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==== Interactions ====
==== Interactions ====
Proteins shown to interact with TMEM261 include [http://www.genecards.org/cgi-bin/carddisp.pl?gene=NAAA NAAA], [http://www.genecards.org/cgi-bin/carddisp.pl?gene=QTRT1&search=d6edd4112f517825968a5a6978882712 QTRT1],[http://www.genecards.org/cgi-bin/carddisp.pl?gene=ZC4H2&search=79ba8f7afa868106306bf83d200ba523 ZC4H2]<ref>{{cite journal|last1=Dash|first1=A et al.|title=Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimens.|journal=Am J Pathol.|date=2002|volume=161|issue=5|pages=1743-1748|doi=10.1016/S0002-9440(10)64451-3|url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1850797/}}</ref> and [http://www.genecards.org/cgi-bin/carddisp.pl?gene=ZNF454&search=68835d4da3192d71bcf7818742536191 ZNF454]<ref>{{cite journal|last1=Rovillain|first1=E et al.|title=An RNA interference screen for identifying downstream effectors of the p53 and pRB tumour suppressor pathways involved in senescence.|journal=BMC Genomics.|date=2011|volume=12|issue=355|doi=10.1186/1471-2164-12-355|pmid=21740549|url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161017/}}</ref><ref>{{cite web|title=c9orf123 protein (Homo Sapiens)- STRING Network View|url=http://string-db.org/newstring_cgi/show_input_page.pl?UserId=65EMVhw9LAhY&sessionId=N5_gHtjz1Wbz|website=STRING - Known and Predicted Protein-Protein Interactions}}</ref>. It has also shown to interact with [http://www.genecards.org/cgi-bin/carddisp.pl?gene=APP APP],[http://www.genecards.org/cgi-bin/carddisp.pl?gene=ARHGEF38&search=1bcacaca34542f4b438e308c6b02cfd2 ARHGEF38] and [http://www.genecards.org/cgi-bin/carddisp.pl?gene=HNRNPD&search=c4b9dd1c49f01a5dfb3c401f24182f32 HNRNPD]<ref>{{cite web|title=9ORF123 chromosome 9 open reading frame 123|url=http://thebiogrid.org/124777/summary/homo-sapiens/c9orf123.html|website=BioGRID: Database of Protein and Genetic Interactions|publisher=TyersLab}}</ref>. These proteins are involved with TMEM261 through a variety of interactions; [[Protein–protein interaction|protein-protein]], RNA-protein and DNA-protein.
Proteins shown to interact with TMEM261 include [http://www.genecards.org/cgi-bin/carddisp.pl?gene=NAAA NAAA], [http://www.genecards.org/cgi-bin/carddisp.pl?gene=QTRT1&search=d6edd4112f517825968a5a6978882712 QTRT1],[http://www.genecards.org/cgi-bin/carddisp.pl?gene=ZC4H2&search=79ba8f7afa868106306bf83d200ba523 ZC4H2]<ref>{{cite journal|last1=Dash|first1=A et al.|title=Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimens.|journal=Am J Pathol.|date=2002|volume=161|issue=5|pages=1743-1748|doi=10.1016/S0002-9440(10)64451-3|url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1850797/}}</ref> and [http://www.genecards.org/cgi-bin/carddisp.pl?gene=ZNF454&search=68835d4da3192d71bcf7818742536191 ZNF454]<ref>{{cite journal|last1=Rovillain|first1=E et al.|title=An RNA interference screen for identifying downstream effectors of the p53 and pRB tumour suppressor pathways involved in senescence.|journal=BMC Genomics.|date=2011|volume=12|issue=355|doi=10.1186/1471-2164-12-355|pmid=21740549|url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161017/}}</ref><ref>{{cite web|title=c9orf123 protein (Homo Sapiens)- STRING Network View|url=http://string-db.org/newstring_cgi/show_input_page.pl?UserId=65EMVhw9LAhY&sessionId=N5_gHtjz1Wbz|website=STRING - Known and Predicted Protein-Protein Interactions}}</ref>. It has also shown to interact with [http://www.genecards.org/cgi-bin/carddisp.pl?gene=APP APP]<ref>{{cite journal|last1=Oláh|first1=J et al.|title=Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein.|journal=J Biol Chem.|date=2011|volume=286|issue=39|pages=34088-34100|doi=10.1074/jbc.M111.243907|url=http://www.jbc.org/content/286/39/34088.long}}</ref>,[http://www.genecards.org/cgi-bin/carddisp.pl?gene=ARHGEF38&search=1bcacaca34542f4b438e308c6b02cfd2 ARHGEF38]<ref>{{cite journal|last1=Huttlin|first1=E L et al.|title=High-Throughput Proteomic Mapping of Human Interaction Networks via Affinity-Purification Mass Spectrometry (Pre-Publication)|journal=Pre-Publication|date=2014|url=http://thebiogrid.org/166968/publication/high-throughput-proteomic-mapping-of-human-interaction-networks-via-affinity-purification-mass-spectrometry.html}}</ref> and [http://www.genecards.org/cgi-bin/carddisp.pl?gene=HNRNPD&search=c4b9dd1c49f01a5dfb3c401f24182f32 HNRNPD]<ref>{{cite journal|last1=Lehner|first1=B|last2=Sanderson|first2=C M|title=A protein interaction framework for human mRNA degradation.|journal=Genome Res.|date=2004|volume=14|issue=7|pages=1315-1323|doi=10.1101/gr.2122004|pmid=15231747|url=http://genome.cshlp.org/content/14/7/1315.long}}</ref><ref>{{cite web|title=9ORF123 chromosome 9 open reading frame 123|url=http://thebiogrid.org/124777/summary/homo-sapiens/c9orf123.html|website=BioGRID: Database of Protein and Genetic Interactions|publisher=TyersLab}}</ref>. These proteins are involved with TMEM261 through a variety of interactions; [[Protein–protein interaction|protein-protein]], RNA-protein and DNA-protein.


==Expression==
==Expression==

Revision as of 01:08, 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[18],ARHGEF38[19] and HNRNPD[20][21]. 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[22]. However, its expression is highest in the gall bladder, urinary bladder[23], pituitary gland, parathyroid and acites[22]. Staining intensity of cancer cells showed intermediate to high expression in breast, colorectal, ovarian, skin, urothelial head and neck cells. [23].TMEM261 and it's locus has been associated with colorectal cancer[24], breast cancer[25] and lymphomas[26][27] 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[28] which diverged from Homo sapiens 462.5 million years ago. [29]. 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][30][28]

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. ^ Oláh, J; et al. (2011). "Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein". J Biol Chem. 286 (39): 34088–34100. doi:10.1074/jbc.M111.243907. {{cite journal}}: Explicit use of et al. in: |first1= (help)CS1 maint: unflagged free DOI (link)
  19. ^ Huttlin, E L; et al. (2014). "High-Throughput Proteomic Mapping of Human Interaction Networks via Affinity-Purification Mass Spectrometry (Pre-Publication)". Pre-Publication. {{cite journal}}: Explicit use of et al. in: |first1= (help)
  20. ^ Lehner, B; Sanderson, C M (2004). "A protein interaction framework for human mRNA degradation". Genome Res. 14 (7): 1315–1323. doi:10.1101/gr.2122004. PMID 15231747.
  21. ^ "9ORF123 chromosome 9 open reading frame 123". BioGRID: Database of Protein and Genetic Interactions. TyersLab.
  22. ^ a b "EST profile: TMEM261". UniGene. National Library of Medicine.
  23. ^ a b "The Human Protein Atlas:TMEM261".
  24. ^ 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.
  25. ^ 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.
  26. ^ 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)
  27. ^ 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)
  28. ^ a b "NCBI BLAST:Basic Local Alignment Search Tool".
  29. ^ 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)
  30. ^ 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)
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