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)

RBM47		location ⇒	8:27077719-27078865		CU929922,CH242-359I10,8:27071033-27082462 (Clone quality: bE359I10 on chr=8; Num_of_Contigs=6; )
RBM47		location ⇒	8:27079734-27079943		CU929922,CH242-359I10,8:27071033-27082462 (Clone quality: bE359I10 on chr=8; Num_of_Contigs=6; )
RBM47		location ⇒	8:27091131-27091374		CU929922,CH242-359I10,8:27082563-27102255 (Clone quality: bE359I10 on chr=8; Num_of_Contigs=6; )
RBM47		location ⇒	8:27091515-27092098		CU929922,CH242-359I10,8:27082563-27102255 (Clone quality: bE359I10 on chr=8; Num_of_Contigs=6; )
RBM4B		ENSSSCG00000012938	2:4185646-4191066		CU928093,CH242-168G1,2:4184696-4195463 (Clone quality: bE168G1 on chr=2; Num_of_Contigs=25; )
RBM5		ENSSSCG00000011395	13:27189501-27222379
RBM6		ENSSSCG00000011394	13:27151597-27179339
RBM7		ENSSSCG00000015057	9:40747836-40754891		CU856090,CH242-161C5,9:40675140-40798853 (Clone quality: bE161C5 on chr=9; Num_of_Contigs=4; )
RBM8A		ENSSSCG00000006684	4:103493559-103495027		CU606940,CH242-153I6,4:103481415-103497382 (Clone quality: bE153I6 on chr=4; Num_of_Contigs=12; )
RBM9		ENSSSCG00000000152	5:8409000-8495590		CU633647,CH242-180N6,5:8389212-8541866 (Clone quality: bE180N6 on chr=5; Num_of_Contigs=6; )
RBMS1		ENSSSCG00000015888	15:62431468-62702311
RBMS1		location ⇒	15:62431802-62431572		CU929017,CH242-136H2,15:62430735-62445379 (Clone quality: bE136H2 on chr=15; Num_of_Contigs=11; )
RBMS1		location ⇒	15:62457723-62457563		CU929017,CH242-136H2,15:62456354-62459542 (Clone quality: bE136H2 on chr=15; Num_of_Contigs=11; )
RBMS1		location ⇒	15:62576324-62576094		CU914319,CH242-243B3,15:62558851-62649103 (Clone quality: bE243B3 on chr=15; Num_of_Contigs=5; )
RBMS1		location ⇒	15:62602129-62601969		CU914319,CH242-243B3,15:62558851-62649103 (Clone quality: bE243B3 on chr=15; Num_of_Contigs=5; )
RBMS3		ENSSSCG00000011222	13:13574196-14311581
RBMXL1		ENSSSCG00000012703	X:109874957-109880255		CU570847,CH242-351O5,X:109870171-109893371 (Clone quality: bE351O5 on chr=X; Num_of_Contigs=9; )
RBP1		ENSSSCG00000011664	13:65472776-65498700
RBP1		ENSSSCG00000005073	1:196253123-196447019
RBP1		ENSSSCG00000003798	6:102195509-102208960		CU442704,CH242-111N2,6:102164133-102241390 (Clone quality: bE111N2 on chr=6; Num_of_Contigs=4; )
RBP2		ENSSSCG00000010928	10:24833795-25022842
RBP2		ENSSSCG00000009748	14:24738561-24803207
RBP2		ENSSSCG00000011663	13:65412959-65438279
RBP3		ENSSSCG00000010374	14:92261734-92271602
RBP3		ENSSSCG00000007268	17:39098043-39102652
RBP3		location ⇒	14:92261847-92262059		FP085539,CH242-432I14,14:92222865-92268499 (Clone quality: bE432I14 on chr=14; Num_of_Contigs=7; )
RBP4		ENSSSCG00000010479	14:110302357-110309289		CT954211,CH242-292E3,14:110255168-110336880 (Clone quality: bE292E3 on chr=14; Num_of_Contigs=2; )
RBP5		ENSSSCG00000000673	5:59718963-59723033
RBP7		ENSSSCG00000003399	6:47357183-47370721
RBPJL		ENSSSCG00000007400	17:49636898-49649031		CU606851,CH242-219J22,17:49636607-49702762 (Clone quality: bE219J22 on chr=17; Num_of_Contigs=12; )
RBPMS		ENSSSCG00000015846	15:51472724-51785193
RBPMS2		ENSSSCG00000004549	1:110453060-110486575
RBPSUH		ENSSSCG00000008760	8:16036992-16250911
RC3H1		ENSSSCG00000015498	9:109107409-109139928
RC3H2		ENSSSCG00000005575	1:278273870-278311394
RCAN1		ENSSSCG00000012050	13:139886822-139896139		CU856466,CH242-288N3,13:139835411-139917533 (Clone quality: bE288N3 on chr=13; Num_of_Contigs=3; )
RCAN2		ENSSSCG00000001716	7:48143620-48394087
RCAN3		ENSSSCG00000003544	6:56720160-56724215		CU972460,CH242-516P3,6:56706916-56730593 (Clone quality: bE516P3 on chr=6; Num_of_Contigs=14; )
RCBTB2		ENSSSCG00000009400	11:18560730-18633515
RCC2		ENSSSCG00000003485	6:52368718-52386009		CU929743,CH242-257G20,6:52347118-52390944 (Clone quality: bE257G20 on chr=6; Num_of_Contigs=9; )
RCCD1		ENSSSCG00000001822	7:59088118-59097518	CT868688,CH242-510G16,7:59026976-59242142 (Clone quality: bE510G16 on chr=7; Num_of_Contigs=3; )
RCE1		ENSSSCG00000012927	2:3950484-3953552		FP089559,CH242-217L14,2:3940112-3995454 (Clone quality: bE217L14 on chr=2; Num_of_Contigs=11; )
RCHY1		ENSSSCG00000008969	8:60707690-60713609		CU929705,CH242-190B8,8:60703238-60714683 (Clone quality: bE190B8 on chr=8; Num_of_Contigs=18; )
RCL1		ENSSSCG00000005217	1:227245469-227307399		CU467061,CH242-40P15,1:227205229-227339524 (Clone quality: bE40P15 on chr=1; Num_of_Contigs=2; )
RCN1		ENSSSCG00000013318	2:26738947-26751145
RCN2		ENSSSCG00000001866	7:62335310-62352710		CT868718,CH242-524I20,7:62326882-62378863 (Clone quality: bE524I20 on chr=7; Num_of_Contigs=2; )
RCOR1		ENSSSCG00000002526	7:131100742-131235608		CT961040,CH242-13H19,7:131055395-131254263 (Clone quality: bE13H19 on chr=7; Num_of_Contigs=2; )
RCOR2		ENSSSCG00000013049	2:6590789-6592722
RCOR3		ENSSSCG00000015605	9:124181858-124274364
RCOR3		location ⇒	9:124184818-124184871		CU915362,CH242-471A15,9:124172567-124187083 (Clone quality: bE471A15 on chr=9; Num_of_Contigs=16; )

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).