Jump to content

User:IChindris/sandbox: Difference between revisions

From Wikipedia, the free encyclopedia
Browse history interactively
← Previous editNext edit →
Content deleted Content added
VisualWikitext
IChindris (talk | contribs)
197 edits
IChindris (talk | contribs)
197 edits
Line 29: Line 29:
==Evolution==
==Evolution==
==== Orthologues ====
==== Orthologues ====
TMEM261 shows conservation in [[vertebrates]] with higher overall conservation of its [[Protein primary structure|primary structure]] in [[mammals]]. High conservation in orthologues, including distant homologues, is seen from the [[domain of unknown function]] (DUF4536) to the [[C-terminus]] region, as the [[N-terminus]] reigon is only conserved highly in mammalian orthologues. The [[Protein secondary structure|secondary structure]] of TMEM261 shows conservation across most orthologues.<ref name = "SDSC Biology ">{{cite web|title= ClustalW|url=http://workbench.sdsc.edu/}}</ref><ref>{{cite journal|last1=Thompson|first1=Julie D|last2=Higgins|first2=Desmond G|last3=Gibson|first3=Toby J|title=CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.|journal=Nucleic Acids Res|date=1994|volume=22|issue=22|pages=4673–4680.|pmid=308517|url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308517/}}</ref><ref name = "NCBI BLAST">{{cite web|title= NCBI BLAST:Basic Local Alignment Search Tool|url=http://blast.ncbi.nlm.nih.gov/Blast.cgi}}</ref>
TMEM261 has [[orthologues]] and [[homologues]] limited to [[vertebrates]], it's oldest homologue dates to that of the [[cartilaginous fishes]]<ref name = "NCBI BLAST">{{cite web|title= NCBI BLAST:Basic Local Alignment Search Tool|url=http://blast.ncbi.nlm.nih.gov/Blast.cgi}}</ref> which diverged from [[Homo sapiens]] 462.5 million years ago. <ref>{{cite journal|last1=Hedges|first1=S. Blaire|last2=Dudley|first2=Joel|last3=Kumar|first3=Sudhir|title=TimeTree: a public knowledge-base of divergence times among organisms|date=22 September 2006|volume=22|issue=23|pages=2971–2972|doi=10.1093/bioinformatics/btl505|url=http://kumarlab.net/pdf_new/HedgesKumar06.pdf|}}</ref>. The [[Protein primary structure|primary structure]] of TMEM261 shows higher overall conservation in [[mammals]], however high conservation of the [[domain of unknown function]] (DUF4536) to the [[C-terminus]] region is seen in all orthologues, including distant homologues. The [[Protein secondary structure|secondary structure]] of TMEM261 shows conservation across most orthologues.<ref name = "SDSC Biology ">{{cite web|title= ClustalW|url=http://workbench.sdsc.edu/}}</ref><ref>{{cite journal|last1=Thompson|first1=Julie D|last2=Higgins|first2=Desmond G|last3=Gibson|first3=Toby J|title=CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.|journal=Nucleic Acids Res|date=1994|volume=22|issue=22|pages=4673–4680.|pmid=308517|url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308517/}}</ref><ref name = "NCBI BLAST">{{cite web|title= NCBI BLAST:Basic Local Alignment Search Tool|url=http://blast.ncbi.nlm.nih.gov/Blast.cgi}}</ref>
{| class="wikitable"
{| class="wikitable"
|-
|-

Revision as of 00:59, 29 April 2015

TMEM261
Transmembrane protein 261 is a protein that in humans is encoded by the TMEM261 gene located on chromosome 9[1]. TMEM261 is also known as C9ORF123, Chromosome 9 Open Reading Frame 123 and Transmembrane Protein C9orf123[2].

Gene Features


TMEM261 is located at 9p24.1,its length is 91,891 base pairs (bp) on the reverse strand.[2]Its neighbouring gene is PTPRD located at 9p23-p24.3 also on the reverse strand and encodes protein tyrosine phosphatase receptor type delta.[1][2] TMEM261 has a contains 2 exons and 1 intron, and 6 transcript variants, the largest consisting of 742bp with a protein 129 amino acids (aa) in length and 13,500 Daltons (Da) in size, and the smallest coding transcript variant being 381bp with a protein 69aa long and 6,100 Da in size.[3][4].

Protein Features

The coding variant of TMEM261 is a protein of 112aa with a molecular weight of 12,300 Da.[5] The isoelectric is predicted to be 10.2Cite error: The <ref> tag has too many names (see the help page)., whilst it's posttranslational modification value is 9.9[4].

Structure

Annotated features of TMEM261 protein including topology and important sites for phosphorylation and Myristoylation as well DUF4536 and transmembrane helical domains.

TMEM261 contains a domain of unknown function, DUF4536 (pfam15055), predicted as a helical membrane spanning domain about 45aa (47-92) in length with no known domain relationships.[6][7] Two further transmembrane helical domains are predicted of lengths 18aa (52-69) and 23aa (81-102)Cite error: The <ref> tag has too many names (see the help page)..There is also a low complexity region spanning 25aa (14-39).[8] The tertiary structure for TMEM261 has not yet been determined, however it's secondary structure is mostly composed of coiled-coils regions with beta strands and alpha helices in the transmembrane and domain of unknown function reigons. The N-terminal region of TMEM261 is composed of a disordered region[9] [10] which contains the low complexity region[8] which is not highly conserved amongst orthologues[11][12].

Modifications

Some proteins found to interact with TMEM261

A N-myristoylation domain is believed to be present in some TMEM261 protein variants.[4] Post-translational modifications include myristoylation of the N-terminal Glycine residue[4][13] of the TMEM261 protein as well as phosphorylation of Threonine 31.[14]

Interactions

Proteins shown to interact with TMEM261 include NAAA, QTRT1,ZC4H2[15] and ZNF454[16][17]. It has also shown to interact with APP,ARHGEF38 and HNRNPD[18]. These proteins are involved with TMEM261 through a variety of interactions; protein-protein, RNA-protein and DNA-protein.

Expression

TMEM261 shows ubiquitous expression in humans detected in almost all tissue types in humans[19]. However, its expression is highest in the gall bladder, urinary bladder[20], pituitary gland, parathyroid and acites[19]. Staining intensity of cancer cells showed intermediate to high expression in breast, colorectal, ovarian, skin, urothelial head and neck cells. [20].TMEM261 and it's locus has been associated with colorectal cancer[21], breast cancer[22] and lymphomas[23][24] relating to gene amplification and rearrangements.

Evolution

Orthologues

TMEM261 has orthologues and homologues limited to vertebrates, it's oldest homologue dates to that of the cartilaginous fishes[25] which diverged from Homo sapiens 462.5 million years ago. [26]. The primary structure of TMEM261 shows higher overall conservation in mammals, however high conservation of the domain of unknown function (DUF4536) to the C-terminus region is seen in all orthologues, including distant homologues. The secondary structure of TMEM261 shows conservation across most orthologues.[11][27][25]

Organism Scientific Name Accession Number Date of Divergence from Humans (million years) Amino acids (bp) Identity (%) Class
Humans Homo sapiens NP_219500.1 0 112 100 Mammalia
Gorilla Gorilla gorilla XP_004047847.1 8.8 112 99 Mammalia
Olive Baboon Papio anubis XP_003911767.1 29 112 84 Mammalia
Sunda Flying Lemur Galeopterus variegatus XP_008587957.1 81.5 112 68 Mammalia
Lesser Egyptian Jerboa Jaculus Jaculus XP_004653029.1 92.3 109 56 Mammalia
Naked Mole Rat Heterocephalus glaber XP_004898193.1 92.3 114 45 Mammalia
White Rhinoceros Ceratotherium simum simum XP_004436891.1 94.2 112 66 Mammalia
Nine-banded armadillo Dasypus novemcinctus XP_004459147.1 104.4 112 59 Mammalia
Green Sea Turtle Chelonia mydas XP_007056940.1 296 85 49 Reptilia
Zebra Finch Taeniopygia Guttata XP_002187613.2 296 72 47 Aves
Western Clawed Frog Xenopus tropicalis XP_002943025.1 371.2 85 45 Amphibia
Haplochromis burtoni Haplochromis burtoni XP_005928614.1 400.1 91 51 Actinopterygii
Australian Ghost Shark Callorhinchus milii XP_007884223.1 426.5 86 43 Chondrichthyes

Paralogues

TMEM261 has no known paralogs.

References

  1. ^ a b "Entrez Protein: TMEM261".
  2. ^ a b c "GeneCards:TMEM261 Gene". Cite error: The named reference "GeneCards" was defined multiple times with different content (see the help page).
  3. ^ Thierry-Mieg, D; Thierry-Mieg, J. (2006). "AceView: a comprehensive cDNA-supported gene and transcripts annotation". Genome Biology. 7 (Suppl 1): S12. doi:10.1186/gb-2006-7-s1-s12. PMC 1810549. PMID 16925834.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  4. ^ a b c d "AceView:Homo sapiens gene C9orf123".
  5. ^ "Ensemble:Transcript TMEM261-003".
  6. ^ "NCBI Conserved Domains: DUF4536".
  7. ^ "EMBL-EBI Interpro: Transmembrane protein 261 (Q96GE9)".
  8. ^ a b "Vega: Transcript: C9orf123-003".
  9. ^ "Protein structure prediction on the web: a case study using the Phyre server". PHYRE: Protein Homology/analogY Recognition Engin.
  10. ^ Kelley, LA (2009). "Stenberg". MJE. 4: 363–371. doi:10.1038/nprot.2009.2. PMID 19247286.
  11. ^ a b "ClustalW".
  12. ^ Thompson, Julie D; Higgins, Desmond G; Gibson, Toby J (1994). "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice". Nucleic Acids Res. 22 (22): 4673–4680. PMID 308517.
  13. ^ Gallo, Vincenzo. "Myristoylation : Proteins Post-translational Modifications". http://flipper.diff.org/. University of Turin. {{cite web}}: External link in |website= (help)
  14. ^ "Nextprot:TMEM261 » Transmembrane protein 261".
  15. ^ Dash, A; et al. (2002). "Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimens". Am J Pathol. 161 (5): 1743–1748. doi:10.1016/S0002-9440(10)64451-3. {{cite journal}}: Explicit use of et al. in: |first1= (help)
  16. ^ Rovillain, E; et al. (2011). "An RNA interference screen for identifying downstream effectors of the p53 and pRB tumour suppressor pathways involved in senescence". BMC Genomics. 12 (355). doi:10.1186/1471-2164-12-355. PMID 21740549. {{cite journal}}: Explicit use of et al. in: |first1= (help)CS1 maint: unflagged free DOI (link)
  17. ^ "c9orf123 protein (Homo Sapiens)- STRING Network View". STRING - Known and Predicted Protein-Protein Interactions.
  18. ^ "9ORF123 chromosome 9 open reading frame 123". BioGRID: Database of Protein and Genetic Interactions. TyersLab.
  19. ^ a b "EST profile: TMEM261". UniGene. National Library of Medicine.
  20. ^ a b "The Human Protein Atlas:TMEM261".
  21. ^ Gaspar, C (2008). "Cross-Species Comparison of Human and Mouse Intestinal Polyps Reveals Conserved Mechanisms in Adenomatous Polyposis Coli (APC)-Driven Tumorigenesis". Am J Pathol. 172 (5): 1363–1380. doi:10.2353/ajpath.2008.070851. PMID 18403596.
  22. ^ Wu, J (2012). "Identification and functional analysis of 9p24 amplified genes in human breast cancer". Oncogene. 31 (3): 333–341. doi:10.1038/onc.2011.227. PMID 21666724.
  23. ^ Twa, D D W; et al. (2014). "Genomic Rearrangements Involving Programmed Death Ligands Are Recurrent in Primary Mediastinal Large B-Cell Lymphoma". Blood. 123 (13): 2062–2065. doi:10.1182/blood-2013-10-535443. PMID 24497532. {{cite journal}}: Explicit use of et al. in: |first1= (help)
  24. ^ Green, M R; et al. (2010). "Integrative Analysis Reveals Selective 9p24.1 Amplification, Increased PD-1 Ligand Expression, and Further Induction via JAK2 in Nodular Sclerosing Hodgkin Lymphoma and Primary Mediastinal Large B-Cell Lymphoma". Blood. 116 (17): 3268–3277. doi:10.1182/blood-2010-05-282780. PMID 20628145. {{cite journal}}: Explicit use of et al. in: |first1= (help)
  25. ^ a b "NCBI BLAST:Basic Local Alignment Search Tool".
  26. ^ Hedges, S. Blaire; Dudley, Joel; Kumar, Sudhir (22 September 2006). "TimeTree: a public knowledge-base of divergence times among organisms" (PDF). 22 (23): 2971–2972. doi:10.1093/bioinformatics/btl505. {{cite journal}}: Cite has empty unknown parameter: |1= (help); Cite journal requires |journal= (help)
  27. ^ Thompson, Julie D; Higgins, Desmond G; Gibson, Toby J (1994). "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice". Nucleic Acids Res. 22 (22): 4673–4680. PMID 308517.

Further Reading

  • Nicholas K. Tonks (2006). "Protein tyrosine phosphatases: from genes, to function, to disease". Cancer Cell. 7: 833–846. doi:10.1038/nrm2039. {{cite journal}}: Unknown parameter |author-separator= ignored (help)
  • Merryweather-Clarke AT; et al. (2011). "Global gene expression analysis of human erythroid progenitors". Blood. 117 (13): e96-108. doi:10.1182/blood-2010-07-290825. PMID 21270440. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |author-separator= ignored (help)
  • Welch JJ, Watts JA, Vakoc CR; et al. (2004). "Global regulation of erythroid gene expression by transcription factor GATA-1". Blood. 104 (10): 3136–3147. doi:10.1182/blood-2004-04-1603. PMID 15297311. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |author-separator= ignored (help)CS1 maint: multiple names: authors list (link)
  • Nickeleit I; et al. (2008). "Argyrin a reveals a critical role for the tumor suppressor protein p27(kip1) in mediating antitumor activities in response to proteasome inhibition". Cancer Cell. 14 (1): 23–35. doi:10.1016/j.ccr.2008.05.016. PMID 18598941. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |author-separator= ignored (help)
Retrieved from "https://en.wikipedia.org/enwiki/w/index.php?title=User:IChindris/sandbox&oldid=659781108"