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)

ADAMTS15		ENSSSCG00000015250	9:55544441-55566169
ADAMTS16		ENSSSCG00000017109	16:73614748-73776808
ADAMTS19		ENSSSCG00000014259	2:119956105-120260068
ADAMTS19		location ⇒	2:120013630-120013796		CU928718,CH242-148C2,2:119882774-120036473 (Clone quality: bE148C2 on chr=2; Num_of_Contigs=3; )
ADAMTS19		location ⇒	2:120021042-120021220		CU928718,CH242-148C2,2:119882774-120036473 (Clone quality: bE148C2 on chr=2; Num_of_Contigs=3; )
ADAMTS19		location ⇒	2:120259604-120259969		CU582902,CH242-69C11,2:120251788-120266606 (Clone quality: bE69C11 on chr=2; Num_of_Contigs=7; )
ADAMTS19		location ⇒	2:120260088-120260903		CU582902,CH242-69C11,2:120251788-120266606 (Clone quality: bE69C11 on chr=2; Num_of_Contigs=7; )
ADAMTS2		ENSSSCG00000014025	2:68746726-68764858
ADAMTS3		ENSSSCG00000008946	8:58291168-58423167
ADAMTS4		ENSSSCG00000006359	4:92769312-92777013		CU606874,CH242-28G15,4:92745461-92814223 (Clone quality: bE28G15 on chr=4; Num_of_Contigs=6; )
ADAMTS5		ENSSSCG00000012027	13:136023163-136067041
ADAMTS6		ENSSSCG00000016943	16:41185422-41287942
ADAMTS7		ENSSSCG00000001765	7:53922220-53938438		CT990622,CH242-240G10,7:53914944-53952138 (Clone quality: bE240G10 on chr=7; Num_of_Contigs=13; )
ADAMTS8		ENSSSCG00000015249	9:55510963-55529896		CU929954,CH242-520O7,9:55502176-55537127 (Clone quality: bE520O7 on chr=9; Num_of_Contigs=3; )
ADAMTS9		ENSSSCG00000011496	13:38738725-38882544
ADAMTSL1		ENSSSCG00000005175	1:212749071-213086835
ADAMTSL3		ENSSSCG00000001793	7:57035102-57206197
ADAMTSL3		location ⇒	7:57273326-57273458		CU457749,CH242-269J20,7:57248528-57327880 (Clone quality: bE269J20 on chr=7; Num_of_Contigs=8; )
ADAMTSL3		location ⇒	7:57309016-57309150		CU457749,CH242-269J20,7:57248528-57327880 (Clone quality: bE269J20 on chr=7; Num_of_Contigs=8; )
ADAMTSL3		location ⇒	7:57346559-57346437		CU457749,CH242-269J20,7:57342380-57347373 (Clone quality: bE269J20 on chr=7; Num_of_Contigs=8; )
ADAMTSL3		location ⇒	7:57402476-57402295		CU468185,CH242-387O22,7:57347374-57522917 (Clone quality: bE387O22 on chr=7; Num_of_Contigs=2; )
ADAMTSL4		ENSSSCG00000006651	4:102498914-102506582		CU655899,CH242-160A10,4:102490407-102528327 (Clone quality: bE160A10 on chr=4; Num_of_Contigs=7; )
ADAMTSL5		ENSSSCG00000013433	2:46524464-46530367		CU972485,CH242-416N2,2:46524462-46568465 (Clone quality: bE416N2 on chr=2; Num_of_Contigs=2; )
ADAP2		ENSSSCG00000017738	12:40553712-40583423
ADAR		ENSSSCG00000006543	4:99245796-99261698	CU469085,CH242-42I4,4:99200352-99380372 (Clone quality: bE42I4 on chr=4; Num_of_Contigs=1; )
ADAR		location ⇒	4:99246900-99247192	CU469085,CH242-42I4,4:99200352-99380372 (Clone quality: bE42I4 on chr=4; Num_of_Contigs=1; )
ADAR		location ⇒	4:99249082-99249266	CU469085,CH242-42I4,4:99200352-99380372 (Clone quality: bE42I4 on chr=4; Num_of_Contigs=1; )
ADAR		location ⇒	4:99249757-99249837	CU469085,CH242-42I4,4:99200352-99380372 (Clone quality: bE42I4 on chr=4; Num_of_Contigs=1; )
ADAR		location ⇒	4:99250489-99250552	CU469085,CH242-42I4,4:99200352-99380372 (Clone quality: bE42I4 on chr=4; Num_of_Contigs=1; )
ADARB1		ENSSSCG00000012089	13:145139965-145174539
ADARB2		ENSSSCG00000011160	10:64172280-64258755
ADAT1		ENSSSCG00000002706	6:8726335-8753037		CU856392,CH242-53K23,6:8631869-8811363 (Clone quality: bE53K23 on chr=6; Num_of_Contigs=1; )
ADAT2		ENSSSCG00000004135	1:22870602-22892413		CU074286,CH242-127C20,1:22835281-23031382 (Clone quality: bE127C20 on chr=1; Num_of_Contigs=1; )
ADAT3		ENSSSCG00000013450	2:47021241-47022296		FP236669,CH242-487E14,2:47021000-47026797 (Clone quality: bE487E14 on chr=2; Num_of_Contigs=9; )
ADC		ENSSSCG00000003619	6:60987324-61025768
ADCK1		ENSSSCG00000002408	7:108842087-108909821		CU633180,CH242-11C4,7:108802684-108938791 (Clone quality: bE11C4 on chr=7; Num_of_Contigs=3; )
ADCK2		ENSSSCG00000016496	18:7539622-7557943		CU861954,CH242-234F22,18:7394978-7580916 (Clone quality: bE234F22 on chr=18; Num_of_Contigs=1; )
ADCK5		ENSSSCG00000005907	4:508167-525002		CU468594,CH242-10O17,4:503788-542119 (Clone quality: bE10O17 on chr=4; Num_of_Contigs=10; )
ADCY1		ENSSSCG00000016726	18:48613579-48619434		FP103017,CH242-169F4,18:48613133-48622407 (Clone quality: bE169F4 on chr=18; Num_of_Contigs=6; )
ADCY10		ENSSSCG00000006305	4:86403206-86509490
ADCY2		ENSSSCG00000017101	16:71563048-71670349		FP015800,CH242-321F21,16:71559413-71670410 (Clone quality: bE321F21 on chr=16; Num_of_Contigs=4; )
ADCY3		ENSSSCG00000008578	3:106100659-106193071
ADCY4		ENSSSCG00000001988	7:81297178-81313143		CU019590,CH242-406B17,7:81281809-81421007 (Clone quality: bE406B17 on chr=7; Num_of_Contigs=4; )
ADCY6		ENSSSCG00000000175	5:13340189-13356370		CU914692,CH242-143P14,5:13271941-13360701 (Clone quality: bE143P14 on chr=5; Num_of_Contigs=6; )
ADCY8		ENSSSCG00000005957	4:8665878-8896498
ADCY9		ENSSSCG00000007948	3:34043306-34317923
ADCYAP1		ENSSSCG00000003698	6:72333470-72337631		CU467582,CH242-420P11,6:72324388-72354995 (Clone quality: bE420P11 on chr=6; Num_of_Contigs=8; )
ADCYAP1R1		ENSSSCG00000016672	18:40391249-40433540
ADD1		ENSSSCG00000008692	8:959244-977790
ADD3		ENSSSCG00000010621	14:126055114-126185351

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, 1751-32

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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).