId=bKzRFr03O9Lu&sessionId=b92QrR5MM6wa)
  25. ^ Grasberger, H., & Bell, G. I. (2005). Subcellular recruitment by TSG118 and TSPYL implicates a role for zinc finger protein 106 in a novel developmental pathway. The international journal of biochemistry & cell biology, 37(7), 1421–1437. https://doi.org/10.1016/j.biocel.2005.01.013
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