| Data
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• 3,624,831 sequence variation sites identified, including 1,190,072 in the Broiler, 1,009,693 in Layer and 1,425,066 in Silkie.
• 35,647 genes or full length cDNAs, including 2,068 GenBank genes, 28,416 Ensembl gene annotations, 1,825 Riken1 full-length cDNAs, 1,943 BBSRC full-length cDNAs, 995 chicken orthologs of human disease genes etc..
• 1,397,577 SNPs are associated with 33,566 Genes.
• 1,480,658 contig-covered (CtgCoV) regions are mapped onto the RJF genome assembly. The percentage length of CtgCoV regions on RJF genome assembly are 25.6% (broiler/RJF), 25.0% (layer/RJF) and 27.3% (Silkie/RJF).
• 2,544,985 raw sequence traces, among which 1,205,058 are SNP-associated.
• 606 QTLs are collected from both cooperative institutions and public resources.
• 884 references are collected with focus on chicken variation and QTL study. |
Users can access the data via modules of Search, MapView and Tools-Blast. Clicking an object's name to enter the Search module. |
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| Gene |
Including a collection and curation of Ensembl gene annotations, GenBank genes, Riken1 full-length cDNAs, BBSRC full-length cDNAs and chicken orthologs of human disease genes. Gene structure, functional classification, gene ontology and InterPro annotations,
gene-associated SNPs, nucleotide/protein sequences, and links to reference Ensembl or GenBank entries are described in “Gene Report”. |
| QTL |
| Including a collection and curation of QTL information from both cooperative institutions and public resources. “QTL Report” includes trait locus, trait description, cross/population, analysis method, reference, linked markers, genes and SNPs etc. |
| Sequence |
| Including RJF genomic sequences, contigs of the broiler, layer and Silkie, nucleotide sequences of SNP flanking regions, genes, cDNA, reads, and the coded protein sequences. |
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| SNP |
| For the convenience of data presentation in ChickVD, different types of sequence variations (substitutions, insertions or deletions) are all referred as ‘SNPs'. ChickVD contains SNPs in the broiler, layer and Silkie. Detailed information for each SNP is displayed in “SNP Report”, including SNP type, allele bases, SNP flanking sequences and designed PCR-primers, SNP location, SNP-associated genes and reads with quality scores, SNP functional site on its host gene ( e.g. , coding region, intron, untranslated regions), and as well as details of any predicted or known functional outcomes ( e.g. , codon and deduced amino-acid changes). |
| References |
| Including a collection of papers with focus on chicken variation and QTL study. Publication date ranges from year 1980 till now. |
| Tracefile |
| Users may search graphics of raw sequence traces by tracefile name or tracefile-related SNPs. |
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