FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs
Non-coding RNAs (ncRNAs) are essential players in many cellular processes, from normal development to oncogenic transformation. Initially, ncRNAs were defined as transcripts that lacked an open reading frame (ORF). However, multiple lines of evidence suggest that certain ncRNAs encode small peptides...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-09-01
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| Series: | Non-Coding RNA |
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| Online Access: | https://www.mdpi.com/2311-553X/6/4/41 |
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| author | Mihnea P. Dragomir Ganiraju C. Manyam Leonie Florence Ott Léa Berland Erik Knutsen Cristina Ivan Leonard Lipovich Bradley M. Broom George A. Calin |
| author_facet | Mihnea P. Dragomir Ganiraju C. Manyam Leonie Florence Ott Léa Berland Erik Knutsen Cristina Ivan Leonard Lipovich Bradley M. Broom George A. Calin |
| author_sort | Mihnea P. Dragomir |
| collection | DOAJ |
| description | Non-coding RNAs (ncRNAs) are essential players in many cellular processes, from normal development to oncogenic transformation. Initially, ncRNAs were defined as transcripts that lacked an open reading frame (ORF). However, multiple lines of evidence suggest that certain ncRNAs encode small peptides of less than 100 amino acids. The sequences encoding these peptides are known as small open reading frames (smORFs), many initiating with the traditional AUG start codon but terminating with atypical stop codons, suggesting a different biogenesis. The ncRNA-encoded peptides (ncPEPs) are gradually becoming appreciated as a new class of functional molecules that contribute to diverse cellular processes, and are deregulated in different diseases contributing to pathogenesis. As multiple publications have identified unique ncPEPs, we appreciated the need for assembling a new web resource that could gather information about these functional ncPEPs. We developed FuncPEP, a new database of functional ncRNA encoded peptides, containing all experimentally validated and functionally characterized ncPEPs. Currently, FuncPEP includes a comprehensive annotation of 112 functional ncPEPs and specific details regarding the ncRNA transcripts that encode these peptides. We believe that FuncPEP will serve as a platform for further deciphering the biologic significance and medical use of ncPEPs. The link for FuncPEP database can be found at the end of the Introduction Section. |
| first_indexed | 2024-03-10T16:06:24Z |
| format | Article |
| id | doaj.art-2f3f0122c22a47daad067a1809263343 |
| institution | Directory Open Access Journal |
| issn | 2311-553X |
| language | English |
| last_indexed | 2024-03-10T16:06:24Z |
| publishDate | 2020-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Non-Coding RNA |
| spelling | doaj.art-2f3f0122c22a47daad067a18092633432023-11-20T14:47:54ZengMDPI AGNon-Coding RNA2311-553X2020-09-01644110.3390/ncrna6040041FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAsMihnea P. Dragomir0Ganiraju C. Manyam1Leonie Florence Ott2Léa Berland3Erik Knutsen4Cristina Ivan5Leonard Lipovich6Bradley M. Broom7George A. Calin8Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USACenter for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USADepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USANon-coding RNAs (ncRNAs) are essential players in many cellular processes, from normal development to oncogenic transformation. Initially, ncRNAs were defined as transcripts that lacked an open reading frame (ORF). However, multiple lines of evidence suggest that certain ncRNAs encode small peptides of less than 100 amino acids. The sequences encoding these peptides are known as small open reading frames (smORFs), many initiating with the traditional AUG start codon but terminating with atypical stop codons, suggesting a different biogenesis. The ncRNA-encoded peptides (ncPEPs) are gradually becoming appreciated as a new class of functional molecules that contribute to diverse cellular processes, and are deregulated in different diseases contributing to pathogenesis. As multiple publications have identified unique ncPEPs, we appreciated the need for assembling a new web resource that could gather information about these functional ncPEPs. We developed FuncPEP, a new database of functional ncRNA encoded peptides, containing all experimentally validated and functionally characterized ncPEPs. Currently, FuncPEP includes a comprehensive annotation of 112 functional ncPEPs and specific details regarding the ncRNA transcripts that encode these peptides. We believe that FuncPEP will serve as a platform for further deciphering the biologic significance and medical use of ncPEPs. The link for FuncPEP database can be found at the end of the Introduction Section.https://www.mdpi.com/2311-553X/6/4/41non-coding RNAslong non-coding RNAsncRNA-encoded peptidessmall open reading framesncRNA translationsmall peptides |
| spellingShingle | Mihnea P. Dragomir Ganiraju C. Manyam Leonie Florence Ott Léa Berland Erik Knutsen Cristina Ivan Leonard Lipovich Bradley M. Broom George A. Calin FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs Non-Coding RNA non-coding RNAs long non-coding RNAs ncRNA-encoded peptides small open reading frames ncRNA translation small peptides |
| title | FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs |
| title_full | FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs |
| title_fullStr | FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs |
| title_full_unstemmed | FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs |
| title_short | FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs |
| title_sort | funcpep a database of functional peptides encoded by non coding rnas |
| topic | non-coding RNAs long non-coding RNAs ncRNA-encoded peptides small open reading frames ncRNA translation small peptides |
| url | https://www.mdpi.com/2311-553X/6/4/41 |
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