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)

CDH19		ENSSSCG00000004885	1:162620292-162680496
CDH19		location ⇒	1:162680092-162680519		CU062608,CH242-88B5,1:162658778-162754263 (Clone quality: bE88B5 on chr=1; Num_of_Contigs=8; )
CDH2		ENSSSCG00000003722	6:77952628-77983828
CDH2		location ⇒	6:77983689-77983829		CU329675,CH242-402B12,6:77982131-77989451 (Clone quality: bE402B12 on chr=6; Num_of_Contigs=21; )
CDH2		location ⇒	6:78001496-78001327		CU329675,CH242-402B12,6:77996796-78004420 (Clone quality: bE402B12 on chr=6; Num_of_Contigs=21; )
CDH20		ENSSSCG00000004903	1:166681872-166740372
CDH20		location ⇒	1:166726803-166726973		FP090891,CH242-127N5,1:166669322-166736579 (Clone quality: bE127N5 on chr=1; Num_of_Contigs=4; )
CDH20		location ⇒	1:166730464-166730586		FP090891,CH242-127N5,1:166669322-166736579 (Clone quality: bE127N5 on chr=1; Num_of_Contigs=4; )
CDH20		location ⇒	1:166731144-166731393		FP090891,CH242-127N5,1:166669322-166736579 (Clone quality: bE127N5 on chr=1; Num_of_Contigs=4; )
CDH20		location ⇒	1:166906627-166906377		CU633360,CH242-197J3,1:166904488-166907527 (Clone quality: bE197J3 on chr=1; Num_of_Contigs=9; )
CDH22		ENSSSCG00000007439	17:50349566-50372213
CDH22		location ⇒	17:50438577-50438702		CU407253,CH242-446C24,17:50437561-50453801 (Clone quality: bE446C24 on chr=17; Num_of_Contigs=11; )
CDH22		location ⇒	17:50451470-50451767		CU407253,CH242-446C24,17:50437561-50453801 (Clone quality: bE446C24 on chr=17; Num_of_Contigs=11; )
CDH22		location ⇒	17:50459948-50460125		CU407253,CH242-446C24,17:50453902-50460365 (Clone quality: bE446C24 on chr=17; Num_of_Contigs=11; )
CDH22		location ⇒	17:50460154-50460296		CU407253,CH242-446C24,17:50453902-50460365 (Clone quality: bE446C24 on chr=17; Num_of_Contigs=11; )
CDH23		ENSSSCG00000010278	14:77772954-77915348
CDH23		location ⇒	14:77836809-77836964		CT954215,CH242-341I21,14:77695739-77877008 (Clone quality: bE341I21 on chr=14; Num_of_Contigs=1; )
CDH23		location ⇒	14:77838047-77838180		CT954215,CH242-341I21,14:77695739-77877008 (Clone quality: bE341I21 on chr=14; Num_of_Contigs=1; )
CDH23		location ⇒	14:77839406-77839536		CT954215,CH242-341I21,14:77695739-77877008 (Clone quality: bE341I21 on chr=14; Num_of_Contigs=1; )
CDH23		location ⇒	14:77840252-77840582		CT954215,CH242-341I21,14:77695739-77877008 (Clone quality: bE341I21 on chr=14; Num_of_Contigs=1; )
CDH24		ENSSSCG00000002037	7:82382731-82390566		CU468526,CH242-14D10,7:82382718-82403264 (Clone quality: bE14D10 on chr=7; Num_of_Contigs=8; )
CDH24		location ⇒	7:82383758-82383945		CU468526,CH242-14D10,7:82382718-82403264 (Clone quality: bE14D10 on chr=7; Num_of_Contigs=8; )
CDH24		location ⇒	7:82384254-82384511		CU468526,CH242-14D10,7:82382718-82403264 (Clone quality: bE14D10 on chr=7; Num_of_Contigs=8; )
CDH24		location ⇒	7:82385744-82385875		CU468526,CH242-14D10,7:82382718-82403264 (Clone quality: bE14D10 on chr=7; Num_of_Contigs=8; )
CDH26		ENSSSCG00000003725	6:79638557-79642691		CU914455,CH242-81E19,6:79634463-79647148 (Clone quality: bE81E19 on chr=6; Num_of_Contigs=29; )
CDH26		location ⇒	17:62606681-62606762		CU915385,CH242-197I13,17:62578020-62643589 (Clone quality: bE197I13 on chr=17; Num_of_Contigs=8; )
CDH29		ENSSSCG00000011391	13:27081523-27088230		CU914539,CH242-222N14,13:27078304-27105846 (Clone quality: bE222N14 on chr=13; Num_of_Contigs=2; )
CDH3		ENSSSCG00000002642	6:312204-320834		FP102614,CH242-198I21,6:311914-324297 (Clone quality: bE198I21 on chr=6; Num_of_Contigs=22; )
CDH4		location ⇒	6:77972598-77972715		CU329675,CH242-402B12,6:77970576-77976274 (Clone quality: bE402B12 on chr=6; Num_of_Contigs=21; )
CDH4		location ⇒	6:77973378-77973563		CU329675,CH242-402B12,6:77970576-77976274 (Clone quality: bE402B12 on chr=6; Num_of_Contigs=21; )
CDH4		location ⇒	6:77976375-77976560
CDH6		ENSSSCG00000016806	16:15506044-15560738		FP003585,CH242-122L12,16:15492559-15575994 (Clone quality: bE122L12 on chr=16; Num_of_Contigs=5; )
CDH6		location ⇒	16:15400048-15400160		FP003585,CH242-122L12,16:15393136-15455780 (Clone quality: bE122L12 on chr=16; Num_of_Contigs=5; )
CDH6		location ⇒	16:15534652-15534359		FP003585,CH242-122L12,16:15492559-15575994 (Clone quality: bE122L12 on chr=16; Num_of_Contigs=5; )
CDH6		location ⇒	16:15560869-15560511		FP003585,CH242-122L12,16:15492559-15575994 (Clone quality: bE122L12 on chr=16; Num_of_Contigs=5; )
CDH7		ENSSSCG00000004885	1:162620292-162680496
CDH7		ENSSSCG00000004886	1:163217352-163297550
CDH7		ENSSSCG00000004903	1:166681872-166740372
CDH7		location ⇒	1:163280956-163280833		CU074302,CH242-156A7,1:163241095-163326045 (Clone quality: bE156A7 on chr=1; Num_of_Contigs=3; )
CDH7		location ⇒	1:163284035-163283864		CU074302,CH242-156A7,1:163241095-163326045 (Clone quality: bE156A7 on chr=1; Num_of_Contigs=3; )
CDH7		location ⇒	1:163291748-163291627		CU074302,CH242-156A7,1:163241095-163326045 (Clone quality: bE156A7 on chr=1; Num_of_Contigs=3; )
CDH7		location ⇒	1:163297342-163297252		CU074302,CH242-156A7,1:163241095-163326045 (Clone quality: bE156A7 on chr=1; Num_of_Contigs=3; )
CDH8		location ⇒	6:14557594-14557668		CU463066,CH242-417O8,6:14552574-14592913 (Clone quality: bE417O8 on chr=6; Num_of_Contigs=4; )
CDH8		location ⇒	6:16472285-16472734		CU929637,CH242-38F15,6:16457369-16478121 (Clone quality: bE38F15 on chr=6; Num_of_Contigs=8; )
CDH8		location ⇒	6:16574956-16575254		CU929637,CH242-38F15,6:16540374-16603122 (Clone quality: bE38F15 on chr=6; Num_of_Contigs=8; )
CDH9		location ⇒	16:11118674-11118515		CU915691,CH242-20H6,16:11080312-11189089 (Clone quality: bE20H6 on chr=16; Num_of_Contigs=1; )
CDH9		location ⇒	16:15506177-15506119		FP003585,CH242-122L12,16:15492559-15575994 (Clone quality: bE122L12 on chr=16; Num_of_Contigs=5; )
CDH9		location ⇒	16:15525019-15524907		FP003585,CH242-122L12,16:15492559-15575994 (Clone quality: bE122L12 on chr=16; Num_of_Contigs=5; )
CDH9		location ⇒	16:15528180-15528043		FP003585,CH242-122L12,16:15492559-15575994 (Clone quality: bE122L12 on chr=16; Num_of_Contigs=5; )
CDK2		ENSSSCG00000000373	5:20332627-20338207

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).