Pig genome annotation: A Gene Wish List

A Wish List of Genes for Annotation (version 3.26)

(Matches to BACs by their Genome Locations Based on Pig Genome Build v.9 (Data Downloads as of Mar. 7, 2010 )

Info:

Purpose: Help users to find where to go from gene names to their genome locations/BACs in order to locate a starting spot in the pig genome to bring into Otterlace for annotations.
Methods: The gene locations are determined in 2 ways: Ensembl predictions and Blasts. Clones are sought based on their overlapping genome locations with that of your gene.
Terms: Finished BACs: A total of 811 "finished" clones that met the "golden standard" of finished sequencing quality. Unfinished clones: Out of 15,837 clones on the "unfinished clones" list, only 1,769 have been processed to have genome locations. FPC clones: 254K+ of those clones in the sequencing pipeline
Related links:

HINTS:

Owner/Status info: : Someone has this gene on their wish-list to annotate. : This gene is to be annotated. : This gene has been annotated (click to check for details - maybe only a gene variant is annotated. The ultimate annotator list is from Otterlace entries; This list only provides a working reference).
Additional info: : have orthologous gene information. : have refseq information. : details (click for more)
Ensembl Gene ID, Genome Locations, and BAC names are all hyper-linked to Ensembl database

( Go to genes whose symbol start with: 1, 5, 7, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z )
Search results:	Show Finished BAC Show unFinished BAC

User Gene List			Genome Location (Chr.:start-end)	Fell within Finished BACs (Contig, BACname, Chr.:Start-End)	Fell within Unfinished Clones (SeqName, Chr.:Start-End)
Symbol	Owner/ Status	Ensembl Gene ID	Genome Location (Chr.:start-end)	Fell within Finished BACs (Contig, BACname, Chr.:Start-End)	Fell within Unfinished Clones (SeqName, Chr.:Start-End)

YWHAZ		location ⇒	10:35713528-35713597		CU633163,CH242-209C6,10:35703134-35847997 (Clone quality: bE209C6 on chr=10; Num_of_Contigs=3; )
YY1		ENSSSCG00000011517	13:45455083-45456428		CU633640,CH242-164P16,13:45386486-45505220 (Clone quality: bE164P16 on chr=13; Num_of_Contigs=4; )
YY1		location ⇒	7:130650761-130649895		CU896696,CH242-232N15,7:130600538-130650859 (Clone quality: bE232N15 on chr=7; Num_of_Contigs=5; )
YY1		location ⇒	7:130651825-130651762		CU896696,CH242-232N15,7:130650960-130679042 (Clone quality: bE232N15 on chr=7; Num_of_Contigs=5; )
YY1		location ⇒	7:130662506-130662355		CU896696,CH242-232N15,7:130650960-130679042 (Clone quality: bE232N15 on chr=7; Num_of_Contigs=5; )
Y_RNA		ENSSSCG00000019803	14:115783678-115783775		CU407002,CH242-427K14,14:115736639-115822002 (Clone quality: bE427K14 on chr=14; Num_of_Contigs=2; )
Y_RNA		ENSSSCG00000019375	9:101884114-101884226		FP103024,CH242-322I13,9:101863037-101887962 (Clone quality: bE322I13 on chr=9; Num_of_Contigs=4; )
Y_RNA		ENSSSCG00000018847	7:53159666-53159758		CT842532,CH242-280I14,7:53095919-53164545 (Clone quality: bE280I14 on chr=7; Num_of_Contigs=4; )
Y_RNA		ENSSSCG00000018723	18:9190314-9190411		FP236752,CH242-135G1,18:9146556-9190823 (Clone quality: bE135G1 on chr=18; Num_of_Contigs=4; )
Y_RNA		ENSSSCG00000018715	9:101909504-101909600		FP103024,CH242-322I13,9:101888063-101933708 (Clone quality: bE322I13 on chr=9; Num_of_Contigs=4; )
Y_RNA		ENSSSCG00000018504	10:4625633-4625730		CU928114,CH242-53P22,10:4620392-4630083 (Clone quality: bE53P22 on chr=10; Num_of_Contigs=15; )
Y_RNA		ENSSSCG00000018249	13:61412890-61412999		CU633685,CH242-265M20,13:61378623-61549248 (Clone quality: bE265M20 on chr=13; Num_of_Contigs=2; )
Y_RNA		ENSSSCG00000018101	9:101887536-101887637		FP103024,CH242-322I13,9:101863037-101887962 (Clone quality: bE322I13 on chr=9; Num_of_Contigs=4; )

Go to records:
1-49, 50-13

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$version: 3.26; Updates: Mar. 6, 2010; Apr. 20, 2010; Aug 21, 2010

Related publications:

Martien Groenen, Alan Archibald, Hirohide Uenishi, Christopher Tuggle, Yasuhiro Takeuchi, Max Rothschild, Claire Rogel-Gaillard, ... Denis Milan, Hendrik-Jan Megens, ... Zhi-Liang Hu, Sean J. Humphray, ... James M. Reecy, ..., Gary A. Rohrer, ... Shuhong Zhao, Jane Rogers, Carol Churcher & Lawrence B. Schook. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491, 393-398 (15 November 2012).