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Home / Equine Research Bank / BMC Genomics / ASlive: a database for alternative splicing atlas in livesto...
BMC genomics2020; 21(1); 97; doi: 10.1186/s12864-020-6472-9

ASlive: a database for alternative splicing atlas in livestock animals.

Abstract: Alternative splicing is an important biological process whose precision must be tightly regulated during growth and development. Although there are species, disease (e.g. cancers), or study specific databases available in many organisms, no database exists in livestock animals specifically tailored for alternative splicing. Methods: We present in this study the development and implementation of a database for alternative splicing atlas in livestock animals (ASlive.org). Using publicly available RNASeq data sets across many tissues, cell types, and biological conditions totaling 28.6 T bases, we built a database of alternative splicing events in five major livestock and poultry animal species (cattle, sheep, pigs, horses, and chickens). The database contains many types of information on alternative splicing events, including basic information such as genomic locations, genes, and event types, quantitative measurements of alternative splicing in the form of percent spliced in (PSI), overlap with known DNA variants, as well as orthologous events across different lineage groups. Conclusions: This database, the first of its kind in livestock animals, will provide a useful exploratory tool to assist functional annotation of animal genomes.
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Publication Date: 2020-01-30 PubMed ID: 32000661PubMed Central: PMC6993437DOI: 10.1186/s12864-020-6472-9Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research article discusses the development and implementation of ASlive, a unique database that provides a comprehensive catalogue of alternative splicing events in livestock animals. It uses publicly available RNASeq data sets across several tissues, cell types, and biological conditions, providing crucial data to aid in functional annotation of animal genomes.

Introduction

  • Alternative splicing is a fundamental biological mechanism which needs precise regulation for growth and development. While there are databases present for a range of organisms, none exists specifically for livestock animals.

ASlive Database Development and Implementation

  • The researchers in this study have developed and implemented a unique database named ASlive.org for the atlas of alternative splicing in livestock animals.
  • This database is built using publicly available RNASeq data sets, collected across a wide range of tissues, cell types, and biological conditions.
  • The data utilized for building the database totals 28.6 trillion bases.
  • The alternative splicing events are cataloged for five major livestock and poultry animal species including cattle, sheep, pigs, horses, and chickens.

Features and Data of ASlive

  • The database contains a plethora of information on alternative splicing events.
  • It offers basic information such as genomic locations, genes involved, and the types of events.
  • Quantitative measures of alternative splicing are included in the form of percentage spliced in (PSI).
  • Overlap with known DNA variants is provided along with orthologous events spread over different lineage groups.

Conclusion

  • This research has led to the creation of the first-ever database of this kind for livestock animals.
  • This useful tool enables exploration and aids in the functional annotation of animal genomes.

Cite This Article

APA
Liu J, Tan S, Huang S, Huang W. (2020). ASlive: a database for alternative splicing atlas in livestock animals. BMC Genomics, 21(1), 97. https://doi.org/10.1186/s12864-020-6472-9

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 21
Issue: 1
Pages: 97
PII: 97

Researcher Affiliations

Liu, Jinding
  • College of Information Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
  • Research Center for Correlation of Domain Knowledge, Nanjing Agricultural University, Nanjing, 210095, China.
  • Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA.
Tan, Suxu
  • Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA.
Huang, Shuiqing
  • College of Information Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China. sqhuang@njau.edu.cn.
  • Research Center for Correlation of Domain Knowledge, Nanjing Agricultural University, Nanjing, 210095, China. sqhuang@njau.edu.cn.
Huang, Wen
  • Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA. huangw53@msu.edu.

MeSH Terms

  • Alternative Splicing
  • Animals
  • Cattle
  • Databases, Genetic
  • Horses
  • Livestock / genetics
  • Sequence Alignment / veterinary
  • Sequence Analysis, RNA / veterinary
  • Sheep
  • Swine

Grant Funding

  • NA / Nanjing Agricultural University
  • NA / Michigan State University

Conflict of Interest Statement

The authors declare that they have no competing interests.

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Citations

This article has been cited 5 times.
  1. Liu J, Lang K, Tan S, Jie W, Zhu Y, Huang S, Huang W. A web-based database server using 43,710 public RNA-seq samples for the analysis of gene expression and alternative splicing in livestock animals.. BMC Genomics 2022 Oct 17;23(1):706.
    doi: 10.1186/s12864-022-08881-2pubmed: 36253723google scholar: lookup
  2. Xia H, Li F, Peng L, Du Y, Hua G, Yang L, Zhou Y. Over-Expression of Two Different Isoforms of Cattle TUSC5 Showed Opposite Effects on Adipogenesis.. Genes (Basel) 2022 Aug 14;13(8).
    doi: 10.3390/genes13081444pubmed: 36011355google scholar: lookup
  3. Tan S, Wang W, Jie W, Liu J. FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species.. Comput Struct Biotechnol J 2022;20:3676-3684.
    doi: 10.1016/j.csbj.2022.07.015pubmed: 35891795google scholar: lookup
  4. Chakraborty D, Sharma N, Kour S, Sodhi SS, Gupta MK, Lee SJ, Son YO. Applications of Omics Technology for Livestock Selection and Improvement.. Front Genet 2022;13:774113.
    doi: 10.3389/fgene.2022.774113pubmed: 35719396google scholar: lookup
  5. Liu J, Yin F, Lang K, Jie W, Tan S, Duan R, Huang S, Huang W. MetazExp: a database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species.. Nucleic Acids Res 2022 Jan 7;50(D1):D1046-D1054.
    doi: 10.1093/nar/gkab933pubmed: 34718719google scholar: lookup
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