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)

CRSP		location ⇒	2:41164862-41164942		CU928260,CH242-273B21,2:41162604-41257476 (Clone quality: bE273B21 on chr=2; Num_of_Contigs=3; )
CRSP		location ⇒	2:41371328-41371464		CU606994,CH242-513N24,2:41325835-41371753 (Clone quality: bE513N24 on chr=2; Num_of_Contigs=5; )
CRSP		location ⇒	2:41384465-41384526		CU606994,CH242-513N24,2:41371854-41392335 (Clone quality: bE513N24 on chr=2; Num_of_Contigs=5; )
CRSP		location ⇒	2:41526966-41526779		CU606994,CH242-513N24,2:41487352-41529702 (Clone quality: bE513N24 on chr=2; Num_of_Contigs=5; )
CRSP-2		ENSSSCG00000013387	2:41287338-41291017		CU928260,CH242-273B21,2:41257577-41300655 (Clone quality: bE273B21 on chr=2; Num_of_Contigs=3; )
CRSP-2		location ⇒	2:41164862-41164942		CU928260,CH242-273B21,2:41162604-41257476 (Clone quality: bE273B21 on chr=2; Num_of_Contigs=3; )
CRSP-2		location ⇒	2:41289928-41290118		CU928260,CH242-273B21,2:41257577-41300655 (Clone quality: bE273B21 on chr=2; Num_of_Contigs=3; )
CRSP-2		location ⇒	2:41290848-41291014		CU928260,CH242-273B21,2:41257577-41300655 (Clone quality: bE273B21 on chr=2; Num_of_Contigs=3; )
CRSP-2		location ⇒	2:41384465-41384526		CU606994,CH242-513N24,2:41371854-41392335 (Clone quality: bE513N24 on chr=2; Num_of_Contigs=5; )
CRSP2		ENSSSCG00000012250	X:36069913-36138839		FP067431,CH242-266E24,X:36049329-36150098 (Clone quality: bE266E24 on chr=X; Num_of_Contigs=2; )
CRSP2		ENSSSCG00000013387	2:41287338-41291017		CU928260,CH242-273B21,2:41257577-41300655 (Clone quality: bE273B21 on chr=2; Num_of_Contigs=3; )
CRSP8		ENSSSCG00000005720	1:287164826-287368710
CRSP8		location ⇒	1:287165370-287164826	CU915472,CH242-25B10,1:287161792-287179273 (Clone quality: bE25B10 on chr=1; Num_of_Contigs=7; )
CRSP8		location ⇒	1:287365995-287365851	CU076045,CH242-172L24,1:287330189-287383682 (Clone quality: bE172L24 on chr=1; Num_of_Contigs=1; )
CRSP8		location ⇒	1:287368710-287368444	CU076045,CH242-172L24,1:287330189-287383682 (Clone quality: bE172L24 on chr=1; Num_of_Contigs=1; )
CRSP8		location ⇒	1:287494726-287494992		CU914799,CH242-187I21,1:287449789-287546806 (Clone quality: bE187I21 on chr=1; Num_of_Contigs=19; )
CRSP9		location ⇒	16:63806642-63807757		CU972395,CH242-203E2,16:63794505-63875272 (Clone quality: bE203E2 on chr=16; Num_of_Contigs=4; )
CRTAC1		ENSSSCG00000010530	14:114084300-114084497		FP016035,CH242-136O3,14:114064456-114092939 (Clone quality: bE136O3 on chr=14; Num_of_Contigs=6; )
CRTAM		ENSSSCG00000015137	9:48323635-48349895		CU639472,CH242-130N11,9:48226708-48363863 (Clone quality: bE130N11 on chr=9; Num_of_Contigs=2; )
CRTC1		ENSSSCG00000013915	2:62782929-62810692		CU914263,CH242-289B6,2:62670241-62856330 (Clone quality: bE289B6 on chr=2; Num_of_Contigs=2; )
CRTC2		ENSSSCG00000006567	4:99963404-99974606		CU407290,CH242-513B13,4:99962788-99976453 (Clone quality: bE513B13 on chr=4; Num_of_Contigs=7; )
CRX		ENSSSCG00000003124	6:37266988-37270453		FP102640,CH242-235B10,6:37266679-37271317 (Clone quality: bE235B10 on chr=6; Num_of_Contigs=12; )
CRY1		ENSSSCG00000000164	5:11490648-11579336
CRY2		ENSSSCG00000013270	2:14888451-14906965		FP101987,CH242-521A18,2:14831953-14928280 (Clone quality: bE521A18 on chr=2; Num_of_Contigs=9; )
CRYAB		ENSSSCG00000015025	9:38490730-38494307		CU928661,CH242-297D12,9:38485160-38494619 (Clone quality: bE297D12 on chr=9; Num_of_Contigs=9; )
CRYAB		location ⇒	9:38490732-38491078		CU928661,CH242-297D12,9:38485160-38494619 (Clone quality: bE297D12 on chr=9; Num_of_Contigs=9; )
CRYAB		location ⇒	9:38492624-38492749		CU928661,CH242-297D12,9:38485160-38494619 (Clone quality: bE297D12 on chr=9; Num_of_Contigs=9; )
CRYAB		location ⇒	9:38493834-38494178		CU928661,CH242-297D12,9:38485160-38494619 (Clone quality: bE297D12 on chr=9; Num_of_Contigs=9; )
CRYBA4		ENSSSCG00000009965	14:44954612-44961093	CT737259,CH242-127E12,14:44858989-45080062 (Clone quality: bE127E12 on chr=14; Num_of_Contigs=2; )
CRYBB1		ENSSSCG00000009964	14:44936153-44950080	CT737259,CH242-127E12,14:44858989-45080062 (Clone quality: bE127E12 on chr=14; Num_of_Contigs=2; )
CRYBB2		ENSSSCG00000009955	14:43702868-43714419		CU468573,CH242-7N20,14:43694395-43717041 (Clone quality: bE7N20 on chr=14; Num_of_Contigs=4; )
CRYBB3		ENSSSCG00000009954	14:43505444-43511833		CU468449,CH242-125C8,14:43366924-43512165 (Clone quality: bE125C8 on chr=14; Num_of_Contigs=2; )
CRYBG3		ENSSSCG00000004371	1:76036302-76054225
CRYGB		ENSSSCG00000016145	15:104157596-104159686		CU570733,CH242-280B12,15:104156630-104167155 (Clone quality: bE280B12 on chr=15; Num_of_Contigs=4; )
CRYGC		ENSSSCG00000016144	15:104148174-104149606		CU570733,CH242-280B12,15:104130222-104153003 (Clone quality: bE280B12 on chr=15; Num_of_Contigs=4; )
CRYGS		ENSSSCG00000011796	13:93955775-93962580		CU466376,CH242-17J7,13:93934222-94016715 (Clone quality: bE17J7 on chr=13; Num_of_Contigs=6; )
CRYL1		ENSSSCG00000009268	11:38976-101722
CRYM		ENSSSCG00000007849	3:22419306-22605940
CRYZ		ENSSSCG00000003780	6:97025343-97047038		CU442729,CH242-136C9,6:97021854-97054997 (Clone quality: bE136C9 on chr=6; Num_of_Contigs=13; )
CS		ENSSSCG00000000388	5:20593671-20596080		CU694915,CH242-453C18,5:20582151-20599340 (Clone quality: bE453C18 on chr=5; Num_of_Contigs=10; )
CSAD		ENSSSCG00000000259	5:16919875-16929254
CSDA		ENSSSCG00000000633	5:57874577-57897965		CU856689,CH242-196F1,5:57868345-57902214 (Clone quality: bE196F1 on chr=5; Num_of_Contigs=2; )
CSDC2		ENSSSCG00000000062	5:3523080-3525667		CU633382,CH242-275I12,5:3520740-3532572 (Clone quality: bE275I12 on chr=5; Num_of_Contigs=9; )
CSDE1		ENSSSCG00000006752	4:110105904-110205160
CSE1L		ENSSSCG00000007459	17:53101193-53115453
CSF1		location ⇒	4:114630521-114630279		CU606863,CH242-71K19,4:114596843-114641017 (Clone quality: bE71K19 on chr=4; Num_of_Contigs=8; )
CSF1		location ⇒	4:114635718-114635547		CU606863,CH242-71K19,4:114596843-114641017 (Clone quality: bE71K19 on chr=4; Num_of_Contigs=8; )
CSF1		location ⇒	4:114766021-114765849		CU570995,CH242-11B15,4:114761098-114774572 (Clone quality: bE11B15 on chr=4; Num_of_Contigs=17; )
CSF1		location ⇒	4:114797430-114797666		CU570995,CH242-11B15,4:114797095-114802542 (Clone quality: bE11B15 on chr=4; Num_of_Contigs=17; )
CSF1R		ENSSSCG00000014441	2:136526706-136552808

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, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-2250, 2251-2300, 2301-2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-2650, 2651-2700, 2701-2750, 2751-2800, 2801-2850, 2851-2900, 2901-2950, 2951-3000, 3001-3050, 3051-3100, 3101-3150, 3151-3200, 3201-3250, 3251-3300, 3301-3350, 3351-3400, 3401-3450, 3451-3500, 3501-3550, 3551-3600, 3601-3650, 3651-3700, 3701-3750, 3751-3800, 3801-3850, 3851-3900, 3901-12

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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).