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)

CADM1		location ⇒	9:41560018-41559956		CU571118,CH242-229F5,9:41547760-41603997 (Clone quality: bE229F5 on chr=9; Num_of_Contigs=4; )
CADM2		ENSSSCG00000011999	13:123897257-123966866
CADM4		ENSSSCG00000003061	6:34964060-34967939
CADPS2		ENSSSCG00000016611	18:22526007-23020267
CAGE1		ENSSSCG00000001023	7:4661135-4780426
CALB1		ENSSSCG00000006125	4:47870808-47893791
CALB2		ENSSSCG00000002730	6:10120471-10149583
CALCA		ENSSSCG00000013386	2:41163705-41168787		CU928260,CH242-273B21,2:41162604-41257476 (Clone quality: bE273B21 on chr=2; Num_of_Contigs=3; )
CALCA		location ⇒	2:41167838-41168026		CU928260,CH242-273B21,2:41162604-41257476 (Clone quality: bE273B21 on chr=2; Num_of_Contigs=3; )
CALCA		location ⇒	2:41288517-41288599		CU928260,CH242-273B21,2:41257577-41300655 (Clone quality: bE273B21 on chr=2; Num_of_Contigs=3; )
CALCA		location ⇒	2:41370725-41370807		CU606994,CH242-513N24,2:41325835-41371753 (Clone quality: bE513N24 on chr=2; Num_of_Contigs=5; )
CALCA		location ⇒	2:41384463-41384532		CU606994,CH242-513N24,2:41371854-41392335 (Clone quality: bE513N24 on chr=2; Num_of_Contigs=5; )
CALCB		ENSSSCG00000013390	2:41526806-41528502		CU606994,CH242-513N24,2:41487352-41529702 (Clone quality: bE513N24 on chr=2; Num_of_Contigs=5; )
CALCOCO2		ENSSSCG00000017543	12:22603567-22633877
CALCR		ENSSSCG00000015320	9:68503267-68547328		CU915449,CH242-148H14,9:68496256-68547592 (Clone quality: bE148H14 on chr=9; Num_of_Contigs=6; )
CALCRL		ENSSSCG00000016031	15:86516621-86637624
CALD1		ENSSSCG00000016535	18:12519922-12636635
CALHM1		ENSSSCG00000010601	14:119502466-119506650		CT956026,CH242-70J4,14:119384903-119545395 (Clone quality: bE70J4 on chr=14; Num_of_Contigs=4; )
CALHM2		ENSSSCG00000010600	14:119495614-119497820		CT956026,CH242-70J4,14:119384903-119545395 (Clone quality: bE70J4 on chr=14; Num_of_Contigs=4; )
CALHM3		ENSSSCG00000010602	14:119521178-119714661
CALM1		ENSSSCG00000002435	7:120017403-120025188		CT827854,CH242-290O13,7:119962492-120179904 (Clone quality: bE290O13 on chr=7; Num_of_Contigs=1; )
CALM2		location ⇒	13:108912990-108911869		FP236287,CH242-278E9,13:108897828-108915422 (Clone quality: bE278E9 on chr=13; Num_of_Contigs=9; )
CALML4		ENSSSCG00000004959	1:173357339-173361042		CU929738,CH242-251L9,1:173356570-173361426 (Clone quality: bE251L9 on chr=1; Num_of_Contigs=5; )
CALML5		ENSSSCG00000011141	10:61695653-61696102		FP016037,CH242-134E10,10:61637842-61759314 (Clone quality: bE134E10 on chr=10; Num_of_Contigs=5; )
CALN1		ENSSSCG00000007729	3:13991532-13991687		CU694836,CH242-189A1,3:13985323-14027227 (Clone quality: bE189A1 on chr=3; Num_of_Contigs=4; )
CALR		ENSSSCG00000013746	2:56285653-56289452		CU463133,CH242-121E19,2:56264935-56304744 (Clone quality: bE121E19 on chr=2; Num_of_Contigs=6; )
CALR		location ⇒	2:56286457-56286663		CU463133,CH242-121E19,2:56264935-56304744 (Clone quality: bE121E19 on chr=2; Num_of_Contigs=6; )
CALR		location ⇒	2:56287272-56287484		CU463133,CH242-121E19,2:56264935-56304744 (Clone quality: bE121E19 on chr=2; Num_of_Contigs=6; )
CALR		location ⇒	2:56287565-56287681		CU463133,CH242-121E19,2:56264935-56304744 (Clone quality: bE121E19 on chr=2; Num_of_Contigs=6; )
CALR		location ⇒	2:56287762-56287891		CU463133,CH242-121E19,2:56264935-56304744 (Clone quality: bE121E19 on chr=2; Num_of_Contigs=6; )
CALR3		ENSSSCG00000013858	2:61028872-61057769		CU694762,CH242-123E16,2:61018016-61070712 (Clone quality: bE123E16 on chr=2; Num_of_Contigs=2; )
CALR3		location ⇒	2:61039553-61039456		CU694762,CH242-123E16,2:61018016-61070712 (Clone quality: bE123E16 on chr=2; Num_of_Contigs=2; )
CALR3		location ⇒	2:61052879-61052671		CU694762,CH242-123E16,2:61018016-61070712 (Clone quality: bE123E16 on chr=2; Num_of_Contigs=2; )
CALR3		location ⇒	2:61057415-61057310		CU694762,CH242-123E16,2:61018016-61070712 (Clone quality: bE123E16 on chr=2; Num_of_Contigs=2; )
CALR3		location ⇒	2:61057769-61057619		CU694762,CH242-123E16,2:61018016-61070712 (Clone quality: bE123E16 on chr=2; Num_of_Contigs=2; )
CALU		ENSSSCG00000016581	18:18068836-18101629		CU861972,CH242-288G22,18:18062282-18138680 (Clone quality: bE288G22 on chr=18; Num_of_Contigs=5; )
CALY		ENSSSCG00000010776	14:148054801-148058279
CAMK1		ENSSSCG00000011550	13:55235073-55245620		CU633418,CH242-443E24,13:55210129-55267796 (Clone quality: bE443E24 on chr=13; Num_of_Contigs=9; )
CAMK1D		ENSSSCG00000011111	10:56168591-56581512
CAMK1G		ENSSSCG00000015619	9:125755932-125772992
CAMK2A		ENSSSCG00000014443	2:136606174-136697322
CAMK2A		location ⇒	2:136625859-136625981		CU914366,CH242-274B11,2:136604505-136635615 (Clone quality: bE274B11 on chr=2; Num_of_Contigs=10; )
CAMK2A		location ⇒	2:136645774-136645868		CU914366,CH242-274B11,2:136635716-136663326 (Clone quality: bE274B11 on chr=2; Num_of_Contigs=10; )
CAMK2A		location ⇒	2:136649410-136649579		CU914366,CH242-274B11,2:136635716-136663326 (Clone quality: bE274B11 on chr=2; Num_of_Contigs=10; )
CAMK2A		location ⇒	2:136762875-136762997		FP102406,CH242-294F6,2:136762372-136765009 (Clone quality: bE294F6 on chr=2; Num_of_Contigs=13; )
CAMK2B		ENSSSCG00000016748	18:49486662-49498903
CAMK2D		ENSSSCG00000009123	8:93598105-93903603
CAMK2G		ENSSSCG00000010311	14:79839232-79894990
CAMK2G		location ⇒	14:79839459-79839250		CU640439,CH242-168L21,14:79822021-79894539 (Clone quality: bE168L21 on chr=14; Num_of_Contigs=4; )
CAMK2G		location ⇒	14:79839459-79839250		CU640439,CH242-168L21,14:79822021-79894539 (Clone quality: bE168L21 on chr=14; Num_of_Contigs=4; )

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).