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)

TTC39C		ENSSSCG00000003710	6:74282503-74340768
TTC4		ENSSSCG00000003844	6:112246724-112281337
TTC5		ENSSSCG00000002145	7:85017072-85037070		CU571042,CH242-348N17,7:84913444-85061275 (Clone quality: bE348N17 on chr=7; Num_of_Contigs=2; )
TTC6		ENSSSCG00000001939	7:68158258-68209114
TTC7A		ENSSSCG00000008434	3:86841621-86978335
TTC7B		ENSSSCG00000002436	7:120127507-120273913
TTC8		ENSSSCG00000002428	7:118605713-118657306
TTC9		ENSSSCG00000002327	7:102676827-102711964
TTC9		location ⇒	7:102672797-102672602		CU469452,CH242-138O16,7:102664955-102698332 (Clone quality: bE138O16 on chr=7; Num_of_Contigs=9; )
TTC9		location ⇒	7:102676910-102676823		CU469452,CH242-138O16,7:102664955-102698332 (Clone quality: bE138O16 on chr=7; Num_of_Contigs=9; )
TTC9		location ⇒	7:102678623-102678451		CU469452,CH242-138O16,7:102664955-102698332 (Clone quality: bE138O16 on chr=7; Num_of_Contigs=9; )
TTC9		location ⇒	7:102711796-102711559		CU469452,CH242-138O16,7:102698433-102712240 (Clone quality: bE138O16 on chr=7; Num_of_Contigs=9; )
TTC9B		ENSSSCG00000002991	6:33573677-33574819		FP102369,CH242-128M4,6:33567029-33575618 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
TTF1		ENSSSCG00000005725	1:287816105-287884063
TTF2		ENSSSCG00000006733	4:107745006-107788523
TTID		ENSSSCG00000014324	2:126969357-126989069
TTID		location ⇒	2:126972355-126972922		CU914347,CH242-386D24,2:126969542-127015139 (Clone quality: bE386D24 on chr=2; Num_of_Contigs=12; )
TTID		location ⇒	2:126984467-126984674		CU914347,CH242-386D24,2:126969542-127015139 (Clone quality: bE386D24 on chr=2; Num_of_Contigs=12; )
TTID		location ⇒	2:126988439-126989035		CU914347,CH242-386D24,2:126969542-127015139 (Clone quality: bE386D24 on chr=2; Num_of_Contigs=12; )
TTID		location ⇒	2:95481650-95481559		CU856087,CH242-137K2,2:95462189-95567867 (Clone quality: bE137K2 on chr=2; Num_of_Contigs=7; )
TTK		ENSSSCG00000004466	1:91055118-91101553
TTLL1		ENSSSCG00000000035	5:2455372-2505617
TTLL10		ENSSSCG00000003336	6:42882145-42889728		FP102596,CH242-173K23,6:42875917-42894303 (Clone quality: bE173K23 on chr=6; Num_of_Contigs=10; )
TTLL12		ENSSSCG00000000034	5:2436938-2486425
TTLL3		ENSSSCG00000011553	13:55281974-55311369
TTLL4		ENSSSCG00000016201	15:113851734-113859380
TTLL5		ENSSSCG00000002384	7:106771574-107140660
TTLL6		ENSSSCG00000017542	12:22540889-22578684		CU928816,CH242-243D3,12:22540379-22621965 (Clone quality: bE243D3 on chr=12; Num_of_Contigs=4; )
TTLL7		ENSSSCG00000003760	6:89447168-89602717
TTLL8		ENSSSCG00000000982	5:100041336-100063703
TTLL9		ENSSSCG00000007236	17:37603228-37646353
TTL_PIG		ENSSSCG00000008100	3:39551078-39592726
TTL_PIG		ENSSSCG00000008097	3:39350640-39592957
TTN		ENSSSCG00000016001	15:79179921-79454720
TTN		location ⇒	15:79317487-79317414		CU466382,CH242-21C8,15:79295534-79351543 (Clone quality: bE21C8 on chr=15; Num_of_Contigs=3; )
TTN		location ⇒	15:79320865-79320800		CU466382,CH242-21C8,15:79295534-79351543 (Clone quality: bE21C8 on chr=15; Num_of_Contigs=3; )
TTN		location ⇒	15:79345996-79345936		CU466382,CH242-21C8,15:79295534-79351543 (Clone quality: bE21C8 on chr=15; Num_of_Contigs=3; )
TTN		location ⇒	15:79438142-79438043		CU466382,CH242-21C8,15:79372116-79476926 (Clone quality: bE21C8 on chr=15; Num_of_Contigs=3; )
TTPA		ENSSSCG00000006225	4:73586046-73597728
TTPAL		ENSSSCG00000007376	17:48721943-48727915
TTRAP		ENSSSCG00000001092	7:20499805-20512211		CU468861,CH242-123E20,7:20499469-20564207 (Clone quality: bE123E20 on chr=7; Num_of_Contigs=4; )
TTYH1		ENSSSCG00000003271	6:40651001-40666839
TTYH2		ENSSSCG00000017238	12:4894101-4934415	CU929509,CH242-210O23,12:4890845-5083024 (Clone quality: bE210O23 on chr=12; Num_of_Contigs=5; )
TTYH3		ENSSSCG00000007565	3:1467669-1478123
TUB		ENSSSCG00000014581	9:829546-847869		CU571015,CH242-18F18,9:773826-881041 (Clone quality: bE18F18 on chr=9; Num_of_Contigs=4; )
TUBA1		ENSSSCG00000016215	15:114286412-114290179		CU457453,CH242-470M7,15:114256624-114294054 (Clone quality: bE470M7 on chr=15; Num_of_Contigs=11; )
TUBA1A		ENSSSCG00000000193	5:13933531-13937474		CU633660,CH242-20J14,5:13896809-13996550 (Clone quality: bE20J14 on chr=5; Num_of_Contigs=3; )
TUBA1C		ENSSSCG00000000194	5:14008194-14016989		CU633660,CH242-20J14,5:13996651-14067250 (Clone quality: bE20J14 on chr=5; Num_of_Contigs=3; )
TUBA3E		ENSSSCG00000010099	14:51690135-51696311		CU633934,CH242-117H20,14:51553625-51738341 (Clone quality: bE117H20 on chr=14; Num_of_Contigs=1; )
TUBA8		ENSSSCG00000000773	5:65886200-65936145

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).