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Protocols

ALDB specifications

Information


Unique identifier OMICS_09892
Name ALDB
Restrictions to use None
Version 1.0
Maintained Yes

Taxon


  • Vertebrates
    • Gallus gallus

Maintainer


  • person_outline Junying Zhang

Publication for ALDB

ALDB citations

 (19)
library_books

Identification and Functional Analysis of Long Intergenic Non coding RNAs Underlying Intramuscular Fat Content in Pigs

2018
Front Genet
PMCID: 5890112
PMID: 29662503
DOI: 10.3389/fgene.2018.00102

[…] ng to 22,329 genes in the pig annotation in Ensembl database, and 12,103 known lincRNA transcripts encoded by 7,381 lincRNA genes in the pig lincRNA annotation in the domestic-animal lncRNA database (ALDB) exist (; ). We used the Kolomogorv–Smirnov-test method to test the differences. We found that overall novel lincRNA transcripts (mean 872 bp) were shorter than known lincRNA transcripts (mean 1, […]

library_books

Dissection of Myogenic Differentiation Signatures in Chickens by RNA Seq Analysis

2018
Genes
PMCID: 5793186
PMID: 29324704
DOI: 10.3390/genes9010034

[…] rough all of the filters mentioned above were collected as a candidate set of lncRNAs and were then blasted against the chicken lncRNAs retrieved from the Domestic-Animal Long Noncoding RNA Database (ALDB) v1.0 []. […]

library_books

Indole 3 acetaldehyde dehydrogenase dependent auxin synthesis contributes to virulence of Pseudomonas syringae strain DC3000

2018
PLoS Pathog
PMCID: 5766252
PMID: 29293681
DOI: 10.1371/journal.ppat.1006811

[…] The pET28a-AldA, pET28a-AldB, and pET28a-AldC constructs used to express protein for biochemical experiments were generated using NdeI and XhoI enzyme sites and transformed into E. coli BL21 (DE3) cells (Agilent Technologies […]

library_books

Differential regulation of mRNAs and lncRNAs related to lipid metabolism in two pig breeds

2017
Oncotarget
PMCID: 5675652
PMID: 29152100
DOI: 10.18632/oncotarget.20978

[…] re applied to assess the protein-coding potential of the above-obtained transcripts and the intersection of results from these software was as the finally result. (4) Identification of known lncRNAs. ALDB (A Domestic-Animal Long Noncoding RNA Database) [] is a database with a focus on the domestic-animal lncRNAs. BLASTN tool was used to align lncRNA candidates to lncRNAs in the database with the s […]

library_books

Systematic analysis of transcription start sites in avian development

2017
PLoS Biol
PMCID: 5600399
PMID: 28873399
DOI: 10.1371/journal.pbio.2002887

[…] s and peak values on galGal5, the latest version of chicken genome assembly. It was also fully integrated with the latest chicken genome annotation resources, including Ensembl, RefSeq, EST, NONCODE, ALDB-lincRNA, and highly conserved elements (HCEs) from 48 representative avian species [,]. Genes and TSSs could be searched and visualized at desirable genomic resolutions, from single nucleotide to […]

library_books

Analyses of Long Non Coding RNA and mRNA profiling using RNA sequencing in chicken testis with extreme sperm motility

2017
Sci Rep
PMCID: 5567338
PMID: 28831078
DOI: 10.1038/s41598-017-08738-9

[…] oding potential in any of the three tools were filtered out.Transcripts that passed all the filters mentioned above were considered as candidate lncRNA and were then blasted to chicken lncRNAs in the ALDB v1.0 database. Refgene annotation was used to search the nearest neighboring genes of lncRNAs, and 100 kb was set as the threshold. […]

Citations

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ALDB institution(s)
School of Computer Science and Technology, Xidian University, XI'an, Shaanxi, China

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