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BGD specifications

Information


Unique identifier OMICS_04529
Name BGD
Alternative name Bovine Genome Database
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Bovine_genome_database

Taxon


  • Mammals
    • Bos taurus

Maintainer


  • person_outline Christine G. Elsik

Publications for Bovine Genome Database

BGD citations

 (8)
library_books

Correction of a Disease Mutation using CRISPR/Cas9 assisted Genome Editing in Japanese Black Cattle

2017
Sci Rep
PMCID: 5736618
PMID: 29259316
DOI: 10.1038/s41598-017-17968-w

[…] The search for off-target effects by the sgRNA sequence was performed using a web server for selecting rational CRISPR/Cas targets (CRISPRdirect, https://crispr.dbcls.jp) against bovine genome database [Cow genome, Bos_taurus_UMD_3.1.1/bosTau8 (Jun, 2014)]. The genomic region flanking the predicted off-target sites were amplified by PCR and sequences were determined by direct […]

library_books

Constructing a comprehensive gene co expression based interactome in Bos taurus

2017
PeerJ
PMCID: 5719962
PMID: 29226034
DOI: 10.7717/peerj.4107

[…] database, some of other datasets (like E-MTAB-2596) only have limited tissues. Therefore, we adopted gene expression data from 92 different tissues from the individual of the reference genome in the bovine genome database (BGD) (). By using RNAseq sequencing and mapping to the reference genome (University of Maryland version 3.1), all the genes in Bos taurus genome was quantified using the FPKM ( […]

call_split

A nonsense mutation in the COL7A1 gene causes epidermolysis bullosa in Vorderwald cattle

2016
BMC Genet
PMCID: 5131490
PMID: 27905875
DOI: 10.1186/s12863-016-0458-2
call_split See protocol

[…] riers. The genotypes of candidate causal variants were validated in 1682 animals from various bovine breeds that were available from the fifth run of the 1000 bull genomes project [] and our in-house bovine genome database [], respectively. Sequence variants that were homozygous for the non-reference allele in healthy animals were excluded as plausible candidate causal variants. The functional con […]

library_books

Global assessment of imprinted gene expression in the bovine conceptus by next generation sequencing

2016
Epigenetics
PMCID: 4939914
PMID: 27245094
DOI: 10.1080/15592294.2016.1184805

[…] e-RefSeq-Ensembl.txt. These parameters require at least 96% sequence identity for the RNAseq reads to be aligned. The known splicing junctions in Ensembl and RefSeq databases were downloaded from the Bovine Genome Database http://www.bovinegenome.org. The alignment of the RNAseq reads to the diploid genome was then merged to identify: i) reads that were aligned to the same single genomic position […]

library_books

Application of Functional Genomics for Bovine Respiratory Disease Diagnostics

2015
Bioinform Biol Insights
PMCID: 4620937
PMID: 26526746
DOI: 10.4137/BBI.S30525

[…] HPIDB can each add additional bits of relevant information to the list of genes, such as pathways represented, involvement in host innate immune responses, activity as TFs, etc. Resources such as the bovine genome database facilitate the analysis of the genomic context of bovine genes, while tissue-specific expression patterns can be inferred from the bovine gene atlas. Utilizing resources such as […]

call_split

Sexual polymorphisms of vomeronasal 1 receptor family gene expression in bulls, steers, and estrous and early luteal phase heifers

2015
PMCID: 4785117
PMID: 26477467
DOI: 10.1292/jvms.15-0300
call_split See protocol

[…] of Physiological Sciences (Physiological Society of Japan) and were approved by the Committee on Animal Experiments of the School of Veterinary Medicine, Yamaguchi University.In silico mining of the bovine genome database: Nucleotide sequences were obtained from NCBI Bos taurus annotation release 103. These genes were predicted by automated computational analysis, best-placed RefSeq Gnomon ver 5. […]

Citations

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BGD institution(s)
Department of Animal Science, Texas A&M University, College Station, TX, USA; Department of Biology, Georgetown University, WA, DC, USA; Department of Plant Biology, Michigan State University, East Lansing, MI, USA
BGD funding source(s)
USDA National Institute of Food and Agriculture – Agriculture and Food Research Initiative [2010-65205-20407, 2010-65205-20647]

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