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)

CEACAM16		ENSSSCG00000003081	6:35737359-35743410		CU929755,CH242-284D18,6:35720744-35751410 (Clone quality: bE284D18 on chr=6; Num_of_Contigs=4; )
CEACAM16		location ⇒	6:35737779-35737359		CU929755,CH242-284D18,6:35720744-35751410 (Clone quality: bE284D18 on chr=6; Num_of_Contigs=4; )
CEACAM16		location ⇒	6:35740168-35739877		CU929755,CH242-284D18,6:35720744-35751410 (Clone quality: bE284D18 on chr=6; Num_of_Contigs=4; )
CEACAM1634		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CEACAM18		ENSSSCG00000003225	6:39280513-39280701		CU694842,CH242-204P3,6:39279332-39353368 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
CEACAM19		ENSSSCG00000003078	6:35586669-35607279
CEACAM19		location ⇒	6:35586764-35586669		CU929755,CH242-284D18,6:35579071-35587157 (Clone quality: bE284D18 on chr=6; Num_of_Contigs=4; )
CEACAM19		location ⇒	6:35589495-35589346		CU929755,CH242-284D18,6:35587258-35702275 (Clone quality: bE284D18 on chr=6; Num_of_Contigs=4; )
CEACAM21		location ⇒	6:34696962-34697029		FP015926,CH242-183C8,6:34688844-34702901 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
CEACAM3		location ⇒	6:33981425-33981586		FP236582,CH242-238L13,6:33980588-33985267 (Clone quality: bE238L13 on chr=6; Num_of_Contigs=11; )
CEACAM3		location ⇒	6:33982893-33983255		FP236582,CH242-238L13,6:33980588-33985267 (Clone quality: bE238L13 on chr=6; Num_of_Contigs=11; )
CEACAM3		location ⇒	6:34707720-34707559		FP015926,CH242-183C8,6:34703002-34716887 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
CEACAM3		location ⇒	6:34837139-34837500		FP102750,CH242-80G20,6:34836564-34839126 (Clone quality: bE80G20 on chr=6; Num_of_Contigs=9; )
CEACAM5		location ⇒	6:33983116-33983193		FP236582,CH242-238L13,6:33980588-33985267 (Clone quality: bE238L13 on chr=6; Num_of_Contigs=11; )
CEACAM5		location ⇒	6:33987142-33987356		FP236582,CH242-238L13,6:33985368-33993670 (Clone quality: bE238L13 on chr=6; Num_of_Contigs=11; )
CEACAM5		location ⇒	6:33987143-33987397		FP236582,CH242-238L13,6:33985368-33993670 (Clone quality: bE238L13 on chr=6; Num_of_Contigs=11; )
CEACAM5		location ⇒	6:34706392-34706339		FP015926,CH242-183C8,6:34703002-34716887 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
CEACAM6		location ⇒	6:33981409-33981586		FP236582,CH242-238L13,6:33980588-33985267 (Clone quality: bE238L13 on chr=6; Num_of_Contigs=11; )
CEACAM6		location ⇒	6:33982893-33983250		FP236582,CH242-238L13,6:33980588-33985267 (Clone quality: bE238L13 on chr=6; Num_of_Contigs=11; )
CEACAM6		location ⇒	6:34707736-34707559		FP015926,CH242-183C8,6:34703002-34716887 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
CEACAM6		location ⇒	6:34837139-34837495		FP102750,CH242-80G20,6:34836564-34839126 (Clone quality: bE80G20 on chr=6; Num_of_Contigs=9; )
CEACAM7		location ⇒	6:33981412-33981586		FP236582,CH242-238L13,6:33980588-33985267 (Clone quality: bE238L13 on chr=6; Num_of_Contigs=11; )
CEACAM7		location ⇒	6:34707733-34707559		FP015926,CH242-183C8,6:34703002-34716887 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
CEACAM7		location ⇒	6:34837139-34837443		FP102750,CH242-80G20,6:34836564-34839126 (Clone quality: bE80G20 on chr=6; Num_of_Contigs=9; )
CEACAM8		location ⇒	6:33987143-33987397		FP236582,CH242-238L13,6:33985368-33993670 (Clone quality: bE238L13 on chr=6; Num_of_Contigs=11; )
CEACAM8		location ⇒	6:34703488-34703234		FP015926,CH242-183C8,6:34703002-34716887 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
CEACAM8		location ⇒	6:34706191-34706134		FP015926,CH242-183C8,6:34703002-34716887 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
CEACAM8		location ⇒	6:34837343-34837438		FP102750,CH242-80G20,6:34836564-34839126 (Clone quality: bE80G20 on chr=6; Num_of_Contigs=9; )
CEBPA		location ⇒	6:28811480-28811117		CU929902,CH242-260F18,6:28809182-28963405 (Clone quality: bE260F18 on chr=6; Num_of_Contigs=2; )
CEBPB		ENSSSCG00000007468	17:53740319-53741359		CU682662,CH242-263E16,17:53739677-53791812 (Clone quality: bE263E16 on chr=17; Num_of_Contigs=5; )
CEBPB		location ⇒	17:53740250-53740434		CU682662,CH242-263E16,17:53739677-53791812 (Clone quality: bE263E16 on chr=17; Num_of_Contigs=5; )
CEBPB		location ⇒	17:53740643-53740800		CU682662,CH242-263E16,17:53739677-53791812 (Clone quality: bE263E16 on chr=17; Num_of_Contigs=5; )
CEBPB		location ⇒	17:53740928-53741390		CU682662,CH242-263E16,17:53739677-53791812 (Clone quality: bE263E16 on chr=17; Num_of_Contigs=5; )
CEBPB		location ⇒	17:53741556-53741826		CU682662,CH242-263E16,17:53739677-53791812 (Clone quality: bE263E16 on chr=17; Num_of_Contigs=5; )
CEBPD		ENSSSCG00000006276	4:82893775-82894545		CU468820,CH242-166J20,4:82887998-82899500 (Clone quality: bE166J20 on chr=4; Num_of_Contigs=10; )
CEBPD		location ⇒	4:82893745-82894022		CU468820,CH242-166J20,4:82887998-82899500 (Clone quality: bE166J20 on chr=4; Num_of_Contigs=10; )
CEBPD		location ⇒	4:82894089-82894188		CU468820,CH242-166J20,4:82887998-82899500 (Clone quality: bE166J20 on chr=4; Num_of_Contigs=10; )
CEBPD		location ⇒	4:82894271-82894517		CU468820,CH242-166J20,4:82887998-82899500 (Clone quality: bE166J20 on chr=4; Num_of_Contigs=10; )
CEBPD		location ⇒	4:82894570-82895276		CU468820,CH242-166J20,4:82887998-82899500 (Clone quality: bE166J20 on chr=4; Num_of_Contigs=10; )
CEBPE		ENSSSCG00000002033	7:82306050-82307480		CU468526,CH242-14D10,7:82261915-82310389 (Clone quality: bE14D10 on chr=7; Num_of_Contigs=8; )
CEBPG		ENSSSCG00000002867	6:28896258-28896713		CU929902,CH242-260F18,6:28809182-28963405 (Clone quality: bE260F18 on chr=6; Num_of_Contigs=2; )
CEBPG		location ⇒	6:28889722-28889913		CU929902,CH242-260F18,6:28809182-28963405 (Clone quality: bE260F18 on chr=6; Num_of_Contigs=2; )
CEBPG		location ⇒	6:28896155-28897457		CU929902,CH242-260F18,6:28809182-28963405 (Clone quality: bE260F18 on chr=6; Num_of_Contigs=2; )
CEBPG		location ⇒	6:28896327-28896905		CU929902,CH242-260F18,6:28809182-28963405 (Clone quality: bE260F18 on chr=6; Num_of_Contigs=2; )
CEBPG		location ⇒	6:28897487-28897540		CU929902,CH242-260F18,6:28809182-28963405 (Clone quality: bE260F18 on chr=6; Num_of_Contigs=2; )
CEBPZ		ENSSSCG00000008493	3:96014184-96038392		CU695023,CH242-129E17,3:96011217-96129629 (Clone quality: bE129E17 on chr=3; Num_of_Contigs=2; )
CECR2		ENSSSCG00000000766	5:65417079-65432963		CU467800,CH242-7B3,5:65416584-65439865 (Clone quality: bE7B3 on chr=5; Num_of_Contigs=13; )
CECR5		ENSSSCG00000000764	5:65172375-65180689
CEECAM1		ENSSSCG00000005650	1:283510871-283514231
CEECAM1		location ⇒	1:283513796-283513937		CU467095,CH242-140K13,1:283511446-283514529 (Clone quality: bE140K13 on chr=1; Num_of_Contigs=19; )

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).