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DoG_CNV : Database of Genomic Copy Number Variants in the dog genome




The LUPA project is a Collaborative Research Project funded by the European Commission under the 7th Research Framework Programme. An initiative of the LUPA group is to identify the catalogue of Copy Number Variants in the canine genome. DoG_CNV is the Database of Genomic Copy Number Variants in the canine genome. [Tutorial] This work is initiated by Hannes Lohi, Kerstin Lindblad-Toh, Matt Webster and Christophe Hitte Reference for this work: Novel origins of copy number variation in the dog genome. Jonas Berglund, Elisa M Nevalainen, Anna-Maja Molin, Michele Perloski, The LUPA consortium, Catherine Andre, Michael C Zody, Ted Sharpe, Christophe Hitte, Kerstin Lindblad-Toh, Hannes Lohi and Matthew T Webster Genome Biology 2012, 13:R73 (23 August 2012) [Abstract] [Provisional PDF] [PubMed] Statistics : Dogs Number of dogs analyzed: n=53 Number of breeds : 17 + Wolf [-Breed name and associated symbol-] CNV Number of high confidence CNVs: n=394 [-CNV dataset-] CNV detected as simple: n=324 [-SIMPLE dataset-] CNV detected as complex n=70 [-COMPLEX dataset-] Shared CNVs (occuring in multiple breeds): n=316 [-shared CNV dataset-] Breed specific CNVs (detected in one breed): n=78 [-breed specific dataset-] Raw graphic data for CNVs [-display graphic-] Cumulated size of CNV: 24,381,201 bp (0,975% of the dog genome)   Search Copy Number Variants by chromosome Select canine chromosome (Cfa): All 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 Search Copy Number Variants gene content Genes overlapping CNV (extract Ensembl link, gene id, gene sequence): [-Gene content dataset-]   Search Copy Number Variant that intersect canine genes Keyword query [gene_symbol, Ensembl_Id] (examples : FBXO2, ENSCAFG00000023373)     Search Copy Number Variant by genomic loci Keyword query [ locus coordinates ] (example : chr18:10000000-20000000)     Search Copy Number Variants by dog breeds Select one Breed : All Breed Border_Terrier Boxer Cavalier_King_Charles_Spaniel Chihuahua Dachshund English_Cocker_Spaniel English_Springer_Spaniel Finnish_Spitz German_Shepherd Golden_Retriever Irish_Wolfhound Labrador_Retriever Nova_Scotia_Duck_Tolling_Retriever Poodle Sarloos Schnauzer Swedish_Elkhound Wolf   Select Breed #1: All Breed Border_Terrier Boxer Cavalier_King_Charles_Spaniel Chihuahua Dachshund English_Cocker_Spaniel English_Springer_Spaniel Finnish_Spitz German_Shepherd Golden_Retriever Irish_Wolfhound Labrador_Retriever Nova_Scotia_Duck_Tolling_Retriever Poodle Sarloos Schnauzer Swedish_Elkhound Wolf Select chromosome: ALL 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38   Select a Breed : Border_Terrier Boxer Cavalier_King_Charles_Spaniel Chihuahua Dachshund English_Cocker_Spaniel English_Springer_Spaniel Finnish_Spitz German_Shepherd Golden_Retriever Irish_Wolfhound Labrador_Retriever Nova_Scotia_Duck_Tolling_Retriever Poodle Sarloos Schnauzer Swedish_Elkhound Wolf Select an other breed: Border_Terrier Boxer Cavalier_King_Charles_Spaniel Chihuahua Dachshund English_Cocker_Spaniel English_Springer_Spaniel Finnish_Spitz German_Shepherd Golden_Retriever Irish_Wolfhound Labrador_Retriever Nova_Scotia_Duck_Tolling_Retriever Poodle Sarloos Schnauzer Swedish_Elkhound Wolf   VISUALIZE Copy Number Variants in UCSC GENOME BROWSER [ - CNVs in UCSC Genome Browser -] - Format exemple : NSD_n=2_-1 Two individuals of the NSD breed present this CNV with -1 deletion - CNVs are represented by red and blue bars according to the consensus color scheme in genomics databases DGV, NCBI, DECIPHER, UCSC and ISCA [red for CNV loss, blue for CNV gain]. - A UCSC track has been customized to display all SNPs from the canine Illumina HD-array



 

 

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