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)

TAPBP		ENSSSCG00000001507	7:34071574-34080040	CU607018,CH242-138E20,7:33930957-34116846 (Clone quality: bE138E20 on chr=7; Num_of_Contigs=1; )
TAPBP		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
TAPBP		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
TAPBP		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
TAPBP		location ⇒	7:4758-4654		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
TAPBPL		ENSSSCG00000000704	5:60207659-60215384		CU633552,CH242-193I18,5:60186767-60298754 (Clone quality: bE193I18 on chr=5; Num_of_Contigs=2; )
TAPBPL		location ⇒	5:60213777-60213608		CU633552,CH242-193I18,5:60186767-60298754 (Clone quality: bE193I18 on chr=5; Num_of_Contigs=2; )
TAPBPL		location ⇒	5:60214136-60213917		CU633552,CH242-193I18,5:60186767-60298754 (Clone quality: bE193I18 on chr=5; Num_of_Contigs=2; )
TAPBPL		location ⇒	5:60215098-60214941		CU633552,CH242-193I18,5:60186767-60298754 (Clone quality: bE193I18 on chr=5; Num_of_Contigs=2; )
TARBP1		ENSSSCG00000010160	14:57868453-57946346
TARBP2		ENSSSCG00000000276	5:17267545-17272606		CU928648,CH242-523B11,5:17264844-17274557 (Clone quality: bE523B11 on chr=5; Num_of_Contigs=8; )
TARDBP		ENSSSCG00000003409	6:48005348-48008632
TARM1		ENSSSCG00000003258	6:40446119-40450342		FP102634,CH242-226O14,6:40430241-40460898 (Clone quality: bE226O14 on chr=6; Num_of_Contigs=5; )
TARS		ENSSSCG00000016817	16:16965835-16979132
TARSL2		ENSSSCG00000005781	1:291862814-291917305
TAS1R1		ENSSSCG00000003382	6:45903003-45911606
TAS1R3		ENSSSCG00000003341	6:42925459-42929754		FP102596,CH242-173K23,6:42905835-42937819 (Clone quality: bE173K23 on chr=6; Num_of_Contigs=10; )
TAS2R10		ENSSSCG00000000630	5:57779167-57780087		CU856689,CH242-196F1,5:57732379-57868244 (Clone quality: bE196F1 on chr=5; Num_of_Contigs=2; )
TAS2R16		ENSSSCG00000016610	18:22439550-22440431	CU457413,CH242-454C22,18:22286896-22481750 (Clone quality: bE454C22 on chr=18; Num_of_Contigs=3; )
TAS2R40		ENSSSCG00000016467	18:6023887-6024660		CU928380,CH242-107B19,18:5998234-6050575 (Clone quality: bE107B19 on chr=18; Num_of_Contigs=4; )
TAS2R41		ENSSSCG00000016457	18:5698352-5699275		FP236461,CH242-143H23,18:5607489-5712405 (Clone quality: bE143H23 on chr=18; Num_of_Contigs=1; )
TAS2R42		ENSSSCG00000000626	5:57642336-57643253		CU468708,CH242-297E5,5:57604615-57646125 (Clone quality: bE297E5 on chr=5; Num_of_Contigs=5; )
TAS2R60		ENSSSCG00000016458	18:5725206-5726141		CU929961,CH242-59I9,18:5712406-5783203 (Clone quality: bE59I9 on chr=18; Num_of_Contigs=6; )
TAS2R7		ENSSSCG00000000632	5:57798863-57799792		CU856689,CH242-196F1,5:57732379-57868244 (Clone quality: bE196F1 on chr=5; Num_of_Contigs=2; )
TAS2R9		ENSSSCG00000000631	5:57790460-57791395		CU856689,CH242-196F1,5:57732379-57868244 (Clone quality: bE196F1 on chr=5; Num_of_Contigs=2; )
TASP1		ENSSSCG00000007074	17:22389622-22644617
TAT		ENSSSCG00000002736	6:10322121-10333630		FP016102,CH242-364C5,6:10306746-10373929 (Clone quality: bE364C5 on chr=6; Num_of_Contigs=10; )
TATDN1		ENSSSCG00000005974	4:14787888-14800725		CU468433,CH242-46N16,4:14769281-14812155 (Clone quality: bE46N16 on chr=4; Num_of_Contigs=6; )
TATDN3		ENSSSCG00000015592	9:123078973-123093358		CU657946,CH242-238G6,9:122996435-123111475 (Clone quality: bE238G6 on chr=9; Num_of_Contigs=3; )
TAX1BP1		ENSSSCG00000016692	18:43317028-43348158
TAX1BP1		location ⇒	18:3051-2966		CU640449,CH242-199L20,18:1-119108 (Clone quality: bE199L20 on chr=18; Num_of_Contigs=4; )
TAX1BP1		location ⇒	18:436-568		CU640449,CH242-199L20,18:1-119108 (Clone quality: bE199L20 on chr=18; Num_of_Contigs=4; )
TAX1BP1		location ⇒	18:6778-6872		CU640449,CH242-199L20,18:1-119108 (Clone quality: bE199L20 on chr=18; Num_of_Contigs=4; )
TAX1BP1		location ⇒	18:7943-8056		CU640449,CH242-199L20,18:1-119108 (Clone quality: bE199L20 on chr=18; Num_of_Contigs=4; )
TAX1BP3		ENSSSCG00000017866	12:47048665-47053532		FP016040,CH242-164K7,12:47045956-47064002 (Clone quality: bE164K7 on chr=12; Num_of_Contigs=2; )
TAX1BP3		location ⇒	12:47049090-47048667		FP016040,CH242-164K7,12:47045956-47064002 (Clone quality: bE164K7 on chr=12; Num_of_Contigs=2; )
TAX1BP3		location ⇒	12:47049651-47049158		FP016040,CH242-164K7,12:47045956-47064002 (Clone quality: bE164K7 on chr=12; Num_of_Contigs=2; )
TAX1BP3		location ⇒	12:47050529-47050408		FP016040,CH242-164K7,12:47045956-47064002 (Clone quality: bE164K7 on chr=12; Num_of_Contigs=2; )
TAX1BP3		location ⇒	12:47053532-47053376		FP016040,CH242-164K7,12:47045956-47064002 (Clone quality: bE164K7 on chr=12; Num_of_Contigs=2; )
TBA1B_PIG		ENSSSCG00000000190	5:13787638-13900905
TBA1B_PIG		ENSSSCG00000000190	5:13787638-13900905
TBB5_PIG		ENSSSCG00000001379	7:27204866-27209280	CU480634,CH242-391N4,7:27128408-27216112 (Clone quality: bE391N4 on chr=7; Num_of_Contigs=11; )
TBC1D1		ENSSSCG00000008774	8:24973284-25051796
TBC1D10A		ENSSSCG00000009999	14:48043485-48115262
TBC1D10B		ENSSSCG00000007798	3:16547078-16556482		CU928725,CH242-25P12,3:16542593-16582945 (Clone quality: bE25P12 on chr=3; Num_of_Contigs=8; )
TBC1D10C		ENSSSCG00000012912	2:3494006-3499453		CU633429,CH242-6G2,2:3486771-3519792 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
TBC1D12		ENSSSCG00000010485	14:111215465-111240295		CU468514,CH242-226D12,14:111166047-111244832 (Clone quality: bE226D12 on chr=14; Num_of_Contigs=3; )
TBC1D13		ENSSSCG00000005660	1:283809809-283824155
TBC1D15		ENSSSCG00000000512	5:34927383-34978518
TBC1D16		ENSSSCG00000017159	12:1511910-1565945	CU464073,CH242-396G1,12:1427255-1662757 (Clone quality: bE396G1 on chr=3; 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, 1851-8

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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).