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)

PRKDC		location ⇒	4:82722068-82722284		CU138488,CH242-2G19,4:82717363-82726035 (Clone quality: bE2G19 on chr=4; Num_of_Contigs=17; )
PRKDC		location ⇒	4:82752364-82752533		CU462857,CH242-78H20,4:82737504-82805324 (Clone quality: bE78H20 on chr=4; Num_of_Contigs=2; )
PRKDC		location ⇒	4:82760835-82761051		CU462857,CH242-78H20,4:82737504-82805324 (Clone quality: bE78H20 on chr=4; Num_of_Contigs=2; )
PRKG1		ENSSSCG00000010429	14:102000139-102453405
PRKG1		location ⇒	14:102000683-102000342		CU467975,CH242-266C2,14:101996830-102020960 (Clone quality: bE266C2 on chr=14; Num_of_Contigs=9; )
PRKG1		location ⇒	14:102013540-102013376		CU467975,CH242-266C2,14:101996830-102020960 (Clone quality: bE266C2 on chr=14; Num_of_Contigs=9; )
PRKG1		location ⇒	14:103242306-103242138		CU467801,CH242-82D21,14:103231374-103267011 (Clone quality: bE82D21 on chr=14; Num_of_Contigs=6; )
PRKG1		location ⇒	14:103405412-103404937		CU406970,CH242-173J8,14:103332816-103461731 (Clone quality: bE173J8 on chr=14; Num_of_Contigs=2; )
PRKG2		ENSSSCG00000009250	8:117779537-117847511
PRKR		ENSSSCG00000008208	3:52496620-52579270		CU464187,CH242-105C21,3:52460473-52637141 (Clone quality: bE105C21 on chr=3; Num_of_Contigs=1; )
PRKR		ENSSSCG00000007684	3:8137632-8166975
PRKRA		ENSSSCG00000015997	15:79088977-79111297		CU550661,CH242-197B9,15:79013886-79117387 (Clone quality: bE197B9 on chr=15; Num_of_Contigs=4; )
PRKRA		location ⇒	15:79089687-79089017		CU550661,CH242-197B9,15:79013886-79117387 (Clone quality: bE197B9 on chr=15; Num_of_Contigs=4; )
PRKRA		location ⇒	15:79093573-79093398		CU550661,CH242-197B9,15:79013886-79117387 (Clone quality: bE197B9 on chr=15; Num_of_Contigs=4; )
PRKRA		location ⇒	15:79110493-79110319		CU550661,CH242-197B9,15:79013886-79117387 (Clone quality: bE197B9 on chr=15; Num_of_Contigs=4; )
PRKRA		location ⇒	15:79111223-79111053		CU550661,CH242-197B9,15:79013886-79117387 (Clone quality: bE197B9 on chr=15; Num_of_Contigs=4; )
PRKRIP1		ENSSSCG00000007684	3:8137632-8166975
PRKRIR		ENSSSCG00000014865	9:10333702-10345088
PRKRIR		location ⇒	9:10335635-10335272		CU942407,CH242-510G2,9:10317474-10343606 (Clone quality: bE510G2 on chr=9; Num_of_Contigs=5; )
PRKRIR		location ⇒	9:10341342-10341235		CU942407,CH242-510G2,9:10317474-10343606 (Clone quality: bE510G2 on chr=9; Num_of_Contigs=5; )
PRKRIR		location ⇒	9:10345088-10344966		CU928935,CH242-34M6,9:10343607-10350262 (Clone quality: bE34M6 on chr=9; Num_of_Contigs=2; )
PRKRIR		location ⇒	9:10448301-10448390		CU928935,CH242-34M6,9:10448082-10455824 (Clone quality: bE34M6 on chr=9; Num_of_Contigs=2; )
PRL		ENSSSCG00000001082	7:18161987-18174367		CU468850,CH242-218K5,7:18049595-18220592 (Clone quality: bE218K5 on chr=7; Num_of_Contigs=3; )
PRL		ENSSSCG00000003605	6:60649606-60660132
PRL		ENSSSCG00000006331	4:89472001-89943215
PRL		ENSSSCG00000016830	16:18175457-18194122		CU972465,CH242-211D21,16:18142569-18195698 (Clone quality: bE211D21 on chr=16; Num_of_Contigs=4; )
PRL		location ⇒	7:18162347-18162011		CU468850,CH242-218K5,7:18049595-18220592 (Clone quality: bE218K5 on chr=7; Num_of_Contigs=3; )
PRL		location ⇒	7:18164955-18164774		CU468850,CH242-218K5,7:18049595-18220592 (Clone quality: bE218K5 on chr=7; Num_of_Contigs=3; )
PRL		location ⇒	7:18169108-18169001		CU468850,CH242-218K5,7:18049595-18220592 (Clone quality: bE218K5 on chr=7; Num_of_Contigs=3; )
PRL		location ⇒	7:18171902-18171718		CU468850,CH242-218K5,7:18049595-18220592 (Clone quality: bE218K5 on chr=7; Num_of_Contigs=3; )
PRLR		ENSSSCG00000016830	16:18175457-18194122		CU972465,CH242-211D21,16:18142569-18195698 (Clone quality: bE211D21 on chr=16; Num_of_Contigs=4; )
PRLR		location ⇒	16:18176492-18175468		CU972465,CH242-211D21,16:18142569-18195698 (Clone quality: bE211D21 on chr=16; Num_of_Contigs=4; )
PRLR		location ⇒	16:18180398-18180255		CU972465,CH242-211D21,16:18142569-18195698 (Clone quality: bE211D21 on chr=16; Num_of_Contigs=4; )
PRLR		location ⇒	16:18182725-18182554		CU972465,CH242-211D21,16:18142569-18195698 (Clone quality: bE211D21 on chr=16; Num_of_Contigs=4; )
PRLR		location ⇒	16:18188427-18188257		CU972465,CH242-211D21,16:18142569-18195698 (Clone quality: bE211D21 on chr=16; Num_of_Contigs=4; )
PRMT1		ENSSSCG00000003189	6:38393510-38405026
PRMT10		ENSSSCG00000009030	8:69933491-69956834
PRMT3		ENSSSCG00000013347	2:36357808-36448731
PRMT7		ENSSSCG00000002763	6:12564926-12575409		CU462933,CH242-310F10,6:12564924-12617393 (Clone quality: bE310F10 on chr=6; Num_of_Contigs=6; )
PRNP		ENSSSCG00000007039	17:13140304-13151006		CU694293,CH242-140G16,17:13136598-13170134 (Clone quality: bE140G16 on chr=17; Num_of_Contigs=2; )
PRNP		location ⇒	17:13142776-13142068		CU694293,CH242-140G16,17:13136598-13170134 (Clone quality: bE140G16 on chr=17; Num_of_Contigs=2; )
PROCA1		ENSSSCG00000017770	12:42645629-42652247		FP016171,CH242-62B5,12:42618725-42654541 (Clone quality: bE62B5 on chr=12; Num_of_Contigs=5; )
PRODH		ENSSSCG00000002913	6:30404514-30418632		CU466979,CH242-510C11,6:30402782-30424187 (Clone quality: bE510C11 on chr=6; Num_of_Contigs=10; )
PRODH2		ENSSSCG00000002913	6:30404514-30418632		CU466979,CH242-510C11,6:30402782-30424187 (Clone quality: bE510C11 on chr=6; Num_of_Contigs=10; )
PRODH2		ENSSSCG00000002914	6:30424289-30430215		CU466979,CH242-510C11,6:30424288-30445425 (Clone quality: bE510C11 on chr=6; Num_of_Contigs=10; )
PROK1		ENSSSCG00000006805	4:114089166-114100689		CU915404,CH242-292M23,4:114077822-114102028 (Clone quality: bE292M23 on chr=4; Num_of_Contigs=12; )
PROK2		location ⇒	13:45142856-45142752		CU466314,CH242-85B5,13:45125720-45156590 (Clone quality: bE85B5 on chr=13; Num_of_Contigs=9; )
PROM1		ENSSSCG00000008745	8:8476692-8571249
PROM1		location ⇒	8:8270226-8270133		FP016042,CH242-20B12,8:8260029-8300650 (Clone quality: bE20B12 on chr=8; Num_of_Contigs=7; )
PROM1		location ⇒	8:8274331-8273907		FP016042,CH242-20B12,8:8260029-8300650 (Clone quality: bE20B12 on chr=8; Num_of_Contigs=7; )

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).