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)

CAPS		ENSSSCG00000013532	2:49553049-49554774		FP089464,CH242-231P22,2:49500853-49563374 (Clone quality: bE231P22 on chr=2; Num_of_Contigs=4; )
CAPS2		ENSSSCG00000000517	5:38550708-38587631
CAPSL		ENSSSCG00000016833	16:18681789-18777615
CAPZA1		ENSSSCG00000006775	4:112156529-112274258
CAPZA3		ENSSSCG00000000589	5:51989283-51990179		CU457757,CH242-219O8,5:51933888-52027325 (Clone quality: bE219O8 on chr=5; Num_of_Contigs=1; )
CAPZB		ENSSSCG00000003493	6:53283378-53317892
CAR		ENSSSCG00000012012	13:131074034-131090971		CU606918,CH242-163L22,13:131072906-131111271 (Clone quality: bE163L22 on chr=13; Num_of_Contigs=12; )
CAR		location ⇒	4:92735018-92735201		CU606874,CH242-28G15,4:92698180-92745360 (Clone quality: bE28G15 on chr=4; Num_of_Contigs=6; )
CAR		location ⇒	4:92735353-92735496		CU606874,CH242-28G15,4:92698180-92745360 (Clone quality: bE28G15 on chr=4; Num_of_Contigs=6; )
CAR		location ⇒	4:92737537-92737706		CU606874,CH242-28G15,4:92698180-92745360 (Clone quality: bE28G15 on chr=4; Num_of_Contigs=6; )
CAR		location ⇒	4:92739804-92740063		CU606874,CH242-28G15,4:92698180-92745360 (Clone quality: bE28G15 on chr=4; Num_of_Contigs=6; )
CARD12		location ⇒	3:101142314-101141890		CU469148,CH242-287E22,3:101138210-101144928 (Clone quality: bE287E22 on chr=3; Num_of_Contigs=23; )
CARD14		location ⇒	12:1266095-1265969		CU655945,CH242-412P7,12:1253941-1266123 (Clone quality: bE412P7 on chr=12; Num_of_Contigs=12; )
CARD14		location ⇒	12:1267092-1266953		CU655945,CH242-412P7,12:1266224-1276795 (Clone quality: bE412P7 on chr=12; Num_of_Contigs=12; )
CARD14		location ⇒	12:1268430-1268201		CU655945,CH242-412P7,12:1266224-1276795 (Clone quality: bE412P7 on chr=12; Num_of_Contigs=12; )
CARD14		location ⇒	12:1270313-1270260		CU655945,CH242-412P7,12:1266224-1276795 (Clone quality: bE412P7 on chr=12; Num_of_Contigs=12; )
CARD15		location ⇒	8:101541211-101541148		CU972368,CH242-513E6,8:101530614-101541848 (Clone quality: bE513E6 on chr=8; Num_of_Contigs=4; )
CARD15		location ⇒	8:101545868-101545805		CU861532,CH242-199D5,8:101545099-101608799 (Clone quality: bE199D5 on chr=8; Num_of_Contigs=7; )
CARD15		location ⇒	8:101707651-101707609		CU861532,CH242-199D5,8:101690658-101715353 (Clone quality: bE199D5 on chr=8; Num_of_Contigs=7; )
CARD15		location ⇒	8:101711355-101711280		CU861532,CH242-199D5,8:101690658-101715353 (Clone quality: bE199D5 on chr=8; Num_of_Contigs=7; )
CARD16		location ⇒	9:34958339-34958126		CU855956,CH242-116E23,9:34933346-35042600 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CARD17		location ⇒	9:34958339-34958126		CU855956,CH242-116E23,9:34933346-35042600 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CARD4		location ⇒	18:40823129-40823572		CU655860,CH242-247K17,18:40794666-40836370 (Clone quality: bE247K17 on chr=18; Num_of_Contigs=10; )
CARD4		location ⇒	18:40826871-40826957		CU655860,CH242-247K17,18:40794666-40836370 (Clone quality: bE247K17 on chr=18; Num_of_Contigs=10; )
CARD4		location ⇒	18:40828716-40828800		CU655860,CH242-247K17,18:40794666-40836370 (Clone quality: bE247K17 on chr=18; Num_of_Contigs=10; )
CARD4		location ⇒	18:40830191-40830274		CU655860,CH242-247K17,18:40794666-40836370 (Clone quality: bE247K17 on chr=18; Num_of_Contigs=10; )
CARHSP1		ENSSSCG00000007911	3:29954006-29965396		FP089531,CH242-200J6,3:29932646-29993310 (Clone quality: bE200J6 on chr=3; Num_of_Contigs=7; )
CARHSP1		location ⇒	3:29961962-29962032		FP089531,CH242-200J6,3:29932646-29993310 (Clone quality: bE200J6 on chr=3; Num_of_Contigs=7; )
CARHSP1		location ⇒	3:29962956-29963078		FP089531,CH242-200J6,3:29932646-29993310 (Clone quality: bE200J6 on chr=3; Num_of_Contigs=7; )
CARHSP1		location ⇒	3:29964984-29965150		FP089531,CH242-200J6,3:29932646-29993310 (Clone quality: bE200J6 on chr=3; Num_of_Contigs=7; )
CARM1		ENSSSCG00000013633	2:52753919-52769313
CARM1L		ENSSSCG00000005226	1:228996562-229102294
CARS		ENSSSCG00000012857	2:449200-523057
CARS2		ENSSSCG00000009547	11:77492603-77728401
CARTPT		ENSSSCG00000016972	16:45371138-45373217		CU915349,CH242-35O2,16:45343637-45377305 (Clone quality: bE35O2 on chr=16; Num_of_Contigs=7; )
CASA2_PIG		ENSSSCG00000009263	8:119824493-119832180		CU929598,CH242-240J23,8:119824277-119843978 (Clone quality: bE240J23 on chr=8; Num_of_Contigs=8; )
CASC1		ENSSSCG00000000562	5:47089015-47089290		CU639400,CH242-190I20,5:47088535-47092126 (Clone quality: bE190I20 on chr=5; Num_of_Contigs=21; )
CASC3		ENSSSCG00000017477	12:19950609-19970663
CASC4		ENSSSCG00000004693	1:133305454-133347944		CU855673,CH242-6A19,1:133304686-133359858 (Clone quality: bE6A19 on chr=1; Num_of_Contigs=6; )
CASC5		ENSSSCG00000004769	1:137207018-137209484		CU469090,CH242-416D6,1:137205926-137211863 (Clone quality: bE416D6 on chr=1; Num_of_Contigs=22; )
CASD1		ENSSSCG00000015327	9:69522303-69611149
CASK		ENSSSCG00000012253	X:36799905-37083358
CASK		ENSSSCG00000009267	8:119975507-119979593
CASK		location ⇒	X:36800155-36800465		CU856415,CH242-203M4,X:36790012-36812631 (Clone quality: bE203M4 on chr=X; Num_of_Contigs=7; )
CASK		location ⇒	X:36804395-36804481		CU856415,CH242-203M4,X:36790012-36812631 (Clone quality: bE203M4 on chr=X; Num_of_Contigs=7; )
CASK		location ⇒	X:36811797-36812000		CU856415,CH242-203M4,X:36790012-36812631 (Clone quality: bE203M4 on chr=X; Num_of_Contigs=7; )
CASK		location ⇒	X:36813882-36813966		CU856415,CH242-203M4,X:36812732-36890208 (Clone quality: bE203M4 on chr=X; Num_of_Contigs=7; )
CASP1		location ⇒	9:34950356-34950206		CU855956,CH242-116E23,9:34933346-35042600 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP1		location ⇒	9:34951008-34950773		CU855956,CH242-116E23,9:34933346-35042600 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP1		location ⇒	9:34951588-34951412		CU855956,CH242-116E23,9:34933346-35042600 (Clone quality: bE116E23 on chr=9; 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).