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)

TSEN2		ENSSSCG00000011580	13:56906516-56946559
TSEN34		ENSSSCG00000003268	6:40616547-40618750		FP102634,CH242-226O14,6:40616083-40619496 (Clone quality: bE226O14 on chr=6; Num_of_Contigs=5; )
TSG101		ENSSSCG00000005613	1:282315432-282358882
TSG101		ENSSSCG00000013364	2:37922280-37946462		CU914200,CH242-284C6,2:37908590-37947452 (Clone quality: bE284C6 on chr=2; Num_of_Contigs=6; )
TSG101		location ⇒	2:37922627-37922284		CU914200,CH242-284C6,2:37908590-37947452 (Clone quality: bE284C6 on chr=2; Num_of_Contigs=6; )
TSG101		location ⇒	2:37924233-37923997		CU914200,CH242-284C6,2:37908590-37947452 (Clone quality: bE284C6 on chr=2; Num_of_Contigs=6; )
TSG101		location ⇒	2:37925707-37925503		CU914200,CH242-284C6,2:37908590-37947452 (Clone quality: bE284C6 on chr=2; Num_of_Contigs=6; )
TSG101		location ⇒	2:37946461-37946395		CU914200,CH242-284C6,2:37908590-37947452 (Clone quality: bE284C6 on chr=2; Num_of_Contigs=6; )
TSGA10		ENSSSCG00000008186	3:50821112-50911378
TSGA10IP		ENSSSCG00000012964	2:4751566-4764693
TSGA13		ENSSSCG00000016551	18:16330009-16347829		FP236769,CH242-254H18,18:16327628-16393279 (Clone quality: bE254H18 on chr=18; Num_of_Contigs=3; )
TSGA14		ENSSSCG00000016556	18:16619729-16649949		CU466438,CH242-113D18,18:16593041-16655722 (Clone quality: bE113D18 on chr=18; Num_of_Contigs=9; )
TSHB		ENSSSCG00000006749	4:109815329-109816276		CU468531,CH242-18P21,4:109767936-109881501 (Clone quality: bE18P21 on chr=4; Num_of_Contigs=5; )
TSHZ1		ENSSSCG00000004861	1:156237051-156240158		CU466243,CH242-93A4,1:156227008-156247923 (Clone quality: bE93A4 on chr=1; Num_of_Contigs=12; )
TSHZ2		ENSSSCG00000007482	17:56597681-56600752	CR974445,CH242-212D21,17:56438563-56632078 (No clone quality info on bE212D21)
TSKS		ENSSSCG00000003191	6:38436829-38442934		CU694867,CH242-269H19,6:38400485-38449566 (Clone quality: bE269H19 on chr=6; Num_of_Contigs=4; )
TSKU		ENSSSCG00000014871	9:10758211-10759275		CU463147,CH242-406N11,9:10741527-10762698 (Clone quality: bE406N11 on chr=9; Num_of_Contigs=11; )
TSLP		ENSSSCG00000014198	2:104436897-104440957		CU928266,CH242-209C17,2:104419374-104442092 (Clone quality: bE209C17 on chr=2; Num_of_Contigs=4; )
TSN		ENSSSCG00000015729	15:28128157-28134149		CU655817,CH242-268L18,15:28127172-28134289 (Clone quality: bE268L18 on chr=15; Num_of_Contigs=17; )
TSNAX		ENSSSCG00000010171	14:61221630-61417298
TSNAXIP1		ENSSSCG00000002767	6:12855929-12877245		FP102672,CH242-302K22,6:12850515-12884873 (Clone quality: bE302K22 on chr=6; Num_of_Contigs=5; )
TSP50		ENSSSCG00000011327	13:24840453-24843985		CU856704,CH242-520E7,13:24840289-24847506 (Clone quality: bE520E7 on chr=13; Num_of_Contigs=12; )
TSPAN1		ENSSSCG00000003910	6:118351212-118353005		CU464168,CH242-477B24,6:118349288-118384356 (Clone quality: bE477B24 on chr=6; Num_of_Contigs=7; )
TSPAN1		location ⇒	6:118284037-118283880		CU694667,CH242-117A15,6:118247749-118318723 (Clone quality: bE117A15 on chr=6; Num_of_Contigs=3; )
TSPAN1		location ⇒	6:118284788-118284582		CU694667,CH242-117A15,6:118247749-118318723 (Clone quality: bE117A15 on chr=6; Num_of_Contigs=3; )
TSPAN1		location ⇒	6:118351263-118351469		CU464168,CH242-477B24,6:118349288-118384356 (Clone quality: bE477B24 on chr=6; Num_of_Contigs=7; )
TSPAN1		location ⇒	6:118352014-118352171		CU464168,CH242-477B24,6:118349288-118384356 (Clone quality: bE477B24 on chr=6; Num_of_Contigs=7; )
TSPAN11		ENSSSCG00000000734	5:62772441-62806918
TSPAN12		ENSSSCG00000016620	18:24204856-24270047
TSPAN13		ENSSSCG00000015362	9:80471534-80479275		CU929484,CH242-397L4,9:80470380-80481380 (Clone quality: bE397L4 on chr=9; Num_of_Contigs=10; )
TSPAN14		ENSSSCG00000010341	14:85816502-85845941		CT737327,CH242-94O23,14:85788343-85946849 (Clone quality: bE94O23 on chr=14; Num_of_Contigs=2; )
TSPAN15		ENSSSCG00000010255	14:75648115-75709042
TSPAN17		ENSSSCG00000014051	2:70286115-70295236		CU915506,CH242-450C12,2:70276939-70304316 (Clone quality: bE450C12 on chr=2; Num_of_Contigs=12; )
TSPAN18		ENSSSCG00000013278	2:15945113-15958192		FP102411,CH242-59A7,2:15908127-15964472 (Clone quality: bE59A7 on chr=2; Num_of_Contigs=3; )
TSPAN2		ENSSSCG00000006748	4:109765407-109803386
TSPAN2		location ⇒	4:109765407-109765505		CU463898,CH242-57E2,4:109624821-109767935 (Clone quality: bE57E2 on chr=4; Num_of_Contigs=7; )
TSPAN2		location ⇒	4:109781330-109781434		CU468531,CH242-18P21,4:109767936-109881501 (Clone quality: bE18P21 on chr=4; Num_of_Contigs=5; )
TSPAN2		location ⇒	4:109792838-109792936		CU468531,CH242-18P21,4:109767936-109881501 (Clone quality: bE18P21 on chr=4; Num_of_Contigs=5; )
TSPAN2		location ⇒	4:109796014-109796112		CU468531,CH242-18P21,4:109767936-109881501 (Clone quality: bE18P21 on chr=4; Num_of_Contigs=5; )
TSPAN25		ENSSSCG00000006800	4:113726728-113756057
TSPAN3		ENSSSCG00000001868	7:62457425-62482522		CT868718,CH242-524I20,7:62378964-62491858 (Clone quality: bE524I20 on chr=7; Num_of_Contigs=2; )
TSPAN3		location ⇒	7:62458042-62457090		CT868718,CH242-524I20,7:62378964-62491858 (Clone quality: bE524I20 on chr=7; Num_of_Contigs=2; )
TSPAN3		location ⇒	7:62465257-62465102		CT868718,CH242-524I20,7:62378964-62491858 (Clone quality: bE524I20 on chr=7; Num_of_Contigs=2; )
TSPAN3		location ⇒	7:62468687-62468499		CT868718,CH242-524I20,7:62378964-62491858 (Clone quality: bE524I20 on chr=7; Num_of_Contigs=2; )
TSPAN3		location ⇒	7:62482516-62482224		CT868718,CH242-524I20,7:62378964-62491858 (Clone quality: bE524I20 on chr=7; Num_of_Contigs=2; )
TSPAN30		ENSSSCG00000000361	5:20079426-20127422
TSPAN33		ENSSSCG00000016570	18:17651524-17671980		CU638846,CH242-272C14,18:17604734-17699485 (Clone quality: bE272C14 on chr=18; Num_of_Contigs=4; )
TSPAN4		ENSSSCG00000012838	2:116721-130007		CU928976,CH242-144M19,2:43742-170991 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
TSPAN6		ENSSSCG00000012481	X:75667842-75673316		CU207261,CH242-166I17,X:75651367-75713469 (Clone quality: bE166I17 on chr=X; Num_of_Contigs=6; )
TSPAN9		ENSSSCG00000000735	5:62812934-62987030

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).