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)

CD3D		location ⇒	9:44526821-44526690		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
CD3D		location ⇒	9:44527485-44527265		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
CD3D		location ⇒	9:44529522-44529465		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
CD3E		ENSSSCG00000015092	9:44505053-44519343		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
CD3E		location ⇒	9:44505233-44505338		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
CD3E		location ⇒	9:44515707-44515922		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
CD3E		location ⇒	9:44516942-44517112		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
CD3E		location ⇒	9:44518723-44519338		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
CD3G		ENSSSCG00000015094	9:44530626-44540271		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
CD3G		location ⇒	9:44535794-44536023		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
CD3G		location ⇒	9:44537556-44537687		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
CD3G		location ⇒	9:44539457-44539546		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
CD3G		location ⇒	9:44540092-44540306		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
CD3Z		ENSSSCG00000006309	4:86799324-86892177	CU151848,CH242-192N14,4:86700413-86905931 (Clone quality: bE192N14 on chr=4; Num_of_Contigs=2; )
CD3Z		location ⇒	4:86799500-86799566	CU151848,CH242-192N14,4:86700413-86905931 (Clone quality: bE192N14 on chr=4; Num_of_Contigs=2; )
CD3Z		location ⇒	4:86881162-86881260	CU151848,CH242-192N14,4:86700413-86905931 (Clone quality: bE192N14 on chr=4; Num_of_Contigs=2; )
CD4		ENSSSCG00000000687	5:59930618-59956620
CD4		ENSSSCG00000012652	X:104537896-104549372
CD4		ENSSSCG00000011201	13:4234402-4328152
CD4		ENSSSCG00000010538	14:115483488-115483955		CT827848,CH242-276N12,14:115431518-115501704 (Clone quality: bE276N12 on chr=14; Num_of_Contigs=5; )
CD4		ENSSSCG00000001059	7:10571782-10589831
CD4		ENSSSCG00000012397	X:56853523-56857235		CU468205,CH242-6A14,X:56849541-56908124 (Clone quality: bE6A14 on chr=X; Num_of_Contigs=4; )
CD4		location ⇒	5:59932106-59931026		CU457492,CH242-370K21,5:59930503-59949398 (Clone quality: bE370K21 on chr=5; Num_of_Contigs=10; )
CD4		location ⇒	5:59933872-59933670		CU457492,CH242-370K21,5:59930503-59949398 (Clone quality: bE370K21 on chr=5; Num_of_Contigs=10; )
CD4		location ⇒	5:59935731-59935392		CU457492,CH242-370K21,5:59930503-59949398 (Clone quality: bE370K21 on chr=5; Num_of_Contigs=10; )
CD4		location ⇒	5:59936955-59936725		CU457492,CH242-370K21,5:59930503-59949398 (Clone quality: bE370K21 on chr=5; Num_of_Contigs=10; )
CD40		ENSSSCG00000007440	17:50399620-50408344
CD40		ENSSSCG00000002525	7:130944988-130993025		CT998550,CH242-445C19,7:130928637-130997560 (Clone quality: bE445C19 on chr=7; Num_of_Contigs=6; )
CD40		location ⇒	17:50400675-50400804		CU407253,CH242-446C24,17:50399620-50412826 (Clone quality: bE446C24 on chr=17; Num_of_Contigs=11; )
CD40		location ⇒	17:50401084-50401230		CU407253,CH242-446C24,17:50399620-50412826 (Clone quality: bE446C24 on chr=17; Num_of_Contigs=11; )
CD40		location ⇒	17:50401571-50401665		CU407253,CH242-446C24,17:50399620-50412826 (Clone quality: bE446C24 on chr=17; Num_of_Contigs=11; )
CD40		location ⇒	17:50407749-50408290		CU407253,CH242-446C24,17:50399620-50412826 (Clone quality: bE446C24 on chr=17; Num_of_Contigs=11; )
CD40L		ENSSSCG00000007440	17:50399620-50408344
CD42b		ENSSSCG00000010127	14:52410111-52411258		CU468497,CH242-430C1,14:52380763-52419017 (Clone quality: bE430C1 on chr=14; Num_of_Contigs=6; )
CD42c		ENSSSCG00000010127	14:52410111-52411258		CU468497,CH242-430C1,14:52380763-52419017 (Clone quality: bE430C1 on chr=14; Num_of_Contigs=6; )
CD42d		ENSSSCG00000011824	13:98944880-98946583		CU928370,CH242-309K5,13:98935619-99004797 (Clone quality: bE309K5 on chr=13; Num_of_Contigs=6; )
CD44		ENSSSCG00000013297	2:24136169-24228899
CD44		location ⇒	2:24135976-24135472	FP102395,CH242-89L24,2:24124384-24190963 (Clone quality: bE89L24 on chr=2; Num_of_Contigs=2; )
CD44		location ⇒	2:24136375-24136058	FP102395,CH242-89L24,2:24124384-24190963 (Clone quality: bE89L24 on chr=2; Num_of_Contigs=2; )
CD44		location ⇒	2:24180722-24180492	FP102395,CH242-89L24,2:24124384-24190963 (Clone quality: bE89L24 on chr=2; Num_of_Contigs=2; )
CD44		location ⇒	2:24228901-24228657	CU972424,CH242-197C9,2:24190964-24366072 (Clone quality: bE197C9 on chr=2; Num_of_Contigs=2; )
CD45		ENSSSCG00000010907	10:22661389-22700150
CD45		ENSSSCG00000010908	10:22721069-22743562		FP067416,CH242-483G3,10:22720837-22744862 (Clone quality: bE483G3 on chr=10; Num_of_Contigs=5; )
CD45		ENSSSCG00000012909	2:3468942-3469568		CU633429,CH242-6G2,2:3468458-3486670 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
CD46		ENSSSCG00000015293	9:63407760-63456410
CD47		ENSSSCG00000011942	13:112560933-112606511		CU914353,CH242-125K22,13:112547929-112616121 (Clone quality: bE125K22 on chr=13; Num_of_Contigs=6; )
CD47		location ⇒	13:112562666-112560949		CU914353,CH242-125K22,13:112547929-112616121 (Clone quality: bE125K22 on chr=13; Num_of_Contigs=6; )
CD47		location ⇒	13:112562666-112560949		CU914353,CH242-125K22,13:112547929-112616121 (Clone quality: bE125K22 on chr=13; Num_of_Contigs=6; )
CD47		location ⇒	13:112606368-112606020		CU914353,CH242-125K22,13:112547929-112616121 (Clone quality: bE125K22 on chr=13; Num_of_Contigs=6; )
CD47		location ⇒	13:112606368-112606020		CU914353,CH242-125K22,13:112547929-112616121 (Clone quality: bE125K22 on chr=13; 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, 1001-1050, 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).