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)

SLA-1*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-10		ENSSSCG00000001227	7:24377123-24396966
SLA-10		ENSSSCG00000001229	7:24459993-24463671		FP085552,CH242-74M17,7:24423533-24504970 (Clone quality: bE74M17 on chr=7; Num_of_Contigs=9; )
SLA-10*		location ⇒	7:4426-4309		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-10*		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-10*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-10*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-11		ENSSSCG00000001341	7:26558428-26569310	CU498826,CH242-119D24,7:26553813-26728014 (Clone quality: bE119D24 on chr=7; Num_of_Contigs=31; )
SLA-2		ENSSSCG00000001229	7:24459993-24463671		FP085552,CH242-74M17,7:24423533-24504970 (Clone quality: bE74M17 on chr=7; Num_of_Contigs=9; )
SLA-2		ENSSSCG00000001231	7:24498283-24532919
SLA-2		ENSSSCG00000001227	7:24377123-24396966
SLA-2*		location ⇒	7:4426-4309		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-2*		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-2*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-2*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-3		ENSSSCG00000001229	7:24459993-24463671		FP085552,CH242-74M17,7:24423533-24504970 (Clone quality: bE74M17 on chr=7; Num_of_Contigs=9; )
SLA-3		ENSSSCG00000001227	7:24377123-24396966
SLA-3*		location ⇒	7:4426-4309		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-3*		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-3*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-3*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-4*		location ⇒	7:4426-4309		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-4*		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-4*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-4*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-5		ENSSSCG00000001227	7:24377123-24396966
SLA-5		ENSSSCG00000001229	7:24459993-24463671		FP085552,CH242-74M17,7:24423533-24504970 (Clone quality: bE74M17 on chr=7; Num_of_Contigs=9; )
SLA-5*		location ⇒	7:4426-4309		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-5*		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-5*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-5*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-6		ENSSSCG00000001398	7:27604072-27608114	CU467793,CH242-60C3,7:27581747-27762222 (Clone quality: bE60C3 on chr=7; Num_of_Contigs=1; )
SLA-6*		location ⇒	7:4426-4309		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-6*		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-6*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-6*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-7		ENSSSCG00000001397	7:27593568-27596822	CU467793,CH242-60C3,7:27581747-27762222 (Clone quality: bE60C3 on chr=7; Num_of_Contigs=1; )
SLA-7*		location ⇒	7:4426-4309		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-7*		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-7*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-7*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-8		ENSSSCG00000001396	7:27580187-27583921
SLA-8*		location ⇒	7:4426-4309		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-8*		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-8*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-8*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-9		ENSSSCG00000001230	7:24483668-24483922		FP085552,CH242-74M17,7:24423533-24504970 (Clone quality: bE74M17 on chr=7; Num_of_Contigs=9; )
SLA-9		ENSSSCG00000001227	7:24377123-24396966
SLA-9		ENSSSCG00000001229	7:24459993-24463671		FP085552,CH242-74M17,7:24423533-24504970 (Clone quality: bE74M17 on chr=7; Num_of_Contigs=9; )
SLA-9*		location ⇒	7:4426-4309		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )

Go to records:
1-49, 50-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-450, 451-500, 501-550, 551-600, 601-650, 651-700, 701-750, 751-800, 801-850, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-2250, 2251-2300, 2301-2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-16

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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).