PUBLICATION
HRGFish: A database of hypoxia responsive genes in fishes
- Authors
- Rashid, I., Nagpure, N.S., Srivastava, P., Kumar, R., Pathak, A.K., Singh, M., Kushwaha, B.
- ID
- ZDB-PUB-170217-3
- Date
- 2017
- Source
- Scientific Reports 7: 42346 (Journal)
- Registered Authors
- Keywords
- none
- MeSH Terms
-
- Animals
- DNA Primers/metabolism
- Databases, Genetic*
- Fishes/genetics*
- Hypoxia/genetics*
- Internet
- Response Elements
- Sequence Alignment
- User-Computer Interface
- PubMed
- 28205556 Full text @ Sci. Rep.
Citation
Rashid, I., Nagpure, N.S., Srivastava, P., Kumar, R., Pathak, A.K., Singh, M., Kushwaha, B. (2017) HRGFish: A database of hypoxia responsive genes in fishes. Scientific Reports. 7:42346.
Abstract
Several studies have highlighted the changes in the gene expression due to the hypoxia response in fishes, but the systematic organization of the information and the analytical platform for such genes are lacking. In the present study, an attempt was made to develop a database of hypoxia responsive genes in fishes (HRGFish), integrated with analytical tools, using LAMPP technology. Genes reported in hypoxia response for fishes were compiled through literature survey and the database presently covers 818 gene sequences and 35 gene types from 38 fishes. The upstream fragments (3,000 bp), covered in this database, enables to compute CG dinucleotides frequencies, motif finding of the hypoxia response element, identification of CpG island and mapping with the reference promoter of zebrafish. The database also includes functional annotation of genes and provides tools for analyzing sequences and designing primers for selected gene fragments. This may be the first database on the hypoxia response genes in fishes that provides a workbench to the scientific community involved in studying the evolution and ecological adaptation of the fish species in relation to hypoxia.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping