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)

PPIC		location ⇒	8:52132638-52132471		CU930023,CH242-296L22,8:52124161-52142921 (Clone quality: bE296L22 on chr=8; Num_of_Contigs=9; )
PPIC		location ⇒	8:52136339-52136154		CU930023,CH242-296L22,8:52124161-52142921 (Clone quality: bE296L22 on chr=8; Num_of_Contigs=9; )
PPID		ENSSSCG00000008878	8:41236401-41250927		CU896689,CH242-1N13,8:41180262-41282411 (Clone quality: bE1N13 on chr=8; Num_of_Contigs=4; )
PPIE		ENSSSCG00000003664	6:65624698-65639794	CR956427,CH242-51O7,6:65474974-65651225 (No clone quality info on bE51O7)
PPIF		ENSSSCG00000010330	14:85205810-85212642		CT827949,CH242-259N24,14:85046239-85223409 (Clone quality: bE259N24 on chr=14; Num_of_Contigs=1; )
PPIG		ENSSSCG00000015934	15:71377171-71407147
PPIH		ENSSSCG00000003964	6:120933170-120951473		CU467721,CH242-292B22,6:120927206-120962427 (Clone quality: bE292B22 on chr=6; Num_of_Contigs=5; )
PPIH		location ⇒	6:120933374-120933170		CU467721,CH242-292B22,6:120927206-120962427 (Clone quality: bE292B22 on chr=6; Num_of_Contigs=5; )
PPIH		location ⇒	6:120940952-120940862		CU467721,CH242-292B22,6:120927206-120962427 (Clone quality: bE292B22 on chr=6; Num_of_Contigs=5; )
PPIH		location ⇒	6:120942643-120942554		CU467721,CH242-292B22,6:120927206-120962427 (Clone quality: bE292B22 on chr=6; Num_of_Contigs=5; )
PPIH		location ⇒	6:120946218-120946125		CU467721,CH242-292B22,6:120927206-120962427 (Clone quality: bE292B22 on chr=6; Num_of_Contigs=5; )
PPIL1		ENSSSCG00000001568	7:37156256-37177532	CU326356,CH242-61G11,7:36975834-37183903 (Clone quality: bE61G11 on chr=7; Num_of_Contigs=4; )
PPIL2		ENSSSCG00000010083	14:51283055-51306558		CU633431,CH242-79C11,14:51180713-51414471 (Clone quality: bE79C11 on chr=14; Num_of_Contigs=4; )
PPIL3		ENSSSCG00000016096	15:98257521-98272029		CU468511,CH242-98M12,15:98176186-98278835 (Clone quality: bE98M12 on chr=15; Num_of_Contigs=5; )
PPIL4		ENSSSCG00000004107	1:17312194-17396895
PPIL5		ENSSSCG00000005004	1:187878146-187889156
PPIL6		ENSSSCG00000004413	1:80481661-80524575		CU075452,CH242-39D23,1:80450203-80633251 (Clone quality: bE39D23 on chr=1; Num_of_Contigs=2; )
PPM1A		ENSSSCG00000005084	1:197977296-197988154		CU550674,CH242-316H7,1:197971229-197995013 (Clone quality: bE316H7 on chr=1; Num_of_Contigs=8; )
PPM1A		location ⇒	1:197977393-197978070		CU550674,CH242-316H7,1:197971229-197995013 (Clone quality: bE316H7 on chr=1; Num_of_Contigs=8; )
PPM1B		ENSSSCG00000008451	3:89624495-89653909
PPM1D		ENSSSCG00000017677	12:35488384-35538446
PPM1E		ENSSSCG00000017647	12:33272112-33295911
PPM1F		ENSSSCG00000010079	14:51055422-51075048		CU468588,CH242-282B12,14:50969832-51085093 (Clone quality: bE282B12 on chr=14; Num_of_Contigs=2; )
PPM1J		ENSSSCG00000006774	4:112096410-112101502
PPM1M		ENSSSCG00000011434	13:29020534-29023922		CU915558,CH242-407L22,13:29012423-29031095 (Clone quality: bE407L22 on chr=13; Num_of_Contigs=4; )
PPME1		ENSSSCG00000014836	9:8218150-8269089
PPOX		ENSSSCG00000006361	4:92792961-92796731		CU606874,CH242-28G15,4:92745461-92814223 (Clone quality: bE28G15 on chr=4; Num_of_Contigs=6; )
PPP1CA		ENSSSCG00000012913	2:3501365-3504471		CU633429,CH242-6G2,2:3486771-3519792 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
PPP1CB		ENSSSCG00000008540	3:103459106-103477888		CU915333,CH242-291B11,3:103448942-103483458 (Clone quality: bE291B11 on chr=3; Num_of_Contigs=4; )
PPP1CC		ENSSSCG00000009828	14:32098179-32119140		CT827876,CH242-281I3,14:32088666-32208462 (Clone quality: bE281I3 on chr=14; Num_of_Contigs=4; )
PPP1CC		location ⇒	14:32099519-32099127		CT827876,CH242-281I3,14:32088666-32208462 (Clone quality: bE281I3 on chr=14; Num_of_Contigs=4; )
PPP1CC		location ⇒	14:32100908-32100772		CT827876,CH242-281I3,14:32088666-32208462 (Clone quality: bE281I3 on chr=14; Num_of_Contigs=4; )
PPP1CC		location ⇒	14:32101338-32101111		CT827876,CH242-281I3,14:32088666-32208462 (Clone quality: bE281I3 on chr=14; Num_of_Contigs=4; )
PPP1CC		location ⇒	14:32106608-32106375		CT827876,CH242-281I3,14:32088666-32208462 (Clone quality: bE281I3 on chr=14; Num_of_Contigs=4; )
PPP1R10		ENSSSCG00000001347	7:26703760-26719978	CU498826,CH242-119D24,7:26553813-26728014 (Clone quality: bE119D24 on chr=7; Num_of_Contigs=31; )
PPP1R10		ENSSSCG00000001369	7:27034482-27043760	CU326403,CH242-198M20,7:26882096-27123407 (Clone quality: bE198M20 on chr=7; Num_of_Contigs=9; )
PPP1R11		ENSSSCG00000001238	7:24722549-24835286
PPP1R12A		ENSSSCG00000000946	5:96011473-96081050
PPP1R12B		ENSSSCG00000010925	10:24518667-24686347
PPP1R13B		ENSSSCG00000002544	7:132767188-132788195
PPP1R14B		ENSSSCG00000013035	2:6249844-6252340		CU861533,CH242-1H13,2:6249822-6260732 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PPP1R14C		ENSSSCG00000004094	1:16670319-16911767
PPP1R14D		ENSSSCG00000004760	1:136982273-137006480
PPP1R15A		ENSSSCG00000003155	6:37823517-37825139		FP102974,CH242-517N5,6:37823193-37829576 (Clone quality: bE517N5 on chr=6; Num_of_Contigs=15; )
PPP1R15B		ENSSSCG00000015282	9:62648375-62655063		CU463238,CH242-21I11,9:62624994-62656733 (Clone quality: bE21I11 on chr=9; Num_of_Contigs=4; )
PPP1R16A		ENSSSCG00000005901	4:419804-423949		CU468594,CH242-10O17,4:360104-442995 (Clone quality: bE10O17 on chr=4; Num_of_Contigs=10; )
PPP1R16B		ENSSSCG00000007350	17:44067558-44148986		CU074389,CH242-105J10,17:44015909-44155339 (Clone quality: bE105J10 on chr=17; Num_of_Contigs=5; )
PPP1R1A		ENSSSCG00000000298	5:18322895-18325689		CU457442,CH242-280E10,5:18321215-18329017 (Clone quality: bE280E10 on chr=5; Num_of_Contigs=18; )
PPP1R1B		ENSSSCG00000017498	12:20579679-20587050		CU640399,CH242-251F23,12:20578579-20644206 (Clone quality: bE251F23 on chr=12; Num_of_Contigs=5; )
PPP1R1C		ENSSSCG00000016014	15:82058849-82060662		CU464031,CH242-439P1,15:82036866-82066712 (Clone quality: bE439P1 on chr=15; Num_of_Contigs=2; )

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

Report problems to zhu

iastate.edu

$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).