Announcements

If you use any data share by this database (PigRIPdb), that means you’ve agreed to these terms.

1. You agree to use data for non-commercial research purposes only;

2. You agree that you will not attempt to link the data provided to a third-party database except permitted by us;

3. You agree not to transfer or disclose all or part of the data to others. Instead, please direct them to this website;

4. You understand and acknowledge that data is protected by copyright and other intellectual property rights. Providers shall have the sole right to prosecute patents and patent application claiming or covering unauthorized data and Inventions;

5. You accept that this agreement will terminate immediately after you violate this agreement, and you will be required to destroy any data you hold;

6. You accept that it may be necessary for the project team or its designated agent to change the terms of this agreement from time to time to solve new problems. Providers reserve the right to change these terms at any time without prior notice. Use of this website will be subject to the terms of use of the latest version published on this website.

 Updates

PigRIPdb version 1; released time 2025-1-1

 Use tutorial

1. You can visually browse the RIPs in specific genome regions through RIPBrower and display basic information about the sites by clicking on the RIP icons. Additionally, in RIPBrower, you can specify whether to display genomic annotation information, making it easy to explore the genomic context surrounding RIPs.

2. In RIPSearch, you can search for site information using a single condition, or you can combine multiple conditions for a more refined search. You can also retrieve information from specific sites or within a certain range around genes. The results include basic information about the sites, the RIP sites present in the region, and provide the corresponding windows in RIPBrower.

3. If you only have a sequence in hand, (1) you can search for the presence of RIP site information in the corresponding reference genomic region by using the “RIP Blast” module in Blast. (2) By using the “Basic Blast” module in Blast, you can blast your query sequence against transposable element sequences from pigs to determine if there are any transposable element components in your query. You can also compare your query sequence with the reference genomic sequence to obtain its position in the genome, which can then be used to retrieve RIP information in RIPSearch.

4. You can also log into the Download module to download the relevant data to your local machine for further scientific research. Please ensure compliance with the announcements in Help.

5. The Tools and Links section provides URLs or descriptions of various databases and tools for reference by related researchers.

6. In Help, we provide basic information, including announcements, data submission tutorial, contact information, and citation guidelines.

 Submission tutorial

1. Please fill in the RIP information in the “RIP_Share_Template” provided below.

2. Please make sure that the data is generated by yourself or your team and does not contain any copyright or ethical issues.

3. Please send your data to cchen@yzu.edu.cn or cysong@yzu.edu.cn. If your file is too large to email, please contact us to provide alternative submission method.

 Contact:

PigRIPdb was developed by Lab of Transposon (https://en.mobilome.cn/)

Chengyi Song, Ph. D. (Principal Investigator)

Email: cysong@yzu.edu.cn

Cai Chen, Ph.D. Email: cchen@yzu.edu.cn

Email: cchen@yzu.edu.cn

Naisu Yang, Ph.D. Email: naisu.yang@yzu.edu.cn

Email: naisu.yang@yzu.edu.cn

 Citation:

The PigRIPdb manuscript is reviewing

 Reference:

1. Chen C, D'Alessandro E, Murani E, Zheng Y, Giosa D, Yang N, Wang X, Gao B, Li K, Wimmers K, Song C. SINE jumping contributes to large-scale polymorphisms in the pig genomes. Mob DNA. 2021 Jun 28;12(1):17. doi: 10.1186/s13100-021-00246-y. PMID: 34183049; PMCID: PMC8240389.

2. Zong W, Zhao R, Wang X, Zhou C, Wang J, Chen C, Niu N, Zheng Y, Chen L, Liu X, Hou X, Zhao F, Wang L, Wang L, Song C, Zhang L. Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig. DNA Res. 2024 Apr 1;31(2):dsae008. doi: 10.1093/dnares/dsae008. PMID: 38447059; PMCID: PMC11090087.

3. Du Z, Chen C, Zheng Y, Wang X, Song C. Retroviral Insertion Polymorphism (RIP) of Porcine Endogenous Retroviruses (PERVs) in Pig Genomes. Animals (Basel). 2024 Feb 15;14(4):621. doi: 10.3390/ani14040621. PMID: 38396589; PMCID: PMC10886097.

4. Chen C, Du Z, Zheng Y, Chen H, Saleh AA, Yang N, Wang M, Azele P, Wang X, Song C. Investigation of Polymorphisms Induced by the Solo Long Terminal Repeats (Solo-LTRs) in Porcine Endogenous Retroviruses (ERVs). Viruses. 2024 Nov 20;16(11):1801. doi: 10.3390/v16111801. PMID: 39599915; PMCID: PMC11598996.

5. Hao, G. U., et al. "A 314-bp SINE insertion in the ZNF2 promoter region may act as a repressor related to regulation of fat deposition in pigs." Journal of Integrative Agriculture 22.2 (2023): 526-536.

6. Zheng Y, Chen C, Wang M, Moawad AS, Wang X, Song C. SINE Insertion in the Pig Carbonic Anhydrase 5B (CA5B) Gene Is Associated with Changes in Gene Expression and Phenotypic Variation. Animals (Basel). 2023 Jun 9;13(12):1942. doi: 10.3390/ani13121942. PMID: 37370452; PMCID: PMC10295633.

7. He J, Yu M, Chi C, Du Z, Zheng Y, Chen C, Moawad AS, Song C, Wang X. Insertion of 643bp Retrotransposon Upstream of PPARγ CDS Is Associated with Backfat of Large White Pigs. Animals (Basel). 2023 Jul 19;13(14):2355. doi: 10.3390/ani13142355. PMID: 37508132; PMCID: PMC10376311.

8. Chi C, He J, Du Z, Zheng Y, D'Alessandro E, Chen C, Moawad AS, Asare E, Song C, Wang X. Two Retrotransposon Elements in Intron of Porcine BMPR1B Is Associated with Phenotypic Variation. Life (Basel). 2022 Oct 20;12(10):1650. doi: 10.3390/life12101650. PMID: 36295085; PMCID: PMC9604734.

9. Wang X, Chi C, He J, Du Z, Zheng Y, D'Alessandro E, Chen C, Moawad AS, Asare E, Song C. SINE Insertion May Act as a Repressor to Affect the Expression of Pig LEPROT and Growth Traits. Genes (Basel). 2022 Aug 10;13(8):1422. doi: 10.3390/genes13081422. PMID: 36011333; PMCID: PMC9407865.

10. Du Z, D'Alessandro E, Asare E, Zheng Y, Wang M, Chen C, Wang X, Song C. Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes. Genes (Basel). 2022 Jul 28;13(8):1359. doi: 10.3390/genes13081359. PMID: 36011270; PMCID: PMC9407582.

11. Wang X, D'Alessandro E, Chi C, Moawad AS, Zong W, Chen C, Song C. Genetic Evaluation and Population Structure of Jiangsu Native Pigs in China Revealed by SINE Insertion Polymorphisms. Animals (Basel). 2022 May 25;12(11):1345. doi: 10.3390/ani12111345. PMID: 35681812; PMCID: PMC9179424.

12. Du Z, D'Alessandro E, Zheng Y, Wang M, Chen C, Wang X, Song C. Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes. Animals (Basel). 2022 Apr 8;12(8):969. doi: 10.3390/ani12080969. PMID: 35454216; PMCID: PMC9031378.

13. Wang X, Chen Z, Murani E, D'Alessandro E, An Y, Chen C, Li K, Galeano G, Wimmers K, Song C. A 192 bp ERV fragment insertion in the first intron of porcine TLR6 may act as an enhancer associated with the increased expressions of TLR6 and TLR1. Mob DNA. 2021 Aug 18;12(1):20. doi: 10.1186/s13100-021-00248-w. PMID: 34407874; PMCID: PMC8375133.

14. Chen C, Zheng Y, Wang M, Murani E, D'Alessandro E, Moawad AS, Wang X, Wimmers K, Song C. SINE Insertion in the Intron of Pig GHR May Decrease Its Expression by Acting as a Repressor. Animals (Basel). 2021 Jun 23;11(7):1871. doi: 10.3390/ani11071871. PMID: 34201672; PMCID: PMC8300111.

15. Chen C, Wang X, Zong W, D'Alessandro E, Giosa D, Guo Y, Mao J, Song C. Genetic Diversity and Population Structures in Chinese Miniature Pigs Revealed by SINE Retrotransposon Insertion Polymorphisms, a New Type of Genetic Markers. Animals (Basel). 2021 Apr 15;11(4):1136. doi: 10.3390/ani11041136. PMID: 33921134; PMCID: PMC8071531.

16. Chen C, Wang W, Wang X, Shen D, Wang S, Wang Y, Gao B, Wimmers K, Mao J, Li K, Song C. Retrotransposons evolution and impact on lncRNA and protein coding genes in pigs. Mob DNA. 2019 May 6;10:19. doi: 10.1186/s13100-019-0161-8. PMID: 31080521; PMCID: PMC6501411.