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)

SOX30		ENSSSCG00000017051	16:63322917-63360179
SOX4		ENSSSCG00000001081	7:17602673-17604106		CT757489,CH242-225M13,7:17493336-17681766 (Clone quality: bE225M13 on chr=7; Num_of_Contigs=1; )
SOX5		ENSSSCG00000000567	5:48241099-48273755
SOX6		ENSSSCG00000013384	2:39826251-40247509
SOX9		ENSSSCG00000017251	12:6867870-6871241		CU640384,CH242-191B18,12:6786606-6876182 (Clone quality: bE191B18 on chr=12; Num_of_Contigs=3; )
SP1		ENSSSCG00000005720	1:287164826-287368710
SP1		ENSSSCG00000004972	1:175589268-175612821
SP1		ENSSSCG00000004196	1:33301523-33339032		CU633754,CH242-254O2,1:33299154-33340304 (Clone quality: bE254O2 on chr=1; Num_of_Contigs=9; )
SP1		ENSSSCG00000000272	5:17144724-17184351
SP1		ENSSSCG00000005291	1:245347992-245459515
SP1		location ⇒	5:17145032-17144768		CU570852,CH242-3N12,5:17130363-17155278 (Clone quality: bE3N12 on chr=5; Num_of_Contigs=3; )
SP1		location ⇒	5:17145631-17145431		CU570852,CH242-3N12,5:17130363-17155278 (Clone quality: bE3N12 on chr=5; Num_of_Contigs=3; )
SP1		location ⇒	5:17263801-17263537		CU928648,CH242-523B11,5:17259296-17264743 (Clone quality: bE523B11 on chr=5; Num_of_Contigs=8; )
SP1		location ⇒	5:17264400-17264200		CU928648,CH242-523B11,5:17259296-17264743 (Clone quality: bE523B11 on chr=5; Num_of_Contigs=8; )
SP100		ENSSSCG00000016263	15:123716827-123759517
SP100		ENSSSCG00000016262	15:123644233-123709027
SP100		location ⇒	15:123738162-123738327		CU683888,CH242-406J22,15:123725143-123760674 (Clone quality: bE406J22 on chr=15; Num_of_Contigs=8; )
SP100		location ⇒	15:123739842-123740010		CU683888,CH242-406J22,15:123725143-123760674 (Clone quality: bE406J22 on chr=15; Num_of_Contigs=8; )
SP100		location ⇒	15:123748294-123748444		CU683888,CH242-406J22,15:123725143-123760674 (Clone quality: bE406J22 on chr=15; Num_of_Contigs=8; )
SP100		location ⇒	15:123759104-123759500		CU683888,CH242-406J22,15:123725143-123760674 (Clone quality: bE406J22 on chr=15; Num_of_Contigs=8; )
SP110		ENSSSCG00000016261	15:123598462-123644609
SP110		location ⇒	15:123590308-123590449		CU683888,CH242-406J22,15:123588967-123625012 (Clone quality: bE406J22 on chr=15; Num_of_Contigs=8; )
SP110		location ⇒	15:123591289-123591360		CU683888,CH242-406J22,15:123588967-123625012 (Clone quality: bE406J22 on chr=15; Num_of_Contigs=8; )
SP140		ENSSSCG00000016262	15:123644233-123709027
SP140		location ⇒	15:123591758-123591660		CU683888,CH242-406J22,15:123588967-123625012 (Clone quality: bE406J22 on chr=15; Num_of_Contigs=8; )
SP140		location ⇒	15:123697421-123697565		CU683888,CH242-406J22,15:123645768-123704794 (Clone quality: bE406J22 on chr=15; Num_of_Contigs=8; )
SP140		location ⇒	15:123707465-123707608		CU683888,CH242-406J22,15:123704895-123725042 (Clone quality: bE406J22 on chr=15; Num_of_Contigs=8; )
SP140		location ⇒	15:123708568-123709026		CU683888,CH242-406J22,15:123704895-123725042 (Clone quality: bE406J22 on chr=15; Num_of_Contigs=8; )
SP2		ENSSSCG00000015086	9:44286708-44320214
SP2		ENSSSCG00000017516	12:21485201-21661479
SP2		location ⇒	12:21659367-21659445		CU681834,CH242-505F23,12:21649184-21661963 (Clone quality: bE505F23 on chr=12; Num_of_Contigs=26; )
SP2		location ⇒	12:21660499-21661185		CU681834,CH242-505F23,12:21649184-21661963 (Clone quality: bE505F23 on chr=12; Num_of_Contigs=26; )
SP3		ENSSSCG00000015962	15:74935057-74973363
SP3		location ⇒	15:74934199-74934120		CU571287,CH242-292M13,15:74930182-74949783 (Clone quality: bE292M13 on chr=15; Num_of_Contigs=3; )
SP3		location ⇒	15:74935579-74934247		CU571287,CH242-292M13,15:74930182-74949783 (Clone quality: bE292M13 on chr=15; Num_of_Contigs=3; )
SP3		location ⇒	15:74973361-74972001		CU571287,CH242-292M13,15:74969923-74976306 (Clone quality: bE292M13 on chr=15; Num_of_Contigs=3; )
SP3		location ⇒	15:75217035-75218395		CU467035,CH242-73L24,15:75212099-75223808 (Clone quality: bE73L24 on chr=15; Num_of_Contigs=6; )
SP4		ENSSSCG00000015378	9:84581314-84650647		CU927937,CH242-126M11,9:84571324-84661105 (Clone quality: bE126M11 on chr=9; Num_of_Contigs=3; )
SP6		ENSSSCG00000017522	12:21613336-21614469		CU655852,CH242-166I5,12:21573723-21615705 (Clone quality: bE166I5 on chr=12; Num_of_Contigs=13; )
SP7		ENSSSCG00000000269	5:17083984-17085282		CU570852,CH242-3N12,5:17057869-17089247 (Clone quality: bE3N12 on chr=5; Num_of_Contigs=3; )
SP8		ENSSSCG00000003052	6:34876750-34879693		FP102750,CH242-80G20,6:34865935-34887494 (Clone quality: bE80G20 on chr=6; Num_of_Contigs=9; )
SPA17		ENSSSCG00000015197	9:50378700-50391049		CU640461,CH242-276C18,9:50367638-50414260 (Clone quality: bE276C18 on chr=9; Num_of_Contigs=3; )
SPA17		location ⇒	9:50379889-50380071		CU640461,CH242-276C18,9:50367638-50414260 (Clone quality: bE276C18 on chr=9; Num_of_Contigs=3; )
SPA17		location ⇒	9:50386812-50386883		CU640461,CH242-276C18,9:50367638-50414260 (Clone quality: bE276C18 on chr=9; Num_of_Contigs=3; )
SPA17		location ⇒	9:50387816-50387892		CU640461,CH242-276C18,9:50367638-50414260 (Clone quality: bE276C18 on chr=9; Num_of_Contigs=3; )
SPA17		location ⇒	9:50390891-50391215		CU640461,CH242-276C18,9:50367638-50414260 (Clone quality: bE276C18 on chr=9; Num_of_Contigs=3; )
SPACA1		ENSSSCG00000004308	1:59107050-59124466
SPACA3		ENSSSCG00000017726	12:39640598-39648712		FP017292,CH242-263E12,12:39622307-39714413 (Clone quality: bE263E12 on chr=12; Num_of_Contigs=2; )
SPACA3		location ⇒	12:39643341-39643211		FP017292,CH242-263E12,12:39622307-39714413 (Clone quality: bE263E12 on chr=12; Num_of_Contigs=2; )
SPACA3		location ⇒	12:39644650-39644360		FP017292,CH242-263E12,12:39622307-39714413 (Clone quality: bE263E12 on chr=12; 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, 2201-2250, 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).