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)

RAB34		ENSSSCG00000017769	12:42638511-42642425		FP016171,CH242-62B5,12:42618725-42654541 (Clone quality: bE62B5 on chr=12; Num_of_Contigs=5; )
RAB36		ENSSSCG00000010048	14:50087986-50099343
RAB37		ENSSSCG00000017233	12:4708500-4716534	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
RAB38		ENSSSCG00000014923	9:21587661-21624236
RAB39		ENSSSCG00000015005	9:35942326-35968604
RAB39B		ENSSSCG00000012810	X:123391991-123396214	CU861979,CH242-305A15,X:123389549-123544360 (Clone quality: bE305A15 on chr=X; Num_of_Contigs=11; )
RAB3A		ENSSSCG00000013897	2:62356629-62363278		CU915655,CH242-228H4,2:62349388-62376255 (Clone quality: bE228H4 on chr=2; Num_of_Contigs=13; )
RAB3B		ENSSSCG00000003869	6:114002983-114059978
RAB3C		ENSSSCG00000016928	16:35511972-35512199		CU914321,CH242-270D14,16:35409456-35535651 (Clone quality: bE270D14 on chr=16; Num_of_Contigs=4; )
RAB3D		ENSSSCG00000013623	2:52312392-52322025
RAB3GAP1		ENSSSCG00000015695	15:15103608-15153604
RAB3GAP2		ENSSSCG00000010824	10:9783270-9874349
RAB3IL1		ENSSSCG00000013074	2:7895299-7903442		CU914654,CH242-267E20,2:7861434-7908597 (Clone quality: bE267E20 on chr=2; Num_of_Contigs=5; )
RAB3IP		ENSSSCG00000000500	5:32847211-32898060
RAB40C		ENSSSCG00000009116	8:90898795-90899639		CU467915,CH242-253M5,8:90869911-90967763 (Clone quality: bE253M5 on chr=8; Num_of_Contigs=1; )
RAB44		ENSSSCG00000001566	7:37021448-37034938	CU326356,CH242-61G11,7:36975834-37183903 (Clone quality: bE61G11 on chr=7; Num_of_Contigs=4; )
RAB4B		ENSSSCG00000002996	6:33680022-33690564		CU928654,CH242-130A3,6:33678287-33731769 (Clone quality: bE130A3 on chr=6; Num_of_Contigs=6; )
RAB5C		ENSSSCG00000017412	12:18346421-18368345		CU856598,CH242-362F6,12:18319906-18418389 (Clone quality: bE362F6 on chr=12; Num_of_Contigs=5; )
RAB6B		ENSSSCG00000011638	13:61420045-61479045		CU633685,CH242-265M20,13:61378623-61549248 (Clone quality: bE265M20 on chr=13; Num_of_Contigs=2; )
RAB7A		ENSSSCG00000011615	13:59266052-59336087
RAB8A		ENSSSCG00000013848	2:60566824-60585810		CU856246,CH242-281F10,2:60562497-60591128 (Clone quality: bE281F10 on chr=2; Num_of_Contigs=6; )
RAB8B		ENSSSCG00000004566	1:112138577-112156112		CU606936,CH242-108A5,1:112133269-112189441 (Clone quality: bE108A5 on chr=1; Num_of_Contigs=6; )
RAB9A		ENSSSCG00000012123	X:9461203-9461808	CU633939,CH242-187N24,X:9427527-9513452 (Clone quality: bE187N24 on chr=X; Num_of_Contigs=4; )
RABAC1		ENSSSCG00000003046	6:34671296-34674226		FP015926,CH242-183C8,6:34669147-34686332 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
RABEP1		ENSSSCG00000017895	12:48725342-48802968
RABEP2		ENSSSCG00000007806	3:16680596-16697708
RABEPK		ENSSSCG00000005599	1:280715947-280738816
RABGAP1		ENSSSCG00000015505	9:110058693-110082077
RABGAP1L		ENSSSCG00000015499	9:109282531-109462850
RABGEF1		ENSSSCG00000007735	3:14584364-14835951
RABGGTA		ENSSSCG00000001992	7:81362672-81368874		CU019590,CH242-406B17,7:81281809-81421007 (Clone quality: bE406B17 on chr=7; Num_of_Contigs=4; )
RABGGTB		ENSSSCG00000003775	6:96114303-96123370		CU929611,CH242-276C23,6:96098364-96199408 (Clone quality: bE276C23 on chr=6; Num_of_Contigs=3; )
RABIF		ENSSSCG00000010932	10:24990068-24995627		CU986276,CH242-319L9,10:24954126-25023165 (Clone quality: bE319L9 on chr=10; Num_of_Contigs=6; )
RABL3		location ⇒	1:188087531-188087474		CU606975,CH242-251A8,1:188036812-188088768 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
RABL3		location ⇒	1:228874394-228874337		CU618324,CH242-276M24,1:228857825-228880847 (Clone quality: bE276M24 on chr=1; Num_of_Contigs=4; )
RABL4		ENSSSCG00000000139	5:7363643-7384518
RABL5		ENSSSCG00000007679	3:7282798-7286558		FP102957,CH242-63P23,3:7280869-7293451 (Clone quality: bE63P23 on chr=3; Num_of_Contigs=9; )
RAC1		ENSSSCG00000014624	9:2561209-2564779		CU972372,CH242-47M8,9:2561067-2567081 (Clone quality: bE47M8 on chr=9; Num_of_Contigs=7; )
RAC1		ENSSSCG00000009229	8:114105524-114148502
RAC1		location ⇒	17:32985310-32985136		CU855762,CH242-249P11,17:32881834-33024828 (Clone quality: bE249P11 on chr=17; Num_of_Contigs=6; )
RAC3		ENSSSCG00000007455	17:51928484-51932437		CU607037,CH242-23K15,17:51928344-51947555 (Clone quality: bE23K15 on chr=17; Num_of_Contigs=16; )
RAC3		location ⇒	9:5657675-5657568		CU914666,CH242-341A4,9:5657425-5670650 (Clone quality: bE341A4 on chr=9; Num_of_Contigs=11; )
RACGAP1		ENSSSCG00000000217	5:14703906-14706709		CU457393,CH242-123B14,5:14700361-14712656 (Clone quality: bE123B14 on chr=5; Num_of_Contigs=20; )
RAD1		ENSSSCG00000016826	16:18041776-18049625		CU914241,CH242-186I1,16:17966592-18131621 (Clone quality: bE186I1 on chr=16; Num_of_Contigs=2; )
RAD17		ENSSSCG00000016960	16:44702893-44795230
RAD21		ENSSSCG00000006015	4:21609768-21631187		CU656020,CH242-384B12,4:21609657-21632738 (Clone quality: bE384B12 on chr=4; Num_of_Contigs=11; )
RAD21		ENSSSCG00000006014	4:21505023-21642997
RAD21		ENSSSCG00000007191	17:35731437-35763331
RAD21L1		ENSSSCG00000007191	17:35731437-35763331
RAD23A		ENSSSCG00000013747	2:56291244-56297121		CU463133,CH242-121E19,2:56264935-56304744 (Clone quality: bE121E19 on chr=2; Num_of_Contigs=6; )

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, 1001-16

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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).