Evidence map›Paper›PMID 32512182›Full record

ArticleGenomics, proteomics & bioinformatics2020

IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites.

Jian Zhao, Yan Li, Cong Wang, Haotian Zhang, Hao Zhang, Bin Jiang, Xuejiang Guo, Xiaofeng Song

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genomics, proteomics & bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.

0numbers the graph read from it
0cells of the map it votes in
65citing papers in PubMed
9.4field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

65 citing papers in PubMed, 114 citations in OpenAlex.

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5 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 2 institutions in 1 country.

Jian ZhaoDepartment of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China.
Yan LiState Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China; Center of Pathology and Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China.
Cong WangDepartment of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China.
Haotian ZhangState Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China.
Hao ZhangState Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China.
Bin JiangCollege of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China.
Xuejiang GuoState Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China. Electronic address: guo_xuejiang@njmu.edu.cn.
Xiaofeng SongDepartment of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China. Electronic address: xfsong@nuaa.edu.cn.
Nanjing Medical University · CNNanjing University of Aeronautics and Astronautics · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Internal ribosome entry sites (IRESs) are functional RNA elements that can directly recruit ribosomes to an internal position of the mRNA in a cap-independent manner to initiate translation. Recently, IRES elements have attracted much attention for their critical roles in various processes including translation initiation of a new type of RNA, circular RNA (circRNA), with no 5' cap to support classical cap-dependent translation. Thus, an integrative data resource of IRES elements with experimental evidence will be useful for further studies. In this study, we present IRESbase, a comprehensive database of IRESs, by curating the experimentally validated functional minimal IRES elements from literature and annotating their host linear and circular RNAs. The current version of IRESbase contains 1328 IRESs, including 774 eukaryotic IRESs and 554 viral IRESs from 11 eukaryotic organisms and 198 viruses, respectively. As IRESbase collects only IRES of minimal length with functional evidence, the median length of IRESs in IRESbase is 174 nucleotides. By mapping IRESs to human circRNAs and long non-coding RNAs (lncRNAs), 2191 circRNAs and 168 lncRNAs were found to contain at least one entire or partial IRES sequence. IRESbase is available at http://reprod.njmu.edu.cn/cgi-bin/iresbase/index.php.

Indexed as

Databases, GeneticBase SequenceHumansInternal Ribosome Entry SitesProtein BiosynthesisRibosomesRNA, MessengerUser-Computer InterfaceInternal Ribosome Entry SitesRNA, MessengerCircular RNAEukaryotic IRESIRESLong non-coding RNAViral IRES

Identifiers

PMID32512182
PMCPMC7646085
OpenAlexW3033368660

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.