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)

PPAPDC1B		ENSSSCG00000015819	15:45828222-45833734		CU570721,CH242-1H2,15:45819566-45835855 (Clone quality: bE1H2 on chr=15; Num_of_Contigs=6; )
PPAPDC2		ENSSSCG00000005220	1:227406552-227407454		CU041279,CH242-42M5,1:227392311-227411627 (Clone quality: bE42M5 on chr=1; Num_of_Contigs=7; )
PPAPDC3		ENSSSCG00000005713	1:286512638-286513147		CU928974,CH242-58K9,1:286511934-286514293 (Clone quality: bE58K9 on chr=1; Num_of_Contigs=32; )
PPAPR3		ENSSSCG00000005393	1:254350768-254688760
PPAPR5		ENSSSCG00000006876	4:123750178-123899065
PPARA		ENSSSCG00000000006	5:142391-161045
PPARA		location ⇒	5:142630-142390		FP016092,CH242-185O3,5:122470-146185 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
PPARA		location ⇒	5:145448-145001		FP016092,CH242-185O3,5:122470-146185 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
PPARA		location ⇒	5:150028-149838		FP016092,CH242-185O3,5:146286-160061 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
PPARA		location ⇒	5:152763-152664		FP016092,CH242-185O3,5:146286-160061 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
PPARBP		ENSSSCG00000017505	12:20802497-20902249
PPARBP		location ⇒	12:20802517-20802732		FP236573,CH242-65A8,12:20790156-20809394 (Clone quality: bE65A8 on chr=12; Num_of_Contigs=3; )
PPARBP		location ⇒	12:20833055-20833837
PPARBP		location ⇒	12:20874033-20874248		CU942400,CH242-320P18,12:20873440-20885634 (Clone quality: bE320P18 on chr=12; Num_of_Contigs=18; )
PPARBP		location ⇒	12:20904520-20905419		CU942400,CH242-320P18,12:20885735-20908189 (Clone quality: bE320P18 on chr=12; Num_of_Contigs=18; )
PPARD		ENSSSCG00000001539	7:35734820-35881353
PPARD		location ⇒	7:35809766-35810217		CU571051,CH242-525J6,7:35801913-35828071 (Clone quality: bE525J6 on chr=7; Num_of_Contigs=14; )
PPARD		location ⇒	7:35810742-35811130		CU571051,CH242-525J6,7:35801913-35828071 (Clone quality: bE525J6 on chr=7; Num_of_Contigs=14; )
PPARD		location ⇒	7:35879913-35880364		CU467978,CH242-397F5,7:35872400-35952461 (Clone quality: bE397F5 on chr=7; Num_of_Contigs=4; )
PPARD		location ⇒	7:36024388-36024839		CU424481,CH242-125B19,7:36018736-36025906 (Clone quality: bE125B19 on chr=7; Num_of_Contigs=28; )
PPARG		ENSSSCG00000011579	13:56728191-56859476
PPARG		location ⇒	13:56809178-56809409		CU915692,CH242-255I14,13:56721460-56821905 (Clone quality: bE255I14 on chr=13; Num_of_Contigs=3; )
PPARG		location ⇒	13:56832449-56832649		CU856559,CH242-162G3,13:56821906-56932064 (Clone quality: bE162G3 on chr=13; Num_of_Contigs=2; )
PPARG		location ⇒	13:56841526-56841976		CU856559,CH242-162G3,13:56821906-56932064 (Clone quality: bE162G3 on chr=13; Num_of_Contigs=2; )
PPARG		location ⇒	13:56859046-56859357		CU856559,CH242-162G3,13:56821906-56932064 (Clone quality: bE162G3 on chr=13; Num_of_Contigs=2; )
PPARGC-1		ENSSSCG00000014437	2:136333826-136357749		CU914383,CH242-278F6,2:136264401-136403937 (Clone quality: bE278F6 on chr=2; Num_of_Contigs=5; )
PPARGC1B		ENSSSCG00000014437	2:136333826-136357749		CU914383,CH242-278F6,2:136264401-136403937 (Clone quality: bE278F6 on chr=2; Num_of_Contigs=5; )
PPEF2		ENSSSCG00000008972	8:60904184-60934482
PPFIA1		ENSSSCG00000012866	2:1411757-1420165
PPFIA1		location ⇒	2:1338613-1338683		CU469203,CH242-236K15,2:1337394-1339399 (Clone quality: bE236K15 on chr=2; Num_of_Contigs=23; )
PPFIA1		location ⇒	2:1427693-1428026		CU469203,CH242-236K15,2:1423279-1429974 (Clone quality: bE236K15 on chr=2; Num_of_Contigs=23; )
PPFIA1		location ⇒	2:1428135-1428212		CU469203,CH242-236K15,2:1423279-1429974 (Clone quality: bE236K15 on chr=2; Num_of_Contigs=23; )
PPFIA1		location ⇒	2:1475696-1475808		CU469203,CH242-236K15,2:1470544-1481779 (Clone quality: bE236K15 on chr=2; Num_of_Contigs=23; )
PPFIA2		ENSSSCG00000000940	5:94410183-94547079		CU633642,CH242-167I17,5:94386592-94554001 (Clone quality: bE167I17 on chr=5; Num_of_Contigs=1; )
PPFIA4		ENSSSCG00000015474	9:106759290-106794554
PPFIBP1		ENSSSCG00000000549	5:44608561-44658126
PPFIBP1		location ⇒	5:44611021-44610885		CU062551,CH242-2G17,5:44513004-44648165 (Clone quality: bE2G17 on chr=5; Num_of_Contigs=3; )
PPFIBP1		location ⇒	5:44612718-44612529		CU062551,CH242-2G17,5:44513004-44648165 (Clone quality: bE2G17 on chr=5; Num_of_Contigs=3; )
PPFIBP1		location ⇒	5:44613362-44613233		CU062551,CH242-2G17,5:44513004-44648165 (Clone quality: bE2G17 on chr=5; Num_of_Contigs=3; )
PPFIBP1		location ⇒	5:44614024-44613902		CU062551,CH242-2G17,5:44513004-44648165 (Clone quality: bE2G17 on chr=5; Num_of_Contigs=3; )
PPFIBP2		ENSSSCG00000014598	9:1352429-1460845
pPGRP-LB		location ⇒	2:60368411-60368363		CU914413,CH242-247L20,2:60356868-60368411 (Clone quality: bE247L20 on chr=2; Num_of_Contigs=8; )
PPHLN1		ENSSSCG00000000793	5:69649053-69763125
PPIA		ENSSSCG00000016737	18:49044555-49048126
PPIA		location ⇒	1:212547010-212547519		CU481860,CH242-123C21,1:212545617-212551176 (Clone quality: bE123C21 on chr=1; Num_of_Contigs=7; )
PPIB		ENSSSCG00000004557	1:111189586-111195194		CU302261,CH242-182N21,1:111189543-111264608 (Clone quality: bE182N21 on chr=1; Num_of_Contigs=3; )
PPIB		ENSSSCG00000004557	1:111189586-111195194		CU302261,CH242-182N21,1:111189543-111264608 (Clone quality: bE182N21 on chr=1; Num_of_Contigs=3; )
PPIC		ENSSSCG00000008915	8:52131970-52140116		CU930023,CH242-296L22,8:52124161-52142921 (Clone quality: bE296L22 on chr=8; Num_of_Contigs=9; )
PPIC		location ⇒	8:52120849-52121033		CU930023,CH242-296L22,8:52120804-52124060 (Clone quality: bE296L22 on chr=8; Num_of_Contigs=9; )
PPIC		location ⇒	8:52132447-52131980		CU930023,CH242-296L22,8:52124161-52142921 (Clone quality: bE296L22 on chr=8; Num_of_Contigs=9; )

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, 2201-21

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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).