CACG: a database for comparative analysis of conjoined genes.
Abstract: A conjoined gene is defined as one formed at the time of transcription by combining at least part of one exon from each of two or more distinct genes that lie on the same chromosome, in the same or opposite orientation, which translate independently into different proteins. We comparatively studied the extent of conjoined genes in thirteen genomes by analyzing the public databases of expressed sequence tags and mRNA sequences using a set of computational tools designed to identify conjoined genes on the same DNA strand or opposite DNA strands of the same genomic locus. The CACG database, available at http://cgc.kribb.re.kr/map/, includes a number of conjoined genes (7131-human, 2-chimpanzee, 5-orangutan, 57-chicken, 4-rhesus monkey, 651-cow, 27-dog, 2512-mouse, 263-rat, 1482-zebrafish, 5-horse, 29-sheep, and 8-medaka) and is very effective and easy to use to analyze the evolutionary process of conjoined genes when comparing different species.
Copyright © 2012 Elsevier Inc. All rights reserved.
Publication Date: 2012-05-11 PubMed ID: 22584068DOI: 10.1016/j.ygeno.2012.05.005Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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This study introduces a database known as Comparative Analysis of Conjoined Genes (CACG) which offers a comprehensive database of conjoined genes across thirteen different species. It provides important insights into the evolution and functions of these conjoined genes.
What are Conjoined Genes?
- Conjoined genes are unique molecular structures where at least part of one exon from two distinct genes combine during transcription.
- These genes lie on the same chromosome and can be oriented in the same or opposite direction.
- Despite being connected, each gene within the conjoined structure translates independently into different proteins.
Database Creation and Analysis
- The researchers studied thirteen different genomes to understand the extent of conjoined genes within them.
- They used available public databases of expressed sequence tags and mRNA sequences for this analysis.
- They developed and utilized computational tools specifically designed to identify conjoined genes on the same DNA strand or opposing DNA strands of the same genomic locus.
The Comparative Analysis of Conjoined Genes (CACG) Database
- The CACG database houses information on a large number of conjoined genes from thirteen diverse species, including humans, chimpanzees, and mice among others.
- An exact count of conjoined genes in each species is given (e.g., 7131-human, 2-chimpanzee).
- This database can be freely accessed online and offers an effective and user-friendly platform for analyzing the evolutionary process of conjoined genes.
Significance of the Database
- This database provides comparative datasets for conjoined genes across multiple species, offering an invaluable tool for understanding the evolution and function of conjoined genes.
- It provides useful insights for clinical research as alterations or mutations in conjoined genes may be associated with certain diseases or health conditions.
Cite This Article
APA
Kim DS, Kim DW, Kim MY, Nam SH, Choi SH, Kim RN, Kang A, Kim A, Park HS.
(2012).
CACG: a database for comparative analysis of conjoined genes.
Genomics, 100(1), 14-17.
https://doi.org/10.1016/j.ygeno.2012.05.005 Publication
Researcher Affiliations
- Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea.
MeSH Terms
- Animals
- Cattle
- Chickens
- Computational Biology / methods
- Databases, Genetic
- Dogs
- Exons / genetics
- Expressed Sequence Tags
- Genome
- Genomics
- Horses
- Humans
- Macaca mulatta
- Mice
- Oryzias
- Pan troglodytes
- Phylogeny
- Pongo
- RNA Splicing / genetics
- RNA, Messenger / genetics
- Rats
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Analysis, RNA
- Sheep
- Zebrafish
Citations
This article has been cited 5 times.- Severgnini M, D'Angiò M, Bungaro S, Cazzaniga G, Cifola I, Fazio G. Conjoined Genes as Common Events in Childhood Acute Lymphoblastic Leukemia. Cancers (Basel) 2022 Jul 20;14(14).
- Patel BV, Yao F, Howenstine A, Takenaka R, Hyatt JA, Sears KE, Shewchuk BM. Emergent Coordination of the CHKB and CPT1B Genes in Eutherian Mammals: Implications for the Origin of Brown Adipose Tissue. J Mol Biol 2020 Nov 20;432(23):6127-6145.
- Qin F, Song Z, Chang M, Song Y, Frierson H, Li H. Recurrent cis-SAGe chimeric RNA, D2HGDH-GAL3ST2, in prostate cancer. Cancer Lett 2016 Sep 28;380(1):39-46.
- Ren G, Zhang Y, Mao X, Liu X, Mercer E, Marzec J, Ding D, Jiao Y, Qiu Q, Sun Y, Zhang B, Yeste-Velasco M, Chelala C, Berney D, Lu YJ. Transcription-mediated chimeric RNAs in prostate cancer: time to revisit old hypothesis?. OMICS 2014 Oct;18(10):615-24.
- Greger L, Su J, Rung J, Ferreira PG, Lappalainen T, Dermitzakis ET, Brazma A. Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants. PLoS One 2014;9(8):e104567.
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