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)

SPEF1		ENSSSCG00000007149	17:33587950-33591556		FP236531,CH242-39P18,17:33587321-33595049 (Clone quality: bE39P18 on chr=17; Num_of_Contigs=7; )
SPEF2		ENSSSCG00000016831	16:18508929-18759937
SPERT		ENSSSCG00000009417	11:20851482-20861311		CU914205,CH242-342O8,11:20851114-20864939 (Clone quality: bE342O8 on chr=11; Num_of_Contigs=14; )
SPG20		ENSSSCG00000009353	11:11806929-11831031		CU582798,CH242-212J9,11:11806928-11834718 (Clone quality: bE212J9 on chr=11; Num_of_Contigs=12; )
SPG21		ENSSSCG00000004544	1:110167827-110192367		CU929866,CH242-13A12,1:110100332-110200592 (Clone quality: bE13A12 on chr=1; Num_of_Contigs=4; )
SPG3A		location ⇒	1:188485275-188484833		CU468394,CH242-205L9,1:188483478-188499538 (Clone quality: bE205L9 on chr=1; Num_of_Contigs=8; )
SPG3A		location ⇒	1:188488972-188488538		CU468394,CH242-205L9,1:188483478-188499538 (Clone quality: bE205L9 on chr=1; Num_of_Contigs=8; )
SPG3A		location ⇒	1:188678161-188678595		CU074392,CH242-137I1,1:188633939-188748299 (Clone quality: bE137I1 on chr=1; Num_of_Contigs=3; )
SPG3A		location ⇒	1:188681858-188682300		CU074392,CH242-137I1,1:188633939-188748299 (Clone quality: bE137I1 on chr=1; Num_of_Contigs=3; )
SPHK1		ENSSSCG00000016256	15:122008922-122052240		CU914375,CH242-15P7,15:121999942-122147383 (Clone quality: bE15P7 on chr=15; Num_of_Contigs=7; )
SPHK1		location ⇒	12:3302716-3302833		CU928356,CH242-33I18,12:3300049-3319333 (Clone quality: bE33I18 on chr=12; Num_of_Contigs=10; )
SPHK1		location ⇒	12:3303124-3303647		CU928356,CH242-33I18,12:3300049-3319333 (Clone quality: bE33I18 on chr=12; Num_of_Contigs=10; )
SPHK1		location ⇒	12:3477728-3477205	CU466934,CH242-34E1,12:3420589-3631790 (Clone quality: bE34E1 on chr=9; Num_of_Contigs=4; )
SPHK1		location ⇒	12:3478136-3478019	CU466934,CH242-34E1,12:3420589-3631790 (Clone quality: bE34E1 on chr=9; Num_of_Contigs=4; )
SPHKAP		ENSSSCG00000016256	15:122008922-122052240		CU914375,CH242-15P7,15:121999942-122147383 (Clone quality: bE15P7 on chr=15; Num_of_Contigs=7; )
SPI		location ⇒	1:210098567-210098622		CU469469,CH242-142L3,1:210062719-210118069 (Clone quality: bE142L3 on chr=1; Num_of_Contigs=6; )
SPI		location ⇒	1:210194046-210193976		CU618316,CH242-254N10,1:210188634-210217788 (Clone quality: bE254N10 on chr=1; Num_of_Contigs=2; )
SPI		location ⇒	1:210330107-210330177		CU651597,CH242-112J16,1:210311258-210361052 (Clone quality: bE112J16 on chr=1; Num_of_Contigs=9; )
SPI		location ⇒	1:210545801-210545880		CU633414,CH242-414D14,1:210407307-210572645 (Clone quality: bE414D14 on chr=1; Num_of_Contigs=1; )
SPI IFN		ENSSSCG00000005149	1:210194352-210194864		CU618316,CH242-254N10,1:210188634-210217788 (Clone quality: bE254N10 on chr=1; Num_of_Contigs=2; )
SPI IFN		ENSSSCG00000000867	5:78143514-78143939		CU856405,CH242-261A10,5:78129753-78144425 (Clone quality: bE261A10 on chr=5; Num_of_Contigs=4; )
SPI IFN		ENSSSCG00000005152	1:210329082-210330177		CU651597,CH242-112J16,1:210311258-210361052 (Clone quality: bE112J16 on chr=1; Num_of_Contigs=9; )
SPI IFN		ENSSSCG00000005288	1:243320848-243391371
SPI1		ENSSSCG00000013237	2:13236585-13254376		CU856312,CH242-38I7,2:13223564-13257570 (Clone quality: bE38I7 on chr=2; Num_of_Contigs=10; )
SPI1		location ⇒	2:13237299-13236586		CU856312,CH242-38I7,2:13223564-13257570 (Clone quality: bE38I7 on chr=2; Num_of_Contigs=10; )
SPI1		location ⇒	2:13237811-13237644		CU856312,CH242-38I7,2:13223564-13257570 (Clone quality: bE38I7 on chr=2; Num_of_Contigs=10; )
SPI1		location ⇒	2:13238815-13238625		CU856312,CH242-38I7,2:13223564-13257570 (Clone quality: bE38I7 on chr=2; Num_of_Contigs=10; )
SPI1		location ⇒	2:13254319-13254142		CU856312,CH242-38I7,2:13223564-13257570 (Clone quality: bE38I7 on chr=2; Num_of_Contigs=10; )
SPIC		ENSSSCG00000000867	5:78143514-78143939		CU856405,CH242-261A10,5:78129753-78144425 (Clone quality: bE261A10 on chr=5; Num_of_Contigs=4; )
SPIN1		ENSSSCG00000007809	3:16742604-16878319
SPIN1		location ⇒	1:30655662-30655551		CU407206,CH242-337H22,1:30645593-30678100 (Clone quality: bE337H22 on chr=1; Num_of_Contigs=9; )
SPIN1		location ⇒	1:30656318-30656228		CU407206,CH242-337H22,1:30645593-30678100 (Clone quality: bE337H22 on chr=1; Num_of_Contigs=9; )
SPIN1		location ⇒	1:30659717-30658711		CU407206,CH242-337H22,1:30645593-30678100 (Clone quality: bE337H22 on chr=1; Num_of_Contigs=9; )
SPIN3		ENSSSCG00000012356	X:48899458-48900234		FP102619,CH242-203B18,X:48898359-48914002 (Clone quality: bE203B18 on chr=X; Num_of_Contigs=9; )
SPINK4		ENSSSCG00000010997	10:31771645-31849736
SPINK5		ENSSSCG00000014422	2:134917206-134987375
SPINK5		location ⇒	2:134922499-134922629		CU928727,CH242-27H11,2:134858172-134943966 (Clone quality: bE27H11 on chr=2; Num_of_Contigs=4; )
SPINK5		location ⇒	2:134932281-134932410		CU928727,CH242-27H11,2:134858172-134943966 (Clone quality: bE27H11 on chr=2; Num_of_Contigs=4; )
SPINK5		location ⇒	2:134938249-134938380		CU928727,CH242-27H11,2:134858172-134943966 (Clone quality: bE27H11 on chr=2; Num_of_Contigs=4; )
SPINK5		location ⇒	2:134942542-134942666		CU928727,CH242-27H11,2:134858172-134943966 (Clone quality: bE27H11 on chr=2; Num_of_Contigs=4; )
SPINK6		ENSSSCG00000014424	2:135082825-135096586		FP017134,CH242-150P12,2:134967630-135167107 (Clone quality: bE150P12 on chr=2; Num_of_Contigs=1; )
SPINK8		ENSSSCG00000011348	13:25965372-25971012		FP102065,CH242-145E9,13:25960235-25992417 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
SPINK9		ENSSSCG00000014426	2:135187923-135192446		FP089465,CH242-369H11,2:135172108-135216486 (Clone quality: bE369H11 on chr=2; Num_of_Contigs=4; )
SPINLW1		location ⇒	4:21571947-21572040		CU467777,CH242-481P3,4:21560537-21600813 (Clone quality: bE481P3 on chr=4; Num_of_Contigs=9; )
SPINLW1		location ⇒	4:21700558-21700465		CU656020,CH242-384B12,4:21691750-21728411 (Clone quality: bE384B12 on chr=4; Num_of_Contigs=11; )
SPINLW1		location ⇒	4:26637302-26637201		CU469100,CH242-252M3,4:26591132-26643958 (Clone quality: bE252M3 on chr=4; Num_of_Contigs=5; )
SPINLW1		location ⇒	4:26828168-26828067		CU571197,CH242-186L13,4:26736369-26919655 (Clone quality: bE186L13 on chr=4; Num_of_Contigs=1; )
SPINT1		ENSSSCG00000004759	1:136950626-136970289
SPINT2		ENSSSCG00000007420	17:50026822-50026971		CU076086,CH242-56C16,17:49960216-50115189 (Clone quality: bE56C16 on chr=17; Num_of_Contigs=2; )
SPINT4		ENSSSCG00000007419	17:50002109-50004608		CU076086,CH242-56C16,17:49960216-50115189 (Clone quality: bE56C16 on chr=17; 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).