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)

CD48		ENSSSCG00000006379	4:93278346-93292708		CU915315,CH242-208F9,4:93261946-93408226 (Clone quality: bE208F9 on chr=4; Num_of_Contigs=2; )
CD48		location ⇒	4:93278364-93278520		CU915315,CH242-208F9,4:93261946-93408226 (Clone quality: bE208F9 on chr=4; Num_of_Contigs=2; )
CD48		location ⇒	4:93286521-93286825		CU915315,CH242-208F9,4:93261946-93408226 (Clone quality: bE208F9 on chr=4; Num_of_Contigs=2; )
CD48		location ⇒	4:93290162-93290422		CU915315,CH242-208F9,4:93261946-93408226 (Clone quality: bE208F9 on chr=4; Num_of_Contigs=2; )
CD49a		ENSSSCG00000016885	16:29202547-29281645
CD49b		ENSSSCG00000016887	16:29427892-29498935		CU928375,CH242-425K19,16:29401619-29534620 (Clone quality: bE425K19 on chr=16; Num_of_Contigs=1; )
CD49c		ENSSSCG00000017578	12:24655910-24790905
CD49d		ENSSSCG00000016009	15:81544892-81624138		CU861559,CH242-348D16,15:81514178-81645419 (Clone quality: bE348D16 on chr=15; Num_of_Contigs=3; )
CD49e		ENSSSCG00000000293	5:18143068-18165627		CU466514,CH242-63P24,5:18141753-18189023 (Clone quality: bE63P24 on chr=5; Num_of_Contigs=10; )
CD5		ENSSSCG00000013115	2:9524678-9534242		CU914270,CH242-323D11,2:9520060-9538986 (Clone quality: bE323D11 on chr=2; Num_of_Contigs=11; )
CD5		ENSSSCG00000006455	4:96025067-96042589	CU137732,CH242-59K14,4:95974742-96142492 (Clone quality: bE59K14 on chr=4; Num_of_Contigs=4; )
CD5		location ⇒	2:9525106-9524675		CU914270,CH242-323D11,2:9520060-9538986 (Clone quality: bE323D11 on chr=2; Num_of_Contigs=11; )
CD5		location ⇒	2:9526900-9526781		CU914270,CH242-323D11,2:9520060-9538986 (Clone quality: bE323D11 on chr=2; Num_of_Contigs=11; )
CD5		location ⇒	2:9528743-9528618		CU914270,CH242-323D11,2:9520060-9538986 (Clone quality: bE323D11 on chr=2; Num_of_Contigs=11; )
CD5		location ⇒	2:9529992-9529696		CU914270,CH242-323D11,2:9520060-9538986 (Clone quality: bE323D11 on chr=2; Num_of_Contigs=11; )
CD51		location ⇒	15:85848518-85848326		CU861617,CH242-300C22,15:85845875-85862091 (Clone quality: bE300C22 on chr=15; Num_of_Contigs=5; )
CD51		location ⇒	15:85853611-85853409		CU861617,CH242-300C22,15:85845875-85862091 (Clone quality: bE300C22 on chr=15; Num_of_Contigs=5; )
CD51		location ⇒	15:85915021-85915223		CU914307,CH242-9E10,15:85898024-85944349 (Clone quality: bE9E10 on chr=15; Num_of_Contigs=1; )
CD51		location ⇒	15:85920115-85920307		CU914307,CH242-9E10,15:85898024-85944349 (Clone quality: bE9E10 on chr=15; Num_of_Contigs=1; )
CD53		ENSSSCG00000006800	4:113726728-113756057
CD53		location ⇒	4:113727589-113726727		CU467047,CH242-12L18,4:113719940-113750653 (Clone quality: bE12L18 on chr=4; Num_of_Contigs=6; )
CD53		location ⇒	4:113737218-113737121		CU467047,CH242-12L18,4:113719940-113750653 (Clone quality: bE12L18 on chr=4; Num_of_Contigs=6; )
CD53		location ⇒	4:113739552-113739363		CU467047,CH242-12L18,4:113719940-113750653 (Clone quality: bE12L18 on chr=4; Num_of_Contigs=6; )
CD53		location ⇒	4:113755980-113755855		CU207230,CH242-384H21,4:113750654-113878957 (Clone quality: bE384H21 on chr=4; Num_of_Contigs=7; )
CD55		ENSSSCG00000015749	15:31993420-32018200
CD55		ENSSSCG00000015664	9:132465109-132465291		CU633410,CH242-391L17,9:132252384-132466044 (Clone quality: bE391L17 on chr=9; Num_of_Contigs=2; )
CD55		location ⇒	9:132464164-132464293		CU633410,CH242-391L17,9:132252384-132466044 (Clone quality: bE391L17 on chr=9; Num_of_Contigs=2; )
CD55		location ⇒	9:132465109-132465295		CU633410,CH242-391L17,9:132252384-132466044 (Clone quality: bE391L17 on chr=9; Num_of_Contigs=2; )
CD56		ENSSSCG00000015045	9:39876973-39943731		CU570935,CH242-240E24,9:39843626-40020360 (Clone quality: bE240E24 on chr=9; Num_of_Contigs=2; )
CD57		ENSSSCG00000015259	9:59287480-59384534
CD58		ENSSSCG00000006738	4:108346796-108569574
CD58		location ⇒	4:108371952-108372249		CU856185,CH242-131P13,4:108243128-108376833 (Clone quality: bE131P13 on chr=4; Num_of_Contigs=7; )
CD58		location ⇒	4:108406453-108406723		CU468823,CH242-63H5,4:108405099-108431457 (Clone quality: bE63H5 on chr=4; Num_of_Contigs=16; )
CD58		location ⇒	4:108540411-108540708		CU481485,CH242-280N19,4:108537543-108558204 (Clone quality: bE280N19 on chr=4; Num_of_Contigs=14; )
CD58		location ⇒	4:108549513-108549783		CU481485,CH242-280N19,4:108537543-108558204 (Clone quality: bE280N19 on chr=4; Num_of_Contigs=14; )
CD59		ENSSSCG00000013309	2:25595826-25616380
CD59		location ⇒	2:25595792-25595860	CU463884,CH242-311M11,2:25413051-25615449 (Clone quality: bE311M11 on chr=2; Num_of_Contigs=2; )
CD59		location ⇒	2:25605218-25605306	CU463884,CH242-311M11,2:25413051-25615449 (Clone quality: bE311M11 on chr=2; Num_of_Contigs=2; )
CD59		location ⇒	2:25609000-25609104	CU463884,CH242-311M11,2:25413051-25615449 (Clone quality: bE311M11 on chr=2; Num_of_Contigs=2; )
CD59		location ⇒	2:25614892-25615408	CU463884,CH242-311M11,2:25413051-25615449 (Clone quality: bE311M11 on chr=2; Num_of_Contigs=2; )
CD5L		ENSSSCG00000006455	4:96025067-96042589	CU137732,CH242-59K14,4:95974742-96142492 (Clone quality: bE59K14 on chr=4; Num_of_Contigs=4; )
CD5L		location ⇒	4:96038700-96039005	CU137732,CH242-59K14,4:95974742-96142492 (Clone quality: bE59K14 on chr=4; Num_of_Contigs=4; )
CD5L		location ⇒	4:96040077-96040361	CU137732,CH242-59K14,4:95974742-96142492 (Clone quality: bE59K14 on chr=4; Num_of_Contigs=4; )
CD6		ENSSSCG00000013111	2:9417713-9458152		CU914270,CH242-323D11,2:9406763-9458191 (Clone quality: bE323D11 on chr=2; Num_of_Contigs=11; )
CD6		location ⇒	2:9589028-9588839		CU914270,CH242-323D11,2:9559695-9593658 (Clone quality: bE323D11 on chr=2; Num_of_Contigs=11; )
CD6		location ⇒	2:9589631-9589526		CU914270,CH242-323D11,2:9559695-9593658 (Clone quality: bE323D11 on chr=2; Num_of_Contigs=11; )
CD6		location ⇒	2:9590169-9589910		CU914270,CH242-323D11,2:9559695-9593658 (Clone quality: bE323D11 on chr=2; Num_of_Contigs=11; )
CD6		location ⇒	2:9592245-9592127		CU914270,CH242-323D11,2:9559695-9593658 (Clone quality: bE323D11 on chr=2; Num_of_Contigs=11; )
CD61		ENSSSCG00000017306	12:14440438-14498372
CD61		location ⇒	12:1264772-1264857		CU655945,CH242-412P7,12:1253941-1266123 (Clone quality: bE412P7 on chr=12; Num_of_Contigs=12; )

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).