RTL6

File:RTL6 gene neighborhood.gifThe gene is on Chromosome 22 (human) at 22q13.31 on the minus strand from 44492570 to 44498125 nt on the GRCh38.p7 assembly of the human genome. Aliases for the gene include LDOC1L, MAR6, MART6, and SIRH3. RTL6 is made up of 2 exons and is encoded by 5556 base pairs of DNA .{{Cite web|url=https://www.ncbi.nlm.nih.gov/gene/84247|title=LDOC1L LDOC1 like [Homo sapiens (human)] - Gene - NCBI|website=www.ncbi.nlm.nih.gov|access-date=2017-02-05}}

RTL6 is a retrotransposon GAG related gene. It is one of eleven MART (Mammalian Retrotransposon Derived) genes in humans related to Sushi-like retrotransposons with long terminal repeats from fish and amphibians. Between 170 and 310 MYA, MART genes lost their ability to retrotranspose and concomitantly gained new, beneficial function for its host organism.{{cite journal | vauthors = Brandt J, Veith AM, Volff JN | title = A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes | journal = Cytogenetic and Genome Research | volume = 110 | issue = 1–4 | pages = 307–17 | date = 2005-01-01 | pmid = 16093683 | doi = 10.1159/000084963 | s2cid = 38398479 }}

RTL6 has an alternate start of transcription 140 base pairs upstream of the normal transcribed region. The lengths of the primary mRNA and that with the upstream start of transcription are 5355 and 5495 base pairs respectively.

The primary amino acid sequence for RTL6 is made up of 239 residues. There are no known alternative splice variants of the protein. The molecular weight of the protein is 26.2 kDa and the isoelectric point is 11.58.Brendel, V., Bucher, P., Nourbakhsh, I.R., Blaisdell, B.E. & Karlin, S. (1992) "Methods and algorithms for statistical analysis of protein sequences" Proc. Natl. Acad. Sci. U.S.A. 89, 2002-2006. RTL6 is a proline and arginine rich protein.File:LDOC1L.jpg]]

RTL6 contains a predicted leucine zipper motif known to participate in nucleic acid binding in other proteins. RTL6 also contains a domain of unknown function from amino acid residues 98-177 . RTL6 is one of a number of genes belonging to the DUF4939 (domain of unknown function) superfamily.{{Cite web|url=https://www.uniprot.org/uniprot/Q6ICC9|title=LDOC1L - Protein LDOC1L - Homo sapiens (Human) - LDOC1L gene & protein|website=www.uniprot.org|language=en|access-date=2017-05-07}}

The secondary structure of RTL6 is made up of largely alpha helices.Garnier, Gibrat, and Robson, Meth. Enzymol., R.F. Doolittle ed. (1996) 266:97-120 One region of RTL6 is also predicted to participate in a coiled-coil structure from amino acid residues 29–63.

There are also two predicted phosphorylation sites for Protein Kinase C with high confidence scores at amino acid residues 6 and 45.{{Cite web|url=http://myhits.isb-sib.ch/cgi-bin/motif_scan|title=Motif Scan|website=myhits.isb-sib.ch|language=en|access-date=2017-05-02}}{{cite journal | vauthors = Blom N, Gammeltoft S, Brunak S | title = Sequence and structure-based prediction of eukaryotic protein phosphorylation sites | journal = Journal of Molecular Biology | volume = 294 | issue = 5 | pages = 1351–62 | date = December 1999 | pmid = 10600390 | doi = 10.1006/jmbi.1999.3310 }} There is also a predicted ubiquitination site with medium-confidence at amino acid residue 8.{{cite journal | vauthors = Radivojac P, Vacic V, Haynes C, Cocklin RR, Mohan A, Heyen JW, Goebl MG, Iakoucheva LM | title = Identification, analysis, and prediction of protein ubiquitination sites | journal = Proteins | volume = 78 | issue = 2 | pages = 365–80 | date = February 2010 | pmid = 19722269 | pmc = 3006176 | doi = 10.1002/prot.22555 }}

File:LDOC1L Protein Annotation.png

RTL6 is expected to be localized to the nucleus and cytosol based on the presence of a leucine zipper domain, the absence of signals indicating secretion or transmembrane domains, and immunohistochemical staining.{{Cite web|url=http://www.genscript.com/psort.html|title=PSORT: Protein Subcellular Localization Prediction Tool|website=www.genscript.com|access-date=2017-05-02}}{{cite journal | vauthors = Lin WZ, Fang JA, Xiao X, Chou KC | title = iLoc-Animal: a multi-label learning classifier for predicting subcellular localization of animal proteins | language = en | journal = Molecular BioSystems | volume = 9 | issue = 4 | pages = 634–44 | date = April 2013 | pmid = 23370050 | doi = 10.1039/c3mb25466f }}{{Cite web|url=https://blast.ncbi.nlm.nih.gov/Blast.cgi|title=BLAST: Basic Local Alignment Search Tool|website=blast.ncbi.nlm.nih.gov|access-date=2017-02-19}}

RTL6 has been shown to be expressed at high levels during all stages of development and in a wide variety of tissues.{{Cite web|url=http://mouse.brain-map.org/gene/show/85967|title=Gene Detail :: Allen Brain Atlas: Mouse Brain|website=mouse.brain-map.org|access-date=2017-05-02}}{{Cite web|url=https://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=258347&TAXID=10090&SEARCH=LDOC1L|title=Leucine zipper, down-regulated in cancer 1-like (Ldoc1l)|website=www.ncbi.nlm.nih.gov|access-date=2017-05-02}}

RTL6 expression has been shown to fall in HeLa cervical cancer cells upon treatment with chemotherapeutic Casiopeinas and in A549 lung cancer cells upon treatment with Actinomycin D.{{cite journal | vauthors = Serment-Guerrero J, Cano-Sanchez P, Reyes-Perez E, Velazquez-Garcia F, Bravo-Gomez ME, Ruiz-Azuara L | title = Genotoxicity of the copper antineoplastic coordination complexes casiopeinas | journal = Toxicology in Vitro | volume = 25 | issue = 7 | pages = 1376–84 | date = October 2011 | pmid = 21601632 | doi = 10.1016/j.tiv.2011.05.008 }}{{cite journal | vauthors = Capranico G, Binaschi M | title = DNA sequence selectivity of topoisomerases and topoisomerase poisons | journal = Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression | volume = 1400 | issue = 1–3 | pages = 185–94 | date = October 1998 | pmid = 9748568 | doi = 10.1016/S0167-4781(98)00135-3 }}

RTL6 has been shown to interact with the following proteins:

The RTL6 protein has been shown to interact with the UXAC protein from Yersinia pestis, the gram-negative bacterium responsible for the bubonic plague.

Eleven paralogs were identified for RTL6 in humans. The paralogs have diverse functions and expression patterns, although many are known to have zinc finger domains and bind nucleic acids:

RTL6 is highly conserved across mammals, including the leucine zipper motif and DUF4939. The gene is also conserved in marsupials such as the opossum but not in birds such as the chicken, suggesting the gene was likely formed after the divergence of mammals and birds but before the divergence of marsupials and mammals (170-310 MYA:{{cite journal | vauthors = Brandt J, Schrauth S, Veith AM, Froschauer A, Haneke T, Schultheis C, Gessler M, Leimeister C, Volff JN | title = Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals | journal = Gene | volume = 345 | issue = 1 | pages = 101–11 | date = January 2005 | pmid = 15716091 | doi = 10.1016/j.gene.2004.11.022 }}

The most distantly detectable organisms with homology in the gene are bony fishes including salmon and the common carp, but similarity to the human protein sequence is markedly less than that of mammals. No traces of the gene can be seen in intermediates between mammals and bony fishes such as reptiles or amphibians:

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Category:Human proteins