Protein or peptide name Chromosome Protein or peptide start site Protein or peptide end site Noncoding RNA start site Noncoding RNA end site Protein or peptide sequence Protein or peptide length Noncoding RNA type Noncoding RNA name Experimental species Experimental techniques Experimental samples (cell line and/or tissue) Description Subcellular location Function Throughput Title of paper PubMed ID Year of publication EntreZ id miPEP160a 2 16339947 16340018 MFCLLIPIFSFVFSPNRHLRLQEQ 24aa pri-miRNA pri-miR160a Arabidopsis thaliana Fluorescence microscopy/Western blotting/Immunoblots Arabidopsis thaliana Five other pri-miRNAs of A. thaliana and M. truncatula encode active miPEPs, suggesting that miPEPs are widespread throughout the plant kingdom. Synthetic miPEP171b and miPEP165a peptides applied to plants specifically trigger the accumulation of miR171b and miR165a, leading to reduction of lateral root development and stimulation of main root growth, respectively, suggesting that miPEPs might have agronomical applications. low Primary transcripts of microRNAs encode regulatory peptides 25807486 2015 miPEP164a 2 19520555 19520665 19520517 19521033 MPSWHGMVLLPYVKHTHASTHTHTHNIYGCACELVFH 37aa pri-miRNA pri-miR164a Arabidopsis thaliana Fluorescence microscopy/Western blotting/Immunoblots Arabidopsis thaliana Five other pri-miRNAs of A. thaliana and M. truncatula encode active miPEPs, suggesting that miPEPs are widespread throughout the plant kingdom. Synthetic miPEP171b and miPEP165a peptides applied to plants specifically trigger the accumulation of miR171b and miR165a, leading to reduction of lateral root development and stimulation of main root growth, respectively, suggesting that miPEPs might have agronomical applications. low Primary transcripts of microRNAs encode regulatory peptides 25807486 2015 miPEP165a 1 79004 79057 MRVKLFQLRGMLSGSRIL 18aa pri-miRNA pri-miR165a Arabidopsis thaliana Fluorescence microscopy/Western blotting/Immunoblots Arabidopsis thaliana The primiR171b of Medicago truncatula and the pri-miR165a of Arabidopsis thaliana produce peptides, which we term miPEP171b and miPEP165a, respectively, that enhance the accumulation of their corresponding mature miRNAs, resulting in downregulation of target genes involved in root development. Synthetic miPEP171b and miPEP165a peptides applied to plants specifically trigger the accumulation of miR171b and miR165a, leading to reduction of lateral root development and stimulation of main root growth, respectively, suggesting that miPEPs might have agronomical applications. low Primary transcripts of microRNAs encode regulatory peptides 25807486 2015 miPEP169d 1 MVKESFMERLKVR 13aa pri-miRNA pri-miR169d Arabidopsis thaliana Fluorescence microscopy/Western blotting/Immunoblots Arabidopsis thaliana Five other pri-miRNAs of A. thaliana and M. truncatula encode active miPEPs, suggesting that miPEPs are widespread throughout the plant kingdom. Synthetic miPEP171b and miPEP165a peptides applied to plants specifically trigger the accumulation of miR171b and miR165a, leading to reduction of lateral root development and stimulation of main root growth, respectively, suggesting that miPEPs might have agronomical applications. low Primary transcripts of microRNAs encode regulatory peptides 25807486 2015 miPEP171b 1 3961210 3961703 MLLHRLSKFCKIERDIVYIS 20aa pri-miRNA pri-miR171b Arabidopsis thaliana Fluorescence microscopy/Western blotting/Immunoblots Arabidopsis thaliana The primiR171b of Medicago truncatula and the pri-miR165a of Arabidopsis thaliana produce peptides, which we term miPEP171b and miPEP165a, respectively, that enhance the accumulation of their corresponding mature miRNAs, resulting in downregulation of target genes involved in root development. Synthetic miPEP171b and miPEP165a peptides applied to plants specifically trigger the accumulation of miR171b and miR165a, leading to reduction of lateral root development and stimulation of main root growth, respectively, suggesting that miPEPs might have agronomical applications. low Primary transcripts of microRNAs encode regulatory peptides 25807486 2015 miPEP319a 4 12352614 12352763 MNIHTYHHLLFPSLVFHQSSDVPNALSLHIHTYEYIIVVIDPFRITLAFR 50aa pri-miRNA pri-miR319a Arabidopsis thaliana Fluorescence microscopy/Western blotting/Immunoblots Arabidopsis thaliana Five other pri-miRNAs of A. thaliana and M. truncatula encode active miPEPs, suggesting that miPEPs are widespread throughout the plant kingdom. Synthetic miPEP171b and miPEP165a peptides applied to plants specifically trigger the accumulation of miR171b and miR165a, leading to reduction of lateral root development and stimulation of main root growth, respectively, suggesting that miPEPs might have agronomical applications. low Primary transcripts of microRNAs encode regulatory peptides 25807486 2015 PLS 4 18329192 18329299 18329094 18329699 MKPRLCFNFRRRSISPCYISISYLLVAKLFKLFKIH 36aa lncRNA PLS Arabidopsis thaliana Microscopy/PCR/Western blotting Arabidopsis thaliana Rapid amplification of cDNA ends PCR, RNA gel blot analysis, and RNase protection assays showed that the PLS ORF is located within a short ( approximately 500 nucleotides) auxin-inducible transcript and encodes a predicted polypeptide of 36 amino acid residues. The sPEP is required for correct auxin-cytokinin homeostasis to modulate root growth and leaf vascular patterning. low The POLARIS gene of Arabidopsis encodes a predicted peptide required for correct root growth and leaf vascular patterning 12172017 2002 3770598 ROTUNDIFOLIA4 2 15534942 15535104 15534739 15535304 MAPEENGTCEPCKTFGQKCSHVVKKQRAKFYILRRCIAMLVCWHDQNHDRKDS 53aa ncRNA ROT4 Arabidopsis thaliana RT-PCR/ in situ hybridization Arabidopsis thaliana The ROT4 open-reading frame (ORF) encodes a novel small peptide that had not been identified in the Arabidopsis genome annotation. plasma membrane Overexpression of a ROT4-green fluorescence protein (GFP) fusion protein in transgenic plants recapitulated the rot4 phenotype, suggesting that ROT4 acts to restrict cell proliferation. low Overexpression of a novel small peptide ROTUNDIFOLIA4 decreases cell proliferation and alters leaf shape in Arabidopsis thaliana 15125775 2004 2745585 CmpA subtilis str. 168 complete genome 527912 528025 527912 528025 MPNWLKKQMQKAFLEKDNYQIKLLNQCWYFYRKKHCS 37aa ncRNA cmpA Bacillus subtilis subsp. subtilis str. 168 GFP fluorescence Bacillus subtilis Here, we describe a sporulation pathway involving SpoVM and a 37-amino-acid-long protein named CmpA that is encoded by a previously un-annotated gene and is expressed under control of two sporulation-specific transcription factors (σ (E) and SpoIIID). surface of the developing spore CmpA localized to the surface of the developing spore and deletion of cmpA resulted in cells progressing through the sporulation programme more quickly. low Small proteins link coat and cortex assembly during sporulation in Bacillus subtilis 22463703 2012 37862802 MciZ subtilis str. 168 complete genome 2459141 2459263 2459141 2459263 VKVHRMPKGVVLVGKAWEIRAKLKEYGRTFQYVKDWISKP 40aa ncRNA mciZ Bacillus subtilis subsp. subtilis str. 168 Fluorescence microscopy/Western blotting Bacillus subtilis Using FtsZ as bait in a two-hybrid screen, we discovered a 40-amino acid peptide, termed MciZ, from Bacillus subtilis that appeared to interact with FtsZ. We conclude that MciZ is a previously unrecognized inhibitor of FtsZ that prevents inappropriate Z-ring formation during sporulation. low PEPTIDE INHIBITOR OF CYTOKINESIS DURING SPORULATION IN BACILLUS SUBTILIS 18284588 2008 37862900 Sda subtilis str. 168 complete genome 2647596 2647456 2647456 2647614 MRKLSDELLIESYFKATEMNLNRDFIELIENEIKRRSLGHIISVSS 46aa ncRNA sda Bacillus subtilis subsp. subtilis str. 168 X-ray Bacillus subtiiis The cytosolic 46-amino acid Sda protein, one of the best characterized small proteins, similarly inhibits the first kinase in the histidine kinase phosphorelay that regulates sporulation-specific genes in B. subtilis. The cytosolic 46-amino acid Sda protein, one of the best characterized small proteins, similarly inhibits the first kinase in the histidine kinase phosphorelay that regulates sporulation-specific genes in B. subtilis. low Structure of the sporulation histidine kinase inhibitor Sda from Bacillus subtilis and insights into its solution state 19465772 2009 2914223 SpoVM subtilis str. 168 complete genome 1655446 1655526 1655446 1655526 MKFYTIKLPKFLGGIVRAMLGSFRKD 26aa ncRNA SpoVM Bacillus subtilis subsp. subtilis str. 168 Western blotting Bacillus subtiiis The spoVM open reading frame is only 26 codons in length and is capable of encoding a polypeptide of 3 kDa. plasma membrane Because spoVM was not strongly required for the transcription of several genes expressed at late times in development, its protein product is likely to play a morphogenetic rather than a regulatory role in sporulation. low An unusually small gene required for sporulation by Bacillus subtilis 8231808 1993 937168 SidA Caulobacter crescentus NA1000 2152374 2152463 2152374 2152463 MIRVARESFALVSVIGFVWMMCTVANLVA 29aa ncRNA sidA Caulobacter vibrioides CB15 Fluorescence microscopy/Western blotting/Immunoblots Caulobacter crescentus Included in the SOS regulon is sidA (SOS-induced inhibitor of cell division A), a membrane protein of only 29 amino acids that helps to delay cell division following DNA damage, but is dispensable in undamaged cells. plasma membrane SidA does not directly disrupt the assembly or stability of the cytokinetic ring protein FtsZ, nor does it affect the recruitment of other components of the cell division machinery. low A DNA damage checkpoint in Caulobacter crescentus inhibits cell division through a direct interaction with FtsW 21685367 2011 7333332 HliR1 Synechocystis sp. PCC 6803, complete genome 1605337 1605447 1605337 1605447 MSNLIAVAFCGYFALLIILFSAKNFLVKDKTSLNLPE 37aa ncRNA hliR1 Cyanobacteria Western blotting Synechocystis sp. PCC 6803 To verify the existence of the respective μ-proteins in vivo, we selected five genes as examples to which a FLAG tag sequence was added and re-introduced them into Synechocystis sp. PCC 6803. These were the previously annotated gene ssr1169, two newly defined genes norf1 and norf4, as well as nsiR6 (nitrogen stress-induced RNA 6) and hliR1 (high light-inducible RNA 1), which originally were considered non-coding. Hence, it is tempting to speculate, that HliR1 is a membrane-bound peptide with a regulatory function on the superoxide dismutase. low Small proteins in cyanobacteria provide a paradigm for the functional analysis of the bacterial micro-proteome 27894276 2016 Norf1 Synechocystis sp. PCC 6803, complete genome 298972 298826 298972 298826 MKLLEMLQDLMQYFTEAFARVFGPSDDEYPAVGVQPFDGEILVNSTEE 48aa ncRNA norf1 Cyanobacteria Western blotting Synechocystis sp. PCC 6803 To verify the existence of the respective μ-proteins in vivo, we selected five genes as examples to which a FLAG tag sequence was added and re-introduced them into Synechocystis sp. PCC 6803. These were the previously annotated gene ssr1169, two newly defined genes norf1 and norf4, as well as nsiR6 (nitrogen stress-induced RNA 6) and hliR1 (high light-inducible RNA 1), which originally were considered non-coding. We conclude that the observed induction of norf1 in response to shifts from light exposure to darkness is under transcriptional control. low Small proteins in cyanobacteria provide a paradigm for the functional analysis of the bacterial micro-proteome 27894276 2016 Norf4 Synechocystis sp. PCC 6803, complete genome 1147885 1147980 1147885 1147980 MTADQLLMLVVLLVPGILLSALVMGSFAKGG 31aa ncRNA norf4 Cyanobacteria Western blotting Synechocystis sp. PCC 6803 To verify the existence of the respective μ-proteins in vivo, we selected five genes as examples to which a FLAG tag sequence was added and re-introduced them into Synechocystis sp. PCC 6803. These were the previously annotated gene ssr1169, two newly defined genes norf1 and norf4, as well as nsiR6 (nitrogen stress-induced RNA 6) and hliR1 (high light-inducible RNA 1), which originally were considered non-coding. Our data suggest that Norf4 is a previously unknown membrane-bound μ-protein and that the norf4 transcript may play a dual role, with a mainly coding function during nitrogen-sufficient conditions and a possibly RNAmediated regulatory function on the gap1 mRNA during nitrogen stress. low Small proteins in cyanobacteria provide a paradigm for the functional analysis of the bacterial micro-proteome 27894276 2016 NsiR6 Synechocystis sp. PCC 6803, complete genome 729173 729370 729173 729370 MSVFPAETCPVCGVTIENGSKVVFSSGPAGTRARLWARVCNFARNTSCINQDEAAIGNVSSRDYYD 66aa ncRNA nsiR6 Cyanobacteria Western blotting Synechocystis sp. PCC 6803 To verify the existence of the respective μ-proteins in vivo, we selected five genes as examples to which a FLAG tag sequence was added and re-introduced them into Synechocystis sp. PCC 6803. These were the previously annotated gene ssr1169, two newly defined genes norf1 and norf4, as well as nsiR6 (nitrogen stress-induced RNA 6) and hliR1 (high light-inducible RNA 1), which originally were considered non-coding. Hence, the putative cysteine pairs in NsiR6 may confer redox control or metal binding. low Small proteins in cyanobacteria provide a paradigm for the functional analysis of the bacterial micro-proteome 27894276 2016 Ssr1169 Synechocystis sp. PCC 6803, complete genome 3081689 3081850 3081689 3081850 MDIVKIICAILLPPLGVFLQVGIGKDFWINLLLTIFGLYILGLVHAIWVIARER 54aa ncRNA ssr1169 Cyanobacteria Western blotting Synechocystis sp. PCC 6803 To verify the existence of the respective μ-proteins in vivo, we selected five genes as examples to which a FLAG tag sequence was added and re-introduced them into Synechocystis sp. PCC 6803. These were the previously annotated gene ssr1169, two newly defined genes norf1 and norf4, as well as nsiR6 (nitrogen stress-induced RNA 6) and hliR1(high light-inducible RNA 1), which originally were considered non-coding. Ssr1169 homologs possess two transmembrane helices that form a Pmp3 domain and might be a stress induced proteolipid membrane modulator. low Small proteins in cyanobacteria provide a paradigm for the functional analysis of the bacterial micro-proteome 27894276 2016 12254832 ELA 1 19667947 19673896 QRPVNLTMRRKLRKHNCLQRRCMPLHSRVPFP 32aa ncRNA ELABELA (ELA) Danio rerio (zebrafish) Immunofluorescence/western blotting/ RT-PCR/qPCR Naive ectodermal cells of the embryo We report here the discovery and characterization of a gene, ELABELA (ELA), encoding a conserved hormone of 32 amino acids. Loss of Ela causes embryos to develop with a rudimentary heart or no heart at all, surprisingly phenocopying the loss of the apelin receptor (aplnr), which we show serves as Ela cognate G protein-coupled receptor. low ELABELA: A Hormone Essential for Heart Development Signals via the Apelin Receptor 24316148 2013 100536023 Toddler 1 19673406 19673579 19667947 19673896 MRFFHPLYLLLLLLTVLVVISADKHGTKHDFLNLRRKYRRHNCPKKRCLPLHSRVPFP 58aa lncRNA Toddler (tdl) Danio rerio (zebrafish) Enhanced green fluorescent protein (eGFP)/MS Zebrafish embryo Toddler is translated and encodes a secreted peptide. Toddler is an activator of APJ/Apelin receptor signaling, promotes gastrulation movements, and might be the first in a series of uncharacterized developmental signals. low Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors 24407481 2014 100536023 CIrcMbl1 circRNA circMbl1 Drosophila melanogaster Western blotting Drosophila S2 cells A Putative CircMbl1-Encoded Protein Is Enriched in Synaptosomes and Modulated by Starvation and FOXO. synaptosomes A Subset of CircRNAs Is Associated with Translating Ribosomes in Fly Heads. low Translation of CircRNAs 28344080 2017 CircMbl3 circRNA circMbl3 Drosophila melanogaster Western blotting Drosophila S2 cells A Putative CircMbl1-Encoded Protein Is Enriched in Synaptosomes and Modulated by Starvation and FOXO. synaptosomes A Subset of CircRNAs Is Associated with Translating Ribosomes in Fly Heads. low Translation of CircRNAs 28344080 2017 Dilp8 3L 17032080 17029812 150aa lncRNA CG14059/dilp8 Drosophila melanogaster Immunoprecipitation/qRT-PCR/Western blotting Drosophila melanogaster dilp8 encodes a peptide for which expression and secretion are sufficient to delay metamorphosis without affecting tissue integrity. The sPEP provides a signal that promotes the delay of metamorphosis in response to conditions that that alter growth in imaginal discs. low Secreted peptide Dilp8 coordinates Drosophila tissue growth with developmental timing 22556251 2012 HSPC300 2R 24027717 24028789 75aa lncRNA HSPC300 Drosophila melanogaster RT-PCR/Immunolabeling/Immunoprecipitations/Western blotting Drosophila melanogaster The WAVE/SCAR complex, consisting of CYFIP (PIR121 or Sra1), Kette (Nap1), Abi, SCAR (WAVE) and HSPC300, is known to regulate the actin nucleating Arp2/3 complex in a Rac1-dependent manner. The sPEP is a component of the WAVE-SCAR complex and is important in nervous system development for axonogenesis and neuromuscular synapse morphogenesis; HSPC300 is orthologous to brk1. low HSPC300 and its role in neuronal connectivity 17894861 2007 246497 Pgc 2R 22332197 22332409 22330200 22332813 MCDYQMEYSFIFEDSSCEGDASMASYDNGFESMWHQVREELQREREMNELCQVFQQNLSLSPPVIADRWRF 71aa lncRNA pgc Drosophila melanogaster Immunostaining/in situ hybridization/Immunoprecipitation/Western blotting Drosophila melanogaster Here we show that, in Drosophila embryos, a small protein encoded by polar granule component (pgc) is essential for repressing CTD Ser 2 phosphorylation in newly formed pole cells, the germline progenitors. Ectopic Pgc expression in somatic cells is sufficient to repress CTD Ser 2 phosphorylation. The sPEP is essential for repressing Ser2 phosphorylation in the carboxy-terminal domain of RNA polymerase II in newly formed pole cells (which are the early germline progenitors) and thus has a fundamental role in germ-cell specification. low Drosophila Pgc protein inhibits P-TEFb recruitment to chromatin in primordial germ cells 18200011 2008 5740599 Pri X 5048273 5070929 11-32aa ncRNA polished rice (pri) sORF gene Drosophila melanogaster Western blotting/Immunoprecipitation Drosophila embryo Here, we show that peptides of 11 to 32 amino acids encoded by the polished rice (pri) sORF gene control epidermal differentiation in Drosophila by modifying the transcription factor Shavenbaby (Svb). nuclei Pri peptides trigger the amino-terminal truncation of the Svb protein, which converts Svb from a repressor to an activator. low Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis 20647469 2010 SclA 2L 16839227 16839310 16837972 16841884 MSEARNLFTTFCILAILLFFLYLIYAVL 28aa lncRNA SclA Drosophila melanogaster in situ hybridization/RT-PCR Drosophila melanogaster Here, we describe two peptides of less than 30 amino acids regulating calcium transport, and hence influencing regular muscle contraction, in the Drosophila heart. Both sPEPs are involved in the regulation of Ca2+ trafficking; alterations result in irregular muscle contractions. low Conserved regulation of cardiac calcium uptake by peptides encoded in small open reading frames 23970561 2013 19835657 SclB 2L 16840296 16840382 16837972 16841884 MNEAKSLFTTFLILAFLLFLLYAFYEAAF 29aa lncRNA SclB Drosophila melanogaster in situ hybridization/RT-PCR Drosophila melanogaster Here, we describe two peptides of less than 30 amino acids regulating calcium transport, and hence influencing regular muscle contraction, in the Drosophila heart. Both sPEPs are involved in the regulation of Ca2+ trafficking; alterations result in irregular muscle contractions. low Conserved regulation of cardiac calcium uptake by peptides encoded in small open reading frames 23970561 2013 19834948 Tal-1A 3R 13813526 13813558 13813109 13814648 MAAYLDPTGQY 11aa ncRNA tarsal-less (tal) Drosophila melanogaster TNT Quick Coupled Transcription/Translationreticulocyte system/GFP fluorescence/Immunohistochemistry Flies embryos /Drosophila S2R+ cells Here we present the characterisation of tarsal-less (tal), a new type of noncanonical gene that had been previously classified as a putative noncoding RNA. We show that tal controls gene expression and tissue folding in Drosophila, thus acting as a link between patterning and morphogenesis. tal function is mediated by several 33-nucleotide long open reading frames (ORFs), which are translated into 11-amino-acid-long peptides. Tal controls gene expression and tissue folding in Drosophila, thus acting as a link between patterning and morphogenesis. low Peptides Encoded by Short ORFs Control Development and Define a New Eukaryotic Gene Family 17439302 2017 7354381 Tal-2A 3R 13813639 13813671 13813109 13814648 MAAYLDPTGQY 11aa ncRNA tarsal-less (tal) Drosophila melanogaster TNT Quick Coupled Transcription/Translationreticulocyte system/GFP fluorescence/Immunohistochemistry Flies embryos /Drosophila S2R+ cells tarsal-less (tal) is a polycistronic transcription unit with 4 non-overlapping reading frames (tal-1A, tal-2A, tal-3A and tal-AA), which encode four peptides. Tal controls gene expression and tissue folding in Drosophila, thus acting as a link between patterning and morphogenesis. low Peptides Encoded by Short ORFs Control Development and Define a New Eukaryotic Gene Family 17439302 2017 7354376 Tal-3A 3R 13813746 13813778 13813109 13814648 MSHDLDPTGTY 11aa ncRNA tarsal-less (tal) Drosophila melanogaster TNT Quick Coupled Transcription/Translationreticulocyte system/GFP fluorescence/Immunohistochemistry Flies embryos /Drosophila S2R+ cells tarsal-less (tal) is a polycistronic transcription unit with 4 non-overlapping reading frames (tal-1A, tal-2A, tal-3A and tal-AA), which encode four peptides. Tal controls gene expression and tissue folding in Drosophila, thus acting as a link between patterning and morphogenesis. low Peptides Encoded by Short ORFs Control Development and Define a New Eukaryotic Gene Family 17439302 2017 7354378 Tal-AA 3R 13813871 13813966 13813109 13814648 MLDPTGTYRRPRDTQDSRQKRRQDCLDPTGQY 32aa ncRNA tarsal-less (tal) Drosophila melanogaster TNT Quick Coupled Transcription/Translationreticulocyte system/GFP fluorescence/Immunohistochemistry Flies embryos /Drosophila S2R+ cells tarsal-less (tal) is a polycistronic transcription unit with 4 non-overlapping reading frames (tal-1A, tal-2A, tal-3A and tal-AA), which encode four peptides. Tal controls gene expression and tissue folding in Drosophila, thus acting as a link between patterning and morphogenesis. low Peptides Encoded by Short ORFs Control Development and Define a New Eukaryotic Gene Family 17439302 2017 7354377 AcrZ K-12 substr. MG1655, complete genome 794773 794922 794773 794922 MLELLKSLVFAVIMVPVVMAIILGLIYGLGEVFNIFSGVGKKDQPGQNH 49aa ncRNA acrZ Escherichia coli Western blotting E. coli Here we show that AcrZ (formerly named YbhT), a 49-amino-acid inner membrane protein, associates with the AcrAB-TolC complex. inner membrane AcrZ may enhance the ability of the AcrAB-TolC pump to export certain classes of substrates. low Conserved small protein associates with the multidrug efflux pump AcrB and differentially affects antibiotic resistance 23010927 2012 945365 Blr K-12 substr. MG1655, complete genome 1704551 1704676 1704551 1704676 MNRLIELTGWIVLVVSVILLGVASHIDNYQPPEQSASVQHK 41aa ncRNA blr Escherichia coli Western blotting E. coli The Blr protein has 41 amino acids, with a single predicted transmembrane helix, but no clear homology to any other protein. transmembrane The Blr protein has 41 amino acids, with a single predicted transmembrane helix, but no clear homology to any other protein. low Intergenic' blr gene in Escherichia coli encodes a 41-residue membrane protein affecting intrinsic susceptibility to certain inhibitors of peptidoglycan synthesis 10931331 2000 2847682 MgrB str. K-12 substr. MG1655, complete genome 1908623 1908766 1908623 1908766 MKKFRWVVLVVVVLACLLLWAQVFNMMCDQDVQFFSGICAINQFIPW 47aa ncRNA mgrB Escherichia coli Fluorescence microscopy/Western blotting E. coli We found that deletion of mgrB (yobG), which encodes a 47 amino acid peptide, results in a potent increase in PhoP-regulated transcription. inner membrane MgrB is a broadly conserved membrane peptide that is a critical mediator of negative feedback in the PhoQ/PhoP circuit. low Feedback inhibition in the PhoQ/PhoP signaling system by a membrane peptide 20041203 2009 946351 MntS str. K-12 substr. MG1655, complete genome 852869 852997 852869 852997 MNEFKRCMRVFSHSPFKVRLMLLSMLCDMVNNKPQQDKPSDK 42aa ncRNA mntS Escherichia coli Western blotting E. coli mntS (formerly the small RNA gene rybA) is repressed by manganese through MntR and encodes an unannotated 42-amino-acid protein. Bacteria control intracellular manganese levels by the transcription regulator MntR. low The Escherichia coli MntR miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis 21908668 2011 14678509 Pentapeptide (E-peptide) Escherichia coli O157:H7 strain Sakai 23S ribosomal RNA gene, complete sequence 1234 1268 5aa rRNA 23S rRNA Escherichia coli PCR E. coli cell A pentapeptide open reading frame equipped with a canonical ribosome-binding site is present in the Escherichia coli 23S rRNA. ribosome Expression of the rRNAencoded peptide is essential for the resistance phenotype. low A functional peptide encoded in the Escherichia coli 23S rRNA 8643630 1996 ENOD40A 2 3408186 3408225 3407569 3408333 MELCWLTTIHGS 12aa ncRNA ENOD40 Glycine max (soybean) MS/Western blotting/Immunoprecipitation Wheat germ In vitro translation of soybean ENOD40 mRNA in wheat germ extracts revealed that the conserved nucleotide sequence at the 5 end (region I) encodes two peptides of 12 and 24 aa residues (peptides A and B). Based on our data we suggest that ENOD40 peptides are involved in the control of sucrose use in nitrogen-fixing nodules. low Soybean ENOD40 encodes two peptides that bind to sucrose synthase 11842484 2002 110740350 ENOD40B 2 3408122 3408197 3407569 3408333 MVLEEAWRERGVRGEGAHSSHSLT 24aa ncRNA ENOD40 Glycine max (soybean) MS/Western blotting/Immunoprecipitation Wheat germ In vitro translation of soybean ENOD40 mRNA in wheat germ extracts revealed that the conserved nucleotide sequence at the 5 end (region I) encodes two peptides of 12 and 24 aa residues (peptides A and B). Based on our data we suggest that ENOD40 peptides are involved in the control of sucrose use in nitrogen-fixing nodules. low Soybean ENOD40 encodes two peptides that bind to sucrose synthase 11842484 2002 547926 miPEP172c 18 MWVLCLFCWPTYTHGS 16aa pri-miRNA pri-miR172c Glycine max (soybean) RT-qPCR Nodules We showed that exogenous application of synthetic miPEP172c could be used to stimulate miR172c expression. The miR172c activation results in a more active repression of its target gene, the AP2 transcription factor NNC1. The miPEP172c treatment ultimately leads to the stimulation of nodulation in soybean, which is one of the most cultivated legumes is the world. Our results showed that, in the same conditions of lack of external nitrogen fertilization, treatment with miPEP172c significantly increased the nodule number observed per plant. low Use of microRNA-encoded peptide miPEP172c to stimulate nodulation in soybean 27105382 2016 pDelta-1 Hepatitis delta virus (HDV) RNA genome 63 359 63 359 PLLSLLSSSLASPPTPSHSSTATGLTPTAASASNSLKGSSGGDKSAHLAVDSSLTVLLAPSGASALQHTALGPSDAQAASKKKHLPLSPSADSPALTGSAPLPQTSLNKLGVVSPTKQNSLP 122aa circRNA pDelta-1 Hepatitis delta virus Electron micrographs/Northern blot hybridization HDV Only one open reading frame gave a stretch of appreciable length (122 amino acids) with a stop codon (TGA)70 bp before the end of the cDNA at nucleotide 370 .It contains three hydrophobic regions ( amino acids 52-59, 79-88 and 105-113) and one strongly hydrophilic region located between amino acids 72-79. One of the first observations of a circRNA behaving as a translational templates is the case of the single-stranded circular RNA genome of the hepatitis δ virus which is a satellite virus of the hepatitis B virus, where encapsulation of HDV with HBV virions results in the production of a single viral protein of 122 amino acids, in a non-canonical manner. low The hepatitis delta virus possesses a circular RNA 2429192 1986 CASIMO1 16 4795735 4795984 4788395 4796491 MAVSTEELEATVQEVLGRLKSHQFFQSTWDTVAFIVFLTFMGTVLLLLLLVVAHCCCCSSPGPRRESPRKERPKGVDNLALEP 83aa ncRNA CASIMO1 Homo sapiens (human) Northern blotting Breast cancer cell lines SKBR3/MCF7/KPL1 It was annotated as a putative non-coding RNA (NR_029453) and contained a potential sORF predicted to form an integral membrane microprotein, hence we named it CASIMO1 for Cancer Associated Small Integral Membrane Open reading frame 1. endosomes CASIMO1 modulates the actin cytoskeleton and impacts cell migration; CASIMO1 influences proliferation and cell cycle progression; CASIMO1 interacts with squalene epoxidase and modulates lipid droplet accumulation. low The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation 29765154 2018 440335 circPPP1R12A-73aa 12 79773563 79935455 MKPVLAFKHGNFDSLPQLMEISSIKKIGWVQWLIPVVSQHFGRLRHVNCLSPGVQDQPGQHGETPSLPKVQN 73aa circRNA circPPP1R12A Homo sapiens (human) SDS-PAGE/LC/MS/Western blotting/qRT-PCR/FISH HT-29/HCT-116/SW480/SW620/LoVo/SW48/DLD-1/Caco2/HCT-15/NCM460/Colon cancer tissue CircPPP1R12A-73aa promoted the growth and metastasis of CC via activating Hippo-YAP signaling pathway. cytoplasm CircPPP1R12A played a critical role in proliferation, migration and invasion of CC cells. low A novel protein encoded by a circular RNA circPPP1R12A promotes tumor pathogenesis and metastasis of colon cancer via Hippo-YAP signaling 30925892 2019 CRNDEP 16 54924882 54925136 54918863 54929189 MLAEIHPKAGLQSLQFIMELLYWLLEGGDSEDKEDATGNVEMKNIQPLVFEISCDVFQSRCKEHGKIKVLEWFKYVLGIPVYRL 84aa lncRNA CRNDE Homo sapiens (human) Immunohistochemical/Western blotting HeLa cells By using bioinformatics methods, we identified the 84-amino acid ORF encoded by one of two CRNDEtranscripts, previously described by our research team. This ORF was cloned into two expression vectors, subsequently utilized in localization studies in HeLa cells. We also developed a polyclonal antibody against CRNDEP. Its specificity was confirmed in immunohistochemical, cellular localization, western blot and immunoprecipitation experiments, as well as by showing a statistically significant decrease of endogenous CRNDEP expression in the cells with transient shRNA mediated knockdown of CRNDE. nuclear Although the exact role of CRNDEP is unknown, our preliminary results suggest that it may be involved in the regulation of the cell proliferation. Possibly, CRNDEP also participates in oxygen metabolism, considering our in silico results, and the correlation between its enforced overexpression and the formation of stress granules. low The Novel Gene CRNDE Encodes a Nuclear Peptide (CRNDEP) Which Is Overexpressed in Highly Proliferating Tissues 25978564 2015 643911 DANCR 4 52713674 52713853 52712394 52720697 MLVATGQCSRCFMFTFSTFSFNCHNSEVDSVRDRLPQDHSAPANSMQLTLTLNTLQLHS 59aa lncRNA DANCR Homo sapiens (human) Western blotting HEK293 cell line Consistent with our prediction, a polypeptide encoded by DANCR was detected with the expected size from the western blot analysis. low Genome-wide identification and differential analysis of translational initiation 29170441 2017 57291 ELABELA 4 164877398 164877494 164877023 164899063 QRPVNLTMRRKLRKHNCLQRRCMPLHSRVPFP 32aa ncRNA APELA (ELA) Homo sapiens (human) Immunofluorescence/western blotting/ RT-PCR/qPCR Embryonic stem cells We report here the discovery and characterization of a gene, ELABELA (ELA), encoding a conserved hormone of 32 amino acids. Loss of Ela causes embryos to develop with a rudimentary heart or no heart at all, surprisingly phenocopying the loss of the apelin receptor (aplnr), which we show serves as Ela cognate G protein-coupled receptor. low ELABELA: A Hormone Essential for Heart Development Signals via the Apelin Receptor 24316148 2013 100506013 FBXW7-185aa 4 152321585 152322104 152320544 152536873 MNQELLSVGSKRRRTGGSLRGNPSSSQVDEEQMNRVVEEEQQQQLRQQEEEHTARNGEVVGVEPRPGGQNDSQQGQLEENNNRFISVDEDSSGNQEEQEEDEEHAGEQDEEDEEEEEMDQESDDFDQSDDSSREDEHTHINSVTNSSSI VDLPVHQLSSPFYTKITKDYFLRIDCQKWSYWVRGM 185aa circRNA circ-FBXW7 Homo sapiens (human) Antibody/LC- MS 293T cells We characterized the circular form of the FBXW7 gene, a well-characterized tumorsuppressive E3 ligase that encodes a novel 185-amino acid protein in human cells, which we termed FBXW7-185aa. Inhibition of proliferation and cell cycle acceleration. low Novel Role of FBXW7 Circular RNA in Repressing Glioma Tumorigenesis 28903484 2018 55294 HOXB-AS3 17 48604008 48604167 48590420 48606414 MPVLPGTQRYPHQRRRFQAAGGGAESGKRGSEEAPGVAWSGSESGRDAATPAW 53aa lncRNA HOXB-AS3 Homo sapiens (human) Western blotting/Immunofluorescence staining HTC-116/SW620 cells/SW480/MDA-MB-231/SK-OV-3/OVCAR-3/S18/S26/HEK293T/Mouse: Male BALB/c nu (3-4 weeks old)/Mouse: Male NOD-SCID (5-6 weeks old) We discovered that the HOXB cluster antisense RNA 3 (HOXB-AS3), which was previously annotated as an lncRNA gene in Homo sapiens, encodes a conserved 53-amino acid small peptide. Suppression of colon cancer (CRC) growth. low A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth 28985503 2017 404266 Humanin (HN) 17 22524062 22524133 22523111 22524665 MAPRGFSCLLLLTSEIDLPVKRRA 24aa rRNA HN1 Homo sapiens (human) Transfection/Immunofluorescence staining F11 cells Here we report a cDNA, encoding a short polypeptide, that suppresses neuronal cell death induced by the three different types of FAD genes and by Ab, designated Humanin (HN). mitochondria Neuroprotective factor against Alzheimer disease-related neurotoxicity. low A rescue factor abolishing neuronal cell death by a wide spectrum of familial Alzheimer’s disease genes and Abeta 11371646 2001 MOLOE-3 2 239193331 239195457 VFDTEIAQVTSDTAVGAR 18aa lncRNA LOC85009 Homo sapiens (human) Fluorescence/MS Melanoma cells Data from in vitro translation experiments and transfection of melanoma cells with bicistronic vectors documented that MELOE-3 is exclusively translated by the classical cap-dependent pathway. Using a sensitive tandem mass spectrometry technique, we detected the presence of MELOE-3 in total lysates of both melanoma cells and normal melanocytes. The poor immunogenicity of MELOE-3 and its expression in melanocytes is consistent with an immune tolerance towards a physiologically expressed protein. In contrast, melanoma-restricted expression of IRES-dependent MELOE-1 may explain its high immunogenicity. In conclusion, within the MELOE family, IRES-dependent antigens represent the best T cell targets for immunotherapy of melanoma. low IRES-dependent translation of the long non coding RNA meloe in melanoma cells produces the most immunogenic MELOE antigens 27486971 2016 85009 MOTS-c MOTS-c gene, complete cds. 1 51 1 51 MRWQEMGYIFYPRKLR 16aa rRNA 12S rRNA Homo sapiens (human) Immunostaining/Western blotting HEK293 cells. Here, we describe the identity of a sORF encoded within the mitochondrial 12S rRNA that yields a bioactivepeptide involved in regulating metabolic homeostasis. mitochondria Regulation of insulin sensitivity and metabolic homeostasis. low The Mitochondrial-Derived Peptide MOTS-c Promotes Metabolic Homeostasis and Reduces Obesity and Insulin Resistance 25738459 2015 Mtln 2 110212358 110212525 110211529 110245420 MADVSERTLQLSVLVAFASGVLLGWQANRLRRRYLDWRKRRLQDKLAATQKKLDLA 56aa lncRNA LINC00116 Homo sapiens (human) Immunoblotting/Immunocytochemistry/Western blotting Human HeLa (ATCC, CCL-2) We show that a skeletal muscle- and heart-enriched long non-coding RNA, LINC00116, encodes a highly conserved 56-amino-acid microprotein that we named mitoregulin (Mtln). inner mitochondrial membrane Studies in cells and mice demonstrate that Mtln localizes to inner mitochondrial membranes, where it interacts with several complexes to influence mitochondrial membrane potential, respiration, Ca2+ retention capacity, ROS,and supercomplex levels. low Mitoregulin: A lncRNA-Encoded Microprotein that Supports Mitochondrial Supercomplexes and Respiratory Efficiency 29949756 2018 205251 Myoregulin (MLN) 10 59737063 59737200 59736692 59753455 MTGKNWILISTTTPKSLEDEIVGRLLKILFVIFVDLISIIYVVITS 46aa lncRNA LINC00948 Homo sapiens (human) CoIPs/Western blot C2C12 cell line We discovered a conserved micropeptide, which we named myoregulin (MLN), encoded by a skeletal muscle-specific RNA annotated as a putative long noncoding RNA. SR membrane MLN interacts directly with SERCA and impedes Ca2+ uptake into the SR. low A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance 25640239 2015 100507027 NoBody X 56729354 56729557 56729242 56819179 MGDQPCASGRSTLPPGNAREAKPPKKRCLLAPRWDYPEGTPNGGSTTLPSAPPPASAGLKSHPPPPEK 68aa lncRNA LINC01420/LOC550643 Homo sapiens (human) LC-MS proteomics/Immunofluorescence K562/H293T/MDA-MB-231 cells Here, we report the discovery and characterization of a 7-kilodalton human microprotein we named non-annotated P-body dissociating polypeptide (NoBody). cytoplasmic Our studies reveal that NoBody interacts with decapping proteins to modulate P-body numbers in cells. low A human microprotein that interacts with the mRNA decapping complex 27918561 2017 550643 PINT87aa 7 131108065 131108325 130877562 131109916 MLWLPDRGSCSARSPSGMLRGAPGGWRYGRRCGRRRQSCCCCCCCSHVGAPLSFHREASLVSHDGHDIMKQHCGEESIRGAHGYKNK 87aa circRNA LINC-PINT Homo sapiens (human) Immunofluorescence/qPCR Glioblastoma tissue/293T cells/u151 cells/A172 cells/Hs683 cells/SW1783 cells We identify an 87-amino-acid peptide encoded by the circular form of the long intergenic non-protein-coding RNA p53-induced transcript (LINC-PINT) that suppresses glioblastoma cell proliferation in vitro and in vivo. This peptide directly interacts with polymerase associated factor complex (PAF1c) and inhibits the transcriptional elongation of multiple oncogenes. low A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma 30367041 2018 378805 SHPRH-146aa 6 145862746 145863142 145857838 145964358 MKIQLRDPGAKALVFSTWQDVLDIISKALTDNNMEFAQISRVKTFQENLSAFKRDPQINILLLPLHTGSNGLTIIEATHVLLVEPILNPAHELQAIGRVHRIGQTKPTIVHRFLIKATIEERMQAMLKTAERRAAILQKWKLWSEL 146aa circRNA circ-SHPRH Homo sapiens (human) LC-MS/MS/Western blotting Human brain glioblastoma cells The circular form of the SNF2 histone linker PHD RING helicase (SHPRH) gene encodes a novel protein that we termed SHPRH-146aa. SHPRH-146aa protects full-length SHPRH from degradation by the ubiquitin proteasome. low A novel protein encoded by the circular form of the SHPRH gene suppresses glioma tumorigenesis 29343848 2018 257218 SPAR 9 35910419 35910688 35909490 35911686 MGAKAPRGPKVAQWAMETAVIGVVVVLFVVTVAITCVLCCFSCDSRAQDPQGGPGRSFTVATFRQEASLFTGPVRHAQPVPSAQDFWTFM 90aa lncRNA LINC00961 Homo sapiens (human) Immunofluorescence staining/Western blotting HeLa/Pc3 cells Here we identify and functionally characterize a novel polypeptide encoded by the lncRNA LINC00961. late endosome/lysosome Activation of mTORC1 and promotes muscle regeneration. low mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide 28024296 2017 158376 miPEP171b 2 72657 72716 MLLHRLSKFCKIERDIVYIS 20aa pri-miRNA pri-miR171b Medicago truncatula Fluorescence microscopy/Western blotting/Immunoblots Medicago truncatula The primiR171b of Medicago truncatula and the pri-miR165a of Arabidopsis thaliana produce peptides, which we term miPEP171b and miPEP165a, respectively, that enhance the accumulation of their corresponding mature miRNAs, resulting in downregulation of target genes involved in root development. Synthetic miPEP171b and miPEP165a peptides applied to plants specifically trigger the accumulation of miR171b and miR165a, leading to reduction of lateral root development and stimulation of main root growth, respectively, suggesting that miPEPs might have agronomical applications. low Primary transcripts of microRNAs encode regulatory peptides 25807486 2015 miPEP171e pri-miRNA pri-miR171e Medicago truncatula Fluorescence microscopy/Western blotting/Immunoblots Medicago truncatula Five other pri-miRNAs of A. thaliana and M. truncatula encode active miPEPs, suggesting that miPEPs are widespread throughout the plant kingdom. Synthetic miPEP171b and miPEP165a peptides applied to plants specifically trigger the accumulation of miR171b and miR165a, leading to reduction of lateral root development and stimulation of main root growth, respectively, suggesting that miPEPs might have agronomical applications. low Primary transcripts of microRNAs encode regulatory peptides 25807486 2015 Aw112010 19 11050156 11050408 11047612 11050566 LSCKMSPIPLIFIFGGVLIICLMQQYLAYKSSKNVVKVFCHQANDVHIYQTQVVMTNTLETSSGKSHPLGRSGEIQSLKKQN 84aa lncRNA Aw112010 Mus musculus Immunoblotting/Immunoprecipitation BMDMs cell We show that the translation of a new ORF hidden within the long non-coding RNA Aw112010 is essential for the orchestration of mucosal immunity during both bacterial infection and colitis. discrete subcellular localizations The translation of the non-canonical ORF in Aw112010 is required for the mucosal inflammatory response. low The translation of non-canonical open reading frames controls mucosal immunity 30542152 2018 107350 DWORF 3 63483726 63483827 63481104 63483906 MAEKESTSPHLMVPILLLVGWIVGCIIVIYIVFF 34aa lncRNA Strit1 Mus musculus Northern blotting Muscle We discovered a putative muscle-specific long noncoding RNA that encodes a peptide of 34 amino acids and that we named dwarf open reading frame (DWORF). DWORF localizes to the SR membrane, where it enhances SERCA activity by displacing the SERCA inhibitors, phospholamban, sarcolipin, and myoregulin. membrane Conversely, slow skeletal muscle lacking DWORF exhibits delayed Ca2+ clearance and relaxation and reduced SERCA activity. DWORF is the only endogenous peptide known to activate the SERCA pump by physical interaction and provides a means for enhancing muscle contractility. low A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle 26816378 2016 102637511 Mtln 2 127792300 127792467 127791377 127792488 MADVSERTLQVSVLVAFASGVVLGWQANRLRRRYLDWRKRRLQDKLATTQKKLDLA 56aa lncRNA 1500011K16Rik Mus musculus Immunoblotting/Immunocytochemistry NIH 3T3/NS0 cells/Brain tissue/Liver tissue/Kidney tissue/Heart tissue/Lung tissue Here we have demonstrated that one such transcript is translated into a 56-aminoacid-long peptide conserved in chordates. mitochondria Interaction of Mtln with NADH-dependent cytochrome b5 reductase stimulates complex I functioning most likely by providing a favorable lipid composition of the membrane. low LINC00116 codes for a mitochondrial peptide linking respiration and lipid metabolism 30796188 2018 67885 Mtln 2 127792300 127792467 127791377 127792488 MADVSERTLQVSVLVAFASGVVLGWQANRLRRRYLDWRKRRLQDKLATTQKKLDLA 56aa lncRNA 1500011K16Rik Mus musculus Immunoblotting/Immunocytochemistry/Western blotting Mouse C2C12 myoblast (ATCC, CRL-1772)/Mouse neuroblastoma N2a (ATCC, CCL-131) We show that a skeletal muscle- and heart-enriched long non-coding RNA, LINC00116, encodes a highly conserved 56-amino-acid microprotein that we named mitoregulin (Mtln). inner mitochondrial membrane Studies in cells and mice demonstrate that Mtln localizes to inner mitochondrial membranes, where it interacts with several complexes to influence mitochondrial membrane potential, respiration, Ca2+ retention capacity, ROS,and supercomplex levels. low Mitoregulin: A lncRNA-Encoded Microprotein that Supports Mitochondrial Supercomplexes and Respiratory Efficiency 29949756 2018 67885 Myoregulin (MLN) 10 70219496 70219633 70204664 70219711 MSGKSWVLISTTSPQSLEDEILGRLLKILFVLFVDLMSIMYVVITS 46aa lncRNA 2310015B20Rik Mus musculus CoIPs/Western blot Skeletal muscle tissue We discovered a conserved micropeptide, which we named myoregulin (MLN), encoded by a skeletal muscle-specific RNA annotated as a putative long noncoding RNA. SR membrane MLN interacts directly with SERCA and impedes Ca2+ uptake into the SR. low A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance 25640239 2015 69563 NCX1 81373105 81738387 600aa circRNA NCX1 Mus musculus Immunoblotting LLC-MK2 A protein, matching the predicted size of about 70 kDa, was expressed, and the transfected cells possessed Na/Ca exchange activity. Although in native tissue we could not detect a protein corresponding exactly to that predicted from the circular transcript, a prominent band of slightly shorter size, possibly representing further proteolytic processing of circular transcript protein, was observed in membranes from LLC-MK2 cells and rat kidney. A protein, matching the predicted size of approximately 70 kDa, was expressed, and the transfected cells possessed Na/Ca exchange activity. low A circularized sodium-calcium exchanger exon 2 transcript 10075718 1999 20541 SPAR 4 43730965 43731189 43730034 43734534 METAVIGMVAVLFVITMAITCILCYFSYDSHTQDPERSSRRSFTVATFHQEASLFTGPALQSRPLPRPQNFWTVV 75aa lncRNA SPAR Mus musculus Immunofluorescence staining/Western blotting Mouse myoblast C2C12 cells Here we identify and functionally characterize a novel polypeptide encoded by the lncRNA LINC00961. late endosome/lysosome Activation of mTORC1 and promotes muscle regeneration. low mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide 28024296 2017 71406 KdpF Mycobacterium_bovis_AF2122/97 1152395 1152487 1152395 1152487 MTTVDNIVGLVIAVALMAFLFAALLFPEKF 30aa ncRNA kdpF Mycobacterium tuberculosis Western blotting Mycobacterium bovis BCG The 30 amino-acid-long KdpF peptide, which is co-transcribed with kdpABC genes and regulated by the KdpDE two-component system, is supposed to stabilize the KdpABC potassium transporter complex but may also exhibit unsuspected regulatory function (s) towards the KdpD sensor kinase. membrane KdpF overexpression reduces intramacrophage growth which may result from alteration of the mycobacterial cell wall. low Overexpression of the KdpF membrane peptide in Mycobacterium bovis BCG results in reduced intramacrophage growth and altered cording morphology 23577107 2013 3205056 rat Humanin (rHN) rRNA Rattus norvegicus (Norway rat) Western blotting/Immunofluorescence staining INS-1 cells In summary, a locally bioactive peptide is derived and translated from an open reading frame (ORF) within rat mitochondrial DNA encoding 16S rRNA. mitochondria Production of reactive oxygen species. low Rat Humanin is encoded and translated in mitochondria and is localized to the mitochondrial compartment where it regulates ROS production 26116236 2015 ScRYMV Rice yellow mottle virus satellite, complete genome 3 218 3 218 MKETAAAKFERQHMDSPDLGTLVPRGSMGYLWIRIRARYPGRPGRLGAVHRASLWSEPGLQGAWRRNRSVGTTRTISHRAPAASSCAGGGDFVSSLTDTDEPRGTWRHPGISPGSTWAARSRAQGVAVERAWPPRGLEAKPVCWDHSDHQSSCSGSFQLRRGRRFCFEPYRHAKRNLEAPRNFTRVDLGGEPCTGRRCGASLASKGPGGETGLLGPLGPSVIVLRQL 227aa circRNA scRYMV rice yellow mottle virus (sobemovirus) MS/Western blotting/Immunoprecipitation E. coli The highly structured (64% GC) covalently closed circular (CCC) RNA (220 nt) of the virusoid associated with rice yellow mottle virus codes for a 16-kDa highly basic protein using novel modalities for coding, translation, and gene expression. This CCC RNA is the smallest among all known viroids and virusoids and the only one that codes proteins. low Novel coding, translation, and gene expression of a replicating covalently closed circular RNA of 220 nt 25253891 2014 932238 sORF-1 II 169637 169873 MQRVRIGQWVYDMEAIHRSDSHECPKRTCGNQTLNPGSIIKEIQYKKYRYILFPPIAANQFTPGCSEYIPILHDAIKD 78aa ncRNA YBL027W-YBL026W intergenic Saccharomyces cerevisiae (yeast) Western blotting Saccharomyces cerevisiae (baker's yeast) We find unannotated RNAs associate with polyribosomes to extents similar to mRNA and that they encode small open reading frames (ORFs) bound by ribosomes.Our data expand the coding capacity of the yeast genome beyond the current annotation and suggest expression of dozens of short polypeptides from transcripts previously predicted to lack coding potential. low Translation of Small Open Reading Frameswithin Unannotated RNA Transcriptsin Saccharomyces cerevisiae 24931603 2014 sORF2 VII 947477 947647 947420 948997 MNVRGNQCIMSIRVFLKAGESSLSFAIKWLKRFEATTKKNQYIQNGWPLKDGNKKRK 57aa ncRNA DIE2 Saccharomyces cerevisiae (yeast) Western blotting BY4741;BY4742 In this study, we further identified this element and observed that overexpression of a small protein (sORF2) of 57 amino acids encoded in this region caused growth inhibition. sORF2 (designated as OTO1) is an orphan ORF that determines the specificity of this species. low Small toxic protein encoded on chromosome VII of Saccharomyces cerevisiae 25781884 2015 853142 sORF-4 XIII 480923 481186 MISMEAINNFIKTAPKHDYLTGGVHHSGNVDVLQLSGNKEDGSLVWNHTFVDVDNNVVAKFEDALEKLESLHRRSSSSTGNEEHANV 87aa ncRNA YKU80-YMR107W intergenic Saccharomyces cerevisiae (yeast) Western blotting Saccharomyces cerevisiae (baker's yeast) We find unannotated RNAs associate with polyribosomes to extents similar to mRNA and that they encode small open reading frames (ORFs) bound by ribosomes.Our data expand the coding capacity of the yeast genome beyond the current annotation and suggest expression of dozens of short polypeptides from transcripts previously predicted to lack coding potential. low Translation of Small Open Reading Frameswithin Unannotated RNA Transcriptsin Saccharomyces cerevisiae 24931603 2014 Mlpt-1 LG9 15959812 159595844 15958600 15959870 MSGLDPTGLY 10aa ncRNA mille-pattes (mlpt) Tribolium castaneum in situ hybridization/ RNAi/Northern blot/ Flour beetle Tribolium embryo The mlpt gene reveals an unusual structure, as it encodes a polycistronic mRNA that codes for four peptides. Mlpt knockdown leads to transformation of the abdominal segments into thoracic segments, providing embryos with up to ten pairs of legs. low A Segmentation Gene in Tribolium Produces a Polycistronic mRNA that Codes for Multiple Conserved Peptides 16901788 2006 657909 Mlpt-2 LG9 15959708 15959746 15958600 15959870 MDGGKLDPTGQY 12aa ncRNA mille-pattes (mlpt) Tribolium castaneum in situ hybridization/ RNAi/Northern blot/ Flour beetle Tribolium embryo The mlpt gene reveals an unusual structure, as it encodes a polycistronic mRNA that codes for four peptides. Mlpt knockdown leads to transformation of the abdominal segments into thoracic segments, providing embryos with up to ten pairs of legs. low A Segmentation Gene in Tribolium Produces a Polycistronic mRNA that Codes for Multiple Conserved Peptides 16901788 2006 657909 Mlpt-3 LG9 15959617 15959664 15958600 15959870 MKLNGGKSLDPTGLY 15aa ncRNA mille-pattes (mlpt) Tribolium castaneum in situ hybridization/ RNAi/Northern blot/ Flour beetle Tribolium embryo The mlpt gene reveals an unusual structure, as it encodes a polycistronic mRNA that codes for four peptides. Mlpt knockdown leads to transformation of the abdominal segments into thoracic segments, providing embryos with up to ten pairs of legs. low A Segmentation Gene in Tribolium Produces a Polycistronic mRNA that Codes for Multiple Conserved Peptides 16901788 2006 657909 Mlpt-4 LG9 15959546 15959617 15958600 15959870 MWHRNRGDGGRPETSSGRRRRLR 23aa ncRNA mille-pattes (mlpt) Tribolium castaneum in situ hybridization/ RNAi/Northern blot/ Flour beetle Tribolium embryo The mlpt gene reveals an unusual structure, as it encodes a polycistronic mRNA that codes for four peptides. Mlpt knockdown leads to transformation of the abdominal segments into thoracic segments, providing embryos with up to ten pairs of legs. low A Segmentation Gene in Tribolium Produces a Polycistronic mRNA that Codes for Multiple Conserved Peptides 16901788 2006 657909 Brk1 5 222623990 22264217 222622762 222624303 MGRGGGMGNPYNYGIAYQADWENREFISNISLNYRRLFDFLLRFEATTKSKLASLNEKLDILERKLEYLEYQYGSATTNPSYFN 84aa lncRNA brk1 Zea mays Northern blot/Western blotting Maize Leaf Epidermal Cells The Brk1 gene encodes a novel, 8 kD protein that is highly conserved in plants and animals, suggesting that BRK1-related proteins may function in actin-dependent aspects of cell polarization in a wide spectrum of eukaryotic organisms. The sPEP promotes multiple actin-dependent cell polarization events in the developing leaf epidermis; brk1 is orthologous to HSPC300. low A small, novel protein highly conserved in plants and animals promotes the polarized growth and division of maize leaf epidermal cells 12015123 2012