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)

STX2		ENSSSCG00000009747	14:24381184-24414065		CU468532,CH242-32J1,14:24369564-24416537 (Clone quality: bE32J1 on chr=14; Num_of_Contigs=7; )
STX3		ENSSSCG00000013119	2:9670666-9708511
STX4		ENSSSCG00000007768	3:15927280-15936241
STX6		ENSSSCG00000015539	9:114969533-115014884
STX7		ENSSSCG00000004190	1:32676785-32728209	CU074298,CH242-141E21,1:32588124-32781733 (Clone quality: bE141E21 on chr=1; Num_of_Contigs=3; )
STXBP1		ENSSSCG00000005617	1:282527722-282566109
STXBP2		ENSSSCG00000013576	2:51049836-51058692		CU929919,CH242-334A8,2:51013584-51060863 (Clone quality: bE334A8 on chr=2; Num_of_Contigs=7; )
STXBP3		ENSSSCG00000006843	4:115746582-115807283
STXBP4		ENSSSCG00000017602	12:28806285-28910551
STXBP5		ENSSSCG00000004113	1:19214945-19376816
STXBP6		ENSSSCG00000001977	7:80545142-80867194
STYK1		ENSSSCG00000000634	5:57940898-57955924		FP017141,CH242-24K3,5:57904188-58023971 (Clone quality: bE24K3 on chr=5; Num_of_Contigs=2; )
STYX		ENSSSCG00000005039	1:190824812-190871702		CU407115,CH242-342H5,1:190778660-191001332 (Clone quality: bE342H5 on chr=1; Num_of_Contigs=1; )
SUCLA2		ENSSSCG00000009405	11:19025551-19079863		CU927974,CH242-412J9,11:19025496-19170114 (Clone quality: bE412J9 on chr=11; Num_of_Contigs=1; )
SUCLG1		ENSSSCG00000008247	3:54911164-54946361
SUCLG2		ENSSSCG00000011501	13:40717893-41010484
SUDS3		ENSSSCG00000009849	14:34474307-34506988		CU468173,CH242-14F4,14:34457877-34508571 (Clone quality: bE14F4 on chr=14; Num_of_Contigs=7; )
SUFU		ENSSSCG00000010586	14:118526054-118648733
SUGT1		ENSSSCG00000009441	11:24949127-24992795
SULF1		ENSSSCG00000006197	4:67782294-67978721
SULF2		ENSSSCG00000007456	17:51936789-52002572
SULT4A1		ENSSSCG00000000026	5:1776610-1797297
SUMF1		ENSSSCG00000011532	13:50902591-50992727		CU928100,CH242-264M15,13:50846452-50995620 (Clone quality: bE264M15 on chr=13; Num_of_Contigs=3; )
SUMO1		ENSSSCG00000011841	13:100446380-100498924
SUMO1		ENSSSCG00000011004	10:32463622-32473371		CU928691,CH242-242E10,10:32318250-32480524 (Clone quality: bE242E10 on chr=10; Num_of_Contigs=1; )
SUMO1		ENSSSCG00000008514	3:100775273-100775578		CU861984,CH242-378M9,3:100767915-100792335 (Clone quality: bE378M9 on chr=3; Num_of_Contigs=9; )
SUMO1		ENSSSCG00000003111	6:36696319-36765843		FP102474,CH242-104M2,6:36670130-36777370 (Clone quality: bE104M2 on chr=6; Num_of_Contigs=1; )
SUMO2		ENSSSCG00000017212	12:4297804-4311546	CU928896,CH242-521B23,12:4294467-4388657 (Clone quality: bE521B23 on chr=12; Num_of_Contigs=4; )
SUMO2		location ⇒	14:29398985-29399987		CU468658,CH242-245F7,14:29355652-29557150 (Clone quality: bE245F7 on chr=14; Num_of_Contigs=1; )
SUMO4		ENSSSCG00000017212	12:4297804-4311546	CU928896,CH242-521B23,12:4294467-4388657 (Clone quality: bE521B23 on chr=12; Num_of_Contigs=4; )
SUOX		ENSSSCG00000000376	5:20400613-20404498
SUPT3H		ENSSSCG00000001709	7:46635097-46963453
SUPT4H1		ENSSSCG00000017639	12:32644393-32650734		CU571372,CH242-73D9,12:32562317-32656104 (Clone quality: bE73D9 on chr=12; Num_of_Contigs=4; )
SUPT7L		ENSSSCG00000008548	3:104211286-104216776
SUPV3L1		ENSSSCG00000010251	14:75394156-75421289		CT737222,CH242-62M1,14:75343233-75510707 (Clone quality: bE62M1 on chr=14; Num_of_Contigs=1; )
SURF6		ENSSSCG00000003765	6:94125005-94125881		CU929925,CH242-365O3,6:94053648-94133388 (Clone quality: bE365O3 on chr=6; Num_of_Contigs=9; )
SUSD1		ENSSSCG00000005465	1:265672951-265793255
SUV39H1		ENSSSCG00000011332	13:24969919-25027220
SUV39H2		ENSSSCG00000011048	10:44576636-44583650		CU929591,CH242-21K12,10:44569457-44680253 (Clone quality: bE21K12 on chr=10; Num_of_Contigs=3; )
SUV420H1		ENSSSCG00000012887	2:3012437-3110208
SUV420H2		ENSSSCG00000003297	6:41359933-41367567
SV2A		ENSSSCG00000006666	4:103153961-103162503
SV2B		ENSSSCG00000002262	7:94615234-94658202	CU367885,CH242-379L2,7:94585905-94792873 (Clone quality: bE379L2 on chr=7; Num_of_Contigs=1; )
SV2C		ENSSSCG00000014085	2:73864764-74074986
SVEP1		ENSSSCG00000005455	1:264076650-264273604
SVIL		ENSSSCG00000011022	10:39474660-39679035
SVOP		ENSSSCG00000009941	14:42103688-42179583		CT954284,CH242-241M1,14:42019840-42206297 (Clone quality: bE241M1 on chr=14; Num_of_Contigs=1; )
SVOPL		ENSSSCG00000016517	18:9197184-9214880		FP236752,CH242-135G1,18:9190924-9218052 (Clone quality: bE135G1 on chr=18; Num_of_Contigs=4; )
SWAP70		ENSSSCG00000013410	2:45880572-45889735		CU928971,CH242-525M1,2:45833429-45891486 (Clone quality: bE525M1 on chr=2; Num_of_Contigs=5; )
SWC8		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )

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).