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)

PRKAG3		ENSSSCG00000016200	15:113847350-113850814		CU914509,CH242-30J4,15:113846889-113851528 (Clone quality: bE30J4 on chr=15; Num_of_Contigs=25; )
PRKAG3		location ⇒	15:113847513-113847356		CU914509,CH242-30J4,15:113846889-113851528 (Clone quality: bE30J4 on chr=15; Num_of_Contigs=25; )
PRKAG3		location ⇒	15:113848033-113847981		CU914509,CH242-30J4,15:113846889-113851528 (Clone quality: bE30J4 on chr=15; Num_of_Contigs=25; )
PRKAG3		location ⇒	15:113849003-113848919		CU914509,CH242-30J4,15:113846889-113851528 (Clone quality: bE30J4 on chr=15; Num_of_Contigs=25; )
PRKAG3		location ⇒	15:113949453-113949537		CU927909,CH242-46J5,15:113947966-113950168 (Clone quality: bE46J5 on chr=15; Num_of_Contigs=21; )
PRKAR1A		ENSSSCG00000017259	12:9945110-9961471		FP085458,CH242-238J2,12:9943590-10107358 (Clone quality: bE238J2 on chr=12; Num_of_Contigs=2; )
PRKAR1A		location ⇒	12:9945499-9945118		FP085458,CH242-238J2,12:9943590-10107358 (Clone quality: bE238J2 on chr=12; Num_of_Contigs=2; )
PRKAR1A		location ⇒	12:9950134-9949975		FP085458,CH242-238J2,12:9943590-10107358 (Clone quality: bE238J2 on chr=12; Num_of_Contigs=2; )
PRKAR1A		location ⇒	12:9953213-9953039		FP085458,CH242-238J2,12:9943590-10107358 (Clone quality: bE238J2 on chr=12; Num_of_Contigs=2; )
PRKAR1A		location ⇒	12:9958432-9958250		FP085458,CH242-238J2,12:9943590-10107358 (Clone quality: bE238J2 on chr=12; Num_of_Contigs=2; )
PRKAR1B		ENSSSCG00000007542	3:42726-114645
PRKAR2A		ENSSSCG00000011363	13:26302044-26391518
PRKAR2A		location ⇒	13:26322469-26322371		CU861514,CH242-101J13,13:26316055-26348726 (Clone quality: bE101J13 on chr=13; Num_of_Contigs=18; )
PRKAR2A		location ⇒	13:26324960-26324850		CU861514,CH242-101J13,13:26316055-26348726 (Clone quality: bE101J13 on chr=13; Num_of_Contigs=18; )
PRKAR2A		location ⇒	13:26332038-26331953		CU861514,CH242-101J13,13:26316055-26348726 (Clone quality: bE101J13 on chr=13; Num_of_Contigs=18; )
PRKAR2A		location ⇒	13:26391346-26391259		CU861514,CH242-101J13,13:26381308-26393392 (Clone quality: bE101J13 on chr=13; Num_of_Contigs=18; )
PRKAR2B		ENSSSCG00000015439	9:100055953-100144799
PRKCA		ENSSSCG00000017268	12:10932486-11257524
PRKCA		ENSSSCG00000000114	5:6364735-6381115		CU633351,CH242-161B9,5:6340838-6445691 (Clone quality: bE161B9 on chr=5; Num_of_Contigs=5; )
PRKCA		location ⇒	12:10932522-10932629		CU694862,CH242-25B15,12:10930548-10936744 (Clone quality: bE25B15 on chr=12; Num_of_Contigs=19; )
PRKCA		location ⇒	12:11074354-11074482		FP102528,CH242-97H10,12:11070590-11077511 (Clone quality: bE97H10 on chr=12; Num_of_Contigs=6; )
PRKCA		location ⇒	12:11197732-11197872		FP085463,CH242-193D1,12:11167230-11262396 (Clone quality: bE193D1 on chr=12; Num_of_Contigs=1; )
PRKCA		location ⇒	12:11198884-11199021		FP085463,CH242-193D1,12:11167230-11262396 (Clone quality: bE193D1 on chr=12; Num_of_Contigs=1; )
PRKCB1		ENSSSCG00000007833	3:20692573-20845692
PRKCB1		location ⇒	3:20722578-20722728		CU855526,CH242-35O6,3:20705349-20739490 (Clone quality: bE35O6 on chr=3; Num_of_Contigs=7; )
PRKCB1		location ⇒	3:20732541-20732638		CU855526,CH242-35O6,3:20705349-20739490 (Clone quality: bE35O6 on chr=3; Num_of_Contigs=7; )
PRKCB1		location ⇒	3:20745289-20745425		CU855526,CH242-35O6,3:20743590-20747687 (Clone quality: bE35O6 on chr=3; Num_of_Contigs=7; )
PRKCB1		location ⇒	3:20747058-20747215		CU855526,CH242-35O6,3:20743590-20747687 (Clone quality: bE35O6 on chr=3; Num_of_Contigs=7; )
PRKCE		ENSSSCG00000008444	3:87746073-87930939
PRKCG		ENSSSCG00000003256	6:40329395-40336735		CU855513,CH242-259K4,6:40326025-40337394 (Clone quality: bE259K4 on chr=6; Num_of_Contigs=12; )
PRKCH		ENSSSCG00000005095	1:199376829-199488557		CU041313,CH242-403I11,1:199362926-199514559 (Clone quality: bE403I11 on chr=1; Num_of_Contigs=3; )
PRKCI		ENSSSCG00000011745	13:82936951-83006835
PRKCQ		ENSSSCG00000011131	10:60823281-60856473
PRKCQ		location ⇒	10:60823313-60823398		CU896695,CH242-128B13,10:60768733-60846417 (Clone quality: bE128B13 on chr=10; Num_of_Contigs=6; )
PRKCQ		location ⇒	10:60826956-60827157		CU896695,CH242-128B13,10:60768733-60846417 (Clone quality: bE128B13 on chr=10; Num_of_Contigs=6; )
PRKCQ		location ⇒	10:60839671-60839835		CU896695,CH242-128B13,10:60768733-60846417 (Clone quality: bE128B13 on chr=10; Num_of_Contigs=6; )
PRKCQ		location ⇒	10:60841117-60841202		CU896695,CH242-128B13,10:60768733-60846417 (Clone quality: bE128B13 on chr=10; Num_of_Contigs=6; )
PRKCSH		ENSSSCG00000013627	2:52398105-52414891		CU855518,CH242-272A5,2:52374247-52417356 (Clone quality: bE272A5 on chr=2; Num_of_Contigs=10; )
PRKD1		ENSSSCG00000001975	7:75842547-75881221
PRKD1		location ⇒	7:75574775-75574910
PRKD1		location ⇒	7:75781251-75781391		CT841524,CH242-276F10,7:75672419-75870162 (Clone quality: bE276F10 on chr=7; Num_of_Contigs=1; )
PRKD1		location ⇒	7:75869106-75869317		CT841524,CH242-276F10,7:75672419-75870162 (Clone quality: bE276F10 on chr=7; Num_of_Contigs=1; )
PRKD1		location ⇒	7:75881000-75881665	CT737415,CH242-158E1,7:75875163-76052284 (Clone quality: bE158E1 on chr=7; Num_of_Contigs=2; )
PRKD3		ENSSSCG00000008495	3:96061360-96101979		CU695023,CH242-129E17,3:96011217-96129629 (Clone quality: bE129E17 on chr=3; Num_of_Contigs=2; )
PRKD3		location ⇒	3:96068472-96068316		CU695023,CH242-129E17,3:96011217-96129629 (Clone quality: bE129E17 on chr=3; Num_of_Contigs=2; )
PRKD3		location ⇒	3:96074422-96074314		CU695023,CH242-129E17,3:96011217-96129629 (Clone quality: bE129E17 on chr=3; Num_of_Contigs=2; )
PRKD3		location ⇒	3:96081559-96081281		CU695023,CH242-129E17,3:96011217-96129629 (Clone quality: bE129E17 on chr=3; Num_of_Contigs=2; )
PRKD3		location ⇒	3:96082817-96082738		CU695023,CH242-129E17,3:96011217-96129629 (Clone quality: bE129E17 on chr=3; Num_of_Contigs=2; )
PRKDC		ENSSSCG00000006274	4:82652523-82866477
PRKDC		location ⇒	4:82694302-82694471		CU138488,CH242-2G19,4:82694105-82697782 (Clone quality: bE2G19 on chr=4; Num_of_Contigs=17; )

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, 2201-21

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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).