User:Olso5610/sandbox

Summary

TMEM260 is a human gene encoding a transmembrane protein of uncharacterized function. TMEM260 is conserved in primates, other mammals, birds, reptiles, and fish. The gene contains a domain, DUF2723, conserved in bacteria and contains ten transmembrane regions.

Gene

TMEM260 is located on chromosome 14 on the q arm at 22.3. It begins at 56,955,072bp from pter and ends at 57,117,324bp pter. The encoded protein is 4,278bp long and 707 amino acids. Aliases include C14orf101, FLJ20392 (clone), and UPF0679 protein C14orf101.

Other genes in the neighborhood of TMEM260 include OTX2, PELI2, RPL36A1 a ribosomal protein, and LINC00520 a long intergenic non-protein coding RNA.

Homology

Orthologs of TMEM260 are found mainly in primates and other mammals such as the elephant and domestic dog. Homologs were identified in reptiles, birds,and fish. no orthologs were identified in invertebrates or drosophila. There are no paralogs of TMEM260. The 3'UTR especially was shown to be conserved. The 5'UTR was only conserved in primates.

Multiple sequence alignment of TMEM260 and select orthologs. Shaded to highlight amino acid conservation.

In the protein sequence, Valine 174, Threonine 313, and Serine 566 were all found to be unique to humans.

Protein

Primary Sequence

Using the program AceView , 13 splice variants were identified to make proteins other than TMEM260. None are experimentally confirmed. AceView also concluded that TMEM260 was produced at 2.2 times the avergage in comparison to the splice variants.

Post-Translational Modifications

In comparison to normal proteins, TMEM260 is pretty insignificant. 22 phosphorylation sites were identified with NetPhos : 14 Serines, 3 Threonines, 5 Tyrosines. NetNGlyc predicted four glycosylated asparagines; found at positions 318, 407, 535, 568. Only one acetylation site, with a score of 0.513, was identified at amino acid 2.

Secondary Structure

TMEM260 was identified to have mainly an α-helix secondary structure with few and small β-sheets using the PSIPRED server.

3° and 4° Structure

Using PHYRE2, similarly structure protein were found. Ranging from amino acids 19-441, PHYRE2 provided an oligosaccharyltransferase protein with 99.4% confidence. Another similar protein structure was found for amino acids 614-696. It was identified to be a tetratricopeptide repeat with a 51.3% confidence.

File:TMEM260 Structure Prediction - Oligosaccharide Transferase.png Oligosaccharide transferase structure predicted for amino acids 19-441

File:TMEM260 Structure Prediction - Tetratricopeptide.png Tetratricopeptide repeat structure predicted for amino acids 614-696

Expression

Attributed by multiple expression maps, TMEM260 is expressed at fairly high levels throughout the body; averaging around the 70 percentile. Expression in current studies is associated with genes in the neighborhood, such as OTX2.

A full gene expression of TMEM260 tested in multiple tissue types.

Biochemistry and Function

Interacting Proteins

Currently no proteins have been identified and confirmed to interact with TMEM260.

Clinical Significance

Altered expression of TMEM260 has been found in studies of medulloblastomas and ovarian carcinomas. However, no single mutation or set of mutations has been linked to any specific disease at the present.