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)

CD302		ENSSSCG00000015884	15:62141546-62172624		CU928024,CH242-216H16,15:62133250-62215175 (Clone quality: bE216H16 on chr=15; Num_of_Contigs=4; )
CD304		ENSSSCG00000011102	10:53376046-53522137
CD31		ENSSSCG00000017277	12:12236539-12292016
CD314		ENSSSCG00000000641	5:58200553-58208785		CU856203,CH242-259K19,5:58140023-58263158 (Clone quality: bE259K19 on chr=5; Num_of_Contigs=4; )
CD316		ENSSSCG00000006392	4:93840441-93848088	CU138477,CH242-105O19,4:93708821-93889364 (Clone quality: bE105O19 on chr=4; Num_of_Contigs=5; )
CD318		ENSSSCG00000011298	13:23480639-23512665
CD319		ENSSSCG00000006378	4:93220455-93235041		CU606866,CH242-143J3,4:93072841-93235164 (Clone quality: bE143J3 on chr=4; Num_of_Contigs=1; )
CD32		ENSSSCG00000006350	4:92582670-92601887		CU468575,CH242-447O4,4:92557884-92605555 (Clone quality: bE447O4 on chr=4; Num_of_Contigs=10; )
CD32		ENSSSCG00000006350	4:92582670-92601887		CU468575,CH242-447O4,4:92557884-92605555 (Clone quality: bE447O4 on chr=4; Num_of_Contigs=10; )
CD325		ENSSSCG00000003722	6:77952628-77983828
CD33		ENSSSCG00000004493	1:99284559-99290281		CU694902,CH242-378G17,1:99170632-99336108 (Clone quality: bE378G17 on chr=1; Num_of_Contigs=1; )
CD33		ENSSSCG00000003236	6:39481730-39501436		CU019573,CH242-21M5,6:39444132-39502362 (Clone quality: bE21M5 on chr=6; Num_of_Contigs=9; )
CD33		ENSSSCG00000003226	6:39295447-39301650		CU694842,CH242-204P3,6:39279332-39353368 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
CD33		location ⇒	6:39260379-39260133		CU694842,CH242-204P3,6:39249252-39279231 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
CD33		location ⇒	6:39272415-39272313		CU694842,CH242-204P3,6:39249252-39279231 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
CD33		location ⇒	6:39295520-39295912		CU694842,CH242-204P3,6:39279332-39353368 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
CD33		location ⇒	6:39296073-39296175		CU694842,CH242-204P3,6:39279332-39353368 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
CD333		ENSSSCG00000008679	8:233929-237967		FP102127,CH242-261D5,8:232868-238907 (Clone quality: bE261D5 on chr=8; Num_of_Contigs=8; )
CD336		ENSSSCG00000001618	7:42015385-42021278		CU306815,CH242-32N5,7:41973045-42041868 (Clone quality: bE32N5 on chr=7; Num_of_Contigs=10; )
CD338		ENSSSCG00000009213	8:112296288-112514103
CD339		ENSSSCG00000007067	17:19688741-19725371
CD33L3		ENSSSCG00000004493	1:99284559-99290281		CU694902,CH242-378G17,1:99170632-99336108 (Clone quality: bE378G17 on chr=1; Num_of_Contigs=1; )
CD33L3		location ⇒	1:99284933-99284578		CU694902,CH242-378G17,1:99170632-99336108 (Clone quality: bE378G17 on chr=1; Num_of_Contigs=1; )
CD33L3		location ⇒	1:99472731-99472376		CU855986,CH242-171G22,1:99451350-99476371 (Clone quality: bE171G22 on chr=1; Num_of_Contigs=18; )
CD34		ENSSSCG00000015622	9:127094351-127118367
CD34		location ⇒	9:127094351-127094597		FP089691,CH242-273B10,9:127073003-127099529 (Clone quality: bE273B10 on chr=9; Num_of_Contigs=7; )
CD34		location ⇒	9:127105543-127105783		FP089691,CH242-273B10,9:127099630-127133313 (Clone quality: bE273B10 on chr=9; Num_of_Contigs=7; )
CD34		location ⇒	9:127106417-127106671		FP089691,CH242-273B10,9:127099630-127133313 (Clone quality: bE273B10 on chr=9; Num_of_Contigs=7; )
CD34		location ⇒	9:127117754-127118989		FP089691,CH242-273B10,9:127099630-127133313 (Clone quality: bE273B10 on chr=9; Num_of_Contigs=7; )
CD340		ENSSSCG00000017497	12:20557656-20578620
CD344		ENSSSCG00000014920	9:20877821-20879122		FP102391,CH242-358A3,9:20873313-20886557 (Clone quality: bE358A3 on chr=9; Num_of_Contigs=7; )
CD350		ENSSSCG00000009751	14:25010134-25011879		CU019576,CH242-288E21,14:24885177-25019758 (Clone quality: bE288E21 on chr=14; Num_of_Contigs=4; )
CD36		ENSSSCG00000015405	9:93201790-93249833		CU694770,CH242-168I5,9:93113331-93272735 (Clone quality: bE168I5 on chr=9; Num_of_Contigs=1; )
CD36		location ⇒	9:93120148-93120095		CU694770,CH242-168I5,9:93113331-93272735 (Clone quality: bE168I5 on chr=9; Num_of_Contigs=1; )
CD36		location ⇒	9:93139263-93139188		CU694770,CH242-168I5,9:93113331-93272735 (Clone quality: bE168I5 on chr=9; Num_of_Contigs=1; )
CD36		location ⇒	9:93162935-93162876		CU694770,CH242-168I5,9:93113331-93272735 (Clone quality: bE168I5 on chr=9; Num_of_Contigs=1; )
CD36		location ⇒	9:93201988-93201460		CU694770,CH242-168I5,9:93113331-93272735 (Clone quality: bE168I5 on chr=9; Num_of_Contigs=1; )
CD38		ENSSSCG00000008742	8:8366135-8381623
CD38		location ⇒	8:8231987-8231486		FP016042,CH242-20B12,8:8224404-8242001 (Clone quality: bE20B12 on chr=8; Num_of_Contigs=7; )
CD38		location ⇒	8:8363052-8362625		FP016042,CH242-20B12,8:8310762-8380249 (Clone quality: bE20B12 on chr=8; Num_of_Contigs=7; )
CD38		location ⇒	8:8380160-8380023		FP016042,CH242-20B12,8:8310762-8380249 (Clone quality: bE20B12 on chr=8; Num_of_Contigs=7; )
CD38		location ⇒	8:8381622-8381492		FP016042,CH242-20B12,8:8380350-8385821 (Clone quality: bE20B12 on chr=8; Num_of_Contigs=7; )
CD39		ENSSSCG00000010497	14:112352301-112444933
CD39		ENSSSCG00000002355	7:105288426-105330499		CT797481,CH242-31K14,7:105227853-105414617 (Clone quality: bE31K14 on chr=7; Num_of_Contigs=1; )
CD39		location ⇒	14:112421242-112421404		CT954285,CH242-291B7,14:112352512-112505527 (Clone quality: bE291B7 on chr=14; Num_of_Contigs=2; )
CD39		location ⇒	14:112422049-112422293		CT954285,CH242-291B7,14:112352512-112505527 (Clone quality: bE291B7 on chr=14; Num_of_Contigs=2; )
CD39		location ⇒	14:112423812-112424072		CT954285,CH242-291B7,14:112352512-112505527 (Clone quality: bE291B7 on chr=14; Num_of_Contigs=2; )
CD39		location ⇒	14:112444180-112444421		CT954285,CH242-291B7,14:112352512-112505527 (Clone quality: bE291B7 on chr=14; Num_of_Contigs=2; )
CD3D		ENSSSCG00000015093	9:44525596-44529625		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
CD3D		location ⇒	9:44526152-44525845		CU914235,CH242-177G19,9:44486144-44604301 (Clone quality: bE177G19 on chr=9; 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).