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)

CWF19L2		ENSSSCG00000015264	9:60317624-60320710		CU929969,CH242-7J8,9:60311833-60333001 (Clone quality: bE7J8 on chr=9; Num_of_Contigs=6; )
CWH43		ENSSSCG00000008830	8:33355438-33509155
CXA1_PIG		ENSSSCG00000004241	1:42737675-42738823		CU914424,CH242-34L11,1:42730624-42754451 (Clone quality: bE34L11 on chr=1; Num_of_Contigs=2; )
CXADR		ENSSSCG00000012012	13:131074034-131090971		CU606918,CH242-163L22,13:131072906-131111271 (Clone quality: bE163L22 on chr=13; Num_of_Contigs=12; )
CXADR		ENSSSCG00000015089	9:44392087-44420224
CXADR		location ⇒	13:131074083-131074243		CU606918,CH242-163L22,13:131072906-131111271 (Clone quality: bE163L22 on chr=13; Num_of_Contigs=12; )
CXADR		location ⇒	13:131079880-131080084		CU606918,CH242-163L22,13:131072906-131111271 (Clone quality: bE163L22 on chr=13; Num_of_Contigs=12; )
CXADR		location ⇒	13:131086919-131087075		CU606918,CH242-163L22,13:131072906-131111271 (Clone quality: bE163L22 on chr=13; Num_of_Contigs=12; )
CXADR		location ⇒	13:131090522-131090826		CU606918,CH242-163L22,13:131072906-131111271 (Clone quality: bE163L22 on chr=13; Num_of_Contigs=12; )
CXCL10		ENSSSCG00000008977	8:61077900-61080208		CU862040,CH242-216J5,8:61077509-61088713 (Clone quality: bE216J5 on chr=8; Num_of_Contigs=10; )
CXCL10		location ⇒	8:61078698-61077900		CU862040,CH242-216J5,8:61077509-61088713 (Clone quality: bE216J5 on chr=8; Num_of_Contigs=10; )
CXCL10		location ⇒	8:61079227-61079136		CU862040,CH242-216J5,8:61077509-61088713 (Clone quality: bE216J5 on chr=8; Num_of_Contigs=10; )
CXCL10		location ⇒	8:61079570-61079442		CU862040,CH242-216J5,8:61077509-61088713 (Clone quality: bE216J5 on chr=8; Num_of_Contigs=10; )
CXCL10		location ⇒	8:61080208-61080087		CU862040,CH242-216J5,8:61077509-61088713 (Clone quality: bE216J5 on chr=8; Num_of_Contigs=10; )
CXCL11		ENSSSCG00000008978	8:61134507-61135728		CU862040,CH242-216J5,8:61126872-61178932 (Clone quality: bE216J5 on chr=8; Num_of_Contigs=10; )
CXCL11		location ⇒	8:61203404-61208568		FP016186,CH242-145A12,8:61197894-61235315 (Clone quality: bE145A12 on chr=8; Num_of_Contigs=1; )
CXCL11		location ⇒	8:7299-7376		FP102972,CH242-47L5,8:6630-11538 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CXCL11		location ⇒	8:7304-7417		FP102972,CH242-47L5,8:6630-11538 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CXCL11		location ⇒	8:7304-7417		FP102972,CH242-47L5,8:6630-11538 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CXCL12		ENSSSCG00000010414	14:95912350-95927577
CXCL12		location ⇒	14:95912378-95912488		CU468943,CH242-199G18,14:95888264-95927178 (Clone quality: bE199G18 on chr=14; Num_of_Contigs=2; )
CXCL12		location ⇒	14:95916710-95916829		CU468943,CH242-199G18,14:95888264-95927178 (Clone quality: bE199G18 on chr=14; Num_of_Contigs=2; )
CXCL12		location ⇒	14:95918987-95919073		CU468943,CH242-199G18,14:95888264-95927178 (Clone quality: bE199G18 on chr=14; Num_of_Contigs=2; )
CXCL12		location ⇒	14:95927304-95927433		CU407064,CH242-295I18,14:95927179-96099489 (Clone quality: bE295I18 on chr=14; Num_of_Contigs=2; )
CXCL13		location ⇒	8:62539992-62539472		CU928317,CH242-28E18,8:62438438-62577755 (Clone quality: bE28E18 on chr=8; Num_of_Contigs=2; )
CXCL14		ENSSSCG00000014310	2:125189121-125198252		CU914284,CH242-458M20,2:125164155-125314737 (Clone quality: bE458M20 on chr=2; Num_of_Contigs=2; )
CXCL14		location ⇒	2:125190320-125190035		CU914284,CH242-458M20,2:125164155-125314737 (Clone quality: bE458M20 on chr=2; Num_of_Contigs=2; )
CXCL14		location ⇒	2:125193465-125193351		CU914284,CH242-458M20,2:125164155-125314737 (Clone quality: bE458M20 on chr=2; Num_of_Contigs=2; )
CXCL14		location ⇒	2:125197775-125197669		CU914284,CH242-458M20,2:125164155-125314737 (Clone quality: bE458M20 on chr=2; Num_of_Contigs=2; )
CXCL14		location ⇒	2:125198169-125197950		CU914284,CH242-458M20,2:125164155-125314737 (Clone quality: bE458M20 on chr=2; Num_of_Contigs=2; )
CXCL16		ENSSSCG00000017920	12:49355045-49359301		CU929524,CH242-164N17,12:49336210-49359359 (Clone quality: bE164N17 on chr=12; Num_of_Contigs=22; )
CXCL17		ENSSSCG00000003048	6:34715572-34728644
CXCL2		ENSSSCG00000008959	8:59528574-59530500		CU928337,CH242-266F15,8:59527661-59536650 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CXCL2		location ⇒	8:59529766-59529917		CU928337,CH242-266F15,8:59527661-59536650 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CXCL2		location ⇒	8:59529766-59529917		CU928337,CH242-266F15,8:59527661-59536650 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CXCL2		location ⇒	8:59529953-59530495		CU928337,CH242-266F15,8:59527661-59536650 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CXCL2		location ⇒	8:59529953-59530495		CU928337,CH242-266F15,8:59527661-59536650 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CXCL2L1		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CXCL2L2		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CXCL3		location ⇒	8:59451609-59451150		CU928337,CH242-266F15,8:59444305-59461464 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CXCL3		location ⇒	8:59452758-59452629		CU928337,CH242-266F15,8:59444305-59461464 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CXCL3		location ⇒	8:59517589-59517716		CU928337,CH242-266F15,8:59511672-59527560 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CXCL3		location ⇒	8:59528838-59528965		CU928337,CH242-266F15,8:59527661-59536650 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CXCL5		location ⇒	8:59499277-59498164		CU928337,CH242-266F15,8:59474833-59511571 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CXCL5		location ⇒	8:59499277-59498164		CU928337,CH242-266F15,8:59474833-59511571 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CXCL5		location ⇒	8:59500300-59500152		CU928337,CH242-266F15,8:59474833-59511571 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CXCL5		location ⇒	8:59500300-59500152		CU928337,CH242-266F15,8:59474833-59511571 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CXCL7_PIG		ENSSSCG00000000244	5:16300076-16302078		CU930049,CH242-185F9,5:16292056-16303046 (Clone quality: bE185F9 on chr=5; Num_of_Contigs=28; )
CXCL7_PIG		ENSSSCG00000008956	8:59485048-59487050		CU928337,CH242-266F15,8:59474833-59511571 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CXCL9		ENSSSCG00000008975	8:61049137-61054194		CU672252,CH242-392J2,8:61030020-61058295 (Clone quality: bE392J2 on chr=8; Num_of_Contigs=2; )

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).