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)

CTTN		location ⇒	2:1455926-1455814		CU469203,CH242-236K15,2:1451789-1460862 (Clone quality: bE236K15 on chr=2; Num_of_Contigs=23; )
CTTN		location ⇒	2:1458940-1458830		CU469203,CH242-236K15,2:1451789-1460862 (Clone quality: bE236K15 on chr=2; Num_of_Contigs=23; )
CTTN		location ⇒	2:1463445-1463352		CU469203,CH242-236K15,2:1460963-1466566 (Clone quality: bE236K15 on chr=2; Num_of_Contigs=23; )
CTTNBP2		ENSSSCG00000016625	18:26939682-27027568		CU914299,CH242-83K4,18:26927247-27039940 (Clone quality: bE83K4 on chr=18; Num_of_Contigs=6; )
CTTNBP2NL		ENSSSCG00000006781	4:112411893-112454113
CTXN1		ENSSSCG00000013590	2:51296669-51296917		CU929699,CH242-182L23,2:51289316-51437705 (Clone quality: bE182L23 on chr=2; Num_of_Contigs=2; )
CTXN2		ENSSSCG00000004660	1:128876836-128877078		CU407256,CH242-454M16,1:128845613-128904942 (Clone quality: bE454M16 on chr=1; Num_of_Contigs=8; )
CTXN3		ENSSSCG00000014253	2:118225224-118225466		CU928767,CH242-12C1,2:118127977-118261112 (Clone quality: bE12C1 on chr=2; Num_of_Contigs=2; )
CUBN		ENSSSCG00000011030	10:41344608-41499207
CUEDC2		ENSSSCG00000010583	14:118463701-118465668		CU498828,CH242-221N13,14:118461285-118465722 (Clone quality: bE221N13 on chr=14; Num_of_Contigs=8; )
CUGBP1		ENSSSCG00000013233	2:13144668-13159069		CU856103,CH242-271O6,2:13144139-13162730 (Clone quality: bE271O6 on chr=2; Num_of_Contigs=3; )
CUGBP2		ENSSSCG00000011121	10:57573759-57728826
CUL1		ENSSSCG00000015455	9:102080685-102096150		CU915471,CH242-253I6,9:102066088-102097050 (Clone quality: bE253I6 on chr=9; Num_of_Contigs=8; )
CUL1		location ⇒	9:1482301-1482418		CU861932,CH242-167P1,9:1469096-1510526 (Clone quality: bE167P1 on chr=9; Num_of_Contigs=7; )
CUL1		location ⇒	9:1571003-1570875		CU571209,CH242-210E24,9:1558736-1597095 (Clone quality: bE210E24 on chr=9; Num_of_Contigs=6; )
CUL1		location ⇒	9:697284-697171		CU638718,CH242-178L14,9:670144-722820 (Clone quality: bE178L14 on chr=9; Num_of_Contigs=6; )
CUL1		location ⇒	9:779473-779590		CU571015,CH242-18F18,9:773826-881041 (Clone quality: bE18F18 on chr=9; Num_of_Contigs=4; )
CUL2		ENSSSCG00000011104	10:54618727-54663918		CU914378,CH242-203J15,10:54614213-54709501 (Clone quality: bE203J15 on chr=10; Num_of_Contigs=5; )
CUL2		ENSSSCG00000005659	1:283774905-283798601
CUL2		location ⇒	10:54657103-54657308		CU914378,CH242-203J15,10:54614213-54709501 (Clone quality: bE203J15 on chr=10; Num_of_Contigs=5; )
CUL2		location ⇒	10:54659556-54659660		CU914378,CH242-203J15,10:54614213-54709501 (Clone quality: bE203J15 on chr=10; Num_of_Contigs=5; )
CUL2		location ⇒	10:54662374-54662498		CU914378,CH242-203J15,10:54614213-54709501 (Clone quality: bE203J15 on chr=10; Num_of_Contigs=5; )
CUL2		location ⇒	10:54663344-54663894		CU914378,CH242-203J15,10:54614213-54709501 (Clone quality: bE203J15 on chr=10; Num_of_Contigs=5; )
CUL3		ENSSSCG00000010931	10:24955012-24986671		CU986276,CH242-319L9,10:24954126-25023165 (Clone quality: bE319L9 on chr=10; Num_of_Contigs=6; )
CUL3		ENSSSCG00000016234	15:118519504-118764756
CUL3		location ⇒	15:122993789-122993669		CU550652,CH242-134E9,15:122978020-123022406 (Clone quality: bE134E9 on chr=15; Num_of_Contigs=5; )
CUL3		location ⇒	15:21659066-21659011		CU972475,CH242-47H5,15:21651785-21667654 (Clone quality: bE47H5 on chr=15; Num_of_Contigs=4; )
CUL3		location ⇒	15:28263063-28262948		CU570904,CH242-119O22,15:28249508-28369816 (Clone quality: bE119O22 on chr=15; Num_of_Contigs=7; )
CUL3		location ⇒	15:7351324-7351438		CU469306,CH242-518F4,15:7344963-7352894 (Clone quality: bE518F4 on chr=15; Num_of_Contigs=20; )
CUL4A		ENSSSCG00000009556	11:78839790-78871059		FP236214,CH242-266L11,11:78807891-78889241 (Clone quality: bE266L11 on chr=11; Num_of_Contigs=10; )
CUL4A		location ⇒	11:78840431-78839861		FP236214,CH242-266L11,11:78807891-78889241 (Clone quality: bE266L11 on chr=11; Num_of_Contigs=10; )
CUL4A		location ⇒	11:78841438-78841286		FP236214,CH242-266L11,11:78807891-78889241 (Clone quality: bE266L11 on chr=11; Num_of_Contigs=10; )
CUL4A		location ⇒	11:78843801-78843625		FP236214,CH242-266L11,11:78807891-78889241 (Clone quality: bE266L11 on chr=11; Num_of_Contigs=10; )
CUL4A		location ⇒	11:78846664-78846548		FP236214,CH242-266L11,11:78807891-78889241 (Clone quality: bE266L11 on chr=11; Num_of_Contigs=10; )
CUL4B		ENSSSCG00000012603	X:95743380-95781252
CUL4B		location ⇒	X:95772552-95772657	CU468368,CH242-64G23,X:95769707-95778344 (Clone quality: bE64G23 on chr=X; Num_of_Contigs=10; )
CUL4B		location ⇒	X:95773349-95773456	CU468368,CH242-64G23,X:95769707-95778344 (Clone quality: bE64G23 on chr=X; Num_of_Contigs=10; )
CUL4B		location ⇒	X:95774456-95774632	CU468368,CH242-64G23,X:95769707-95778344 (Clone quality: bE64G23 on chr=X; Num_of_Contigs=10; )
CUL4B		location ⇒	X:95776995-95777148	CU468368,CH242-64G23,X:95769707-95778344 (Clone quality: bE64G23 on chr=X; Num_of_Contigs=10; )
CUL5		location ⇒	9:109012080-109012009		FP102036,CH242-81O13,9:109007528-109022822 (Clone quality: bE81O13 on chr=9; Num_of_Contigs=6; )
CUL5		location ⇒	9:46177701-46177593		CU595407,CH242-180M7,9:46155254-46179001 (Clone quality: bE180M7 on chr=9; Num_of_Contigs=16; )
CUL5		location ⇒	9:68384528-68384578		FP101868,CH242-199M2,9:68368290-68392326 (Clone quality: bE199M2 on chr=9; Num_of_Contigs=3; )
CUL5		location ⇒	9:7986486-7986560		CU855642,CH242-23A3,9:7946296-8000820 (Clone quality: bE23A3 on chr=9; Num_of_Contigs=4; )
CUL7		ENSSSCG00000001657	7:43944828-43961710
CUTA		ENSSSCG00000001512	7:34127466-34129092	CU498854,CH242-216B14,7:34116847-34138577 (Clone quality: bE216B14 on chr=7; Num_of_Contigs=6; )
CUTC		ENSSSCG00000010542	14:115656295-115681889		CT868685,CH242-211E15,14:115597313-115736638 (Clone quality: bE211E15 on chr=14; Num_of_Contigs=2; )
CUX1		ENSSSCG00000007681	3:7733351-8215757
CUX2		ENSSSCG00000009831	14:32589939-32635021		CT737261,CH242-157F24,14:32468838-32654912 (Clone quality: bE157F24 on chr=14; Num_of_Contigs=1; )
CWC15		ENSSSCG00000014961	9:27373590-27384894		CU571278,CH242-203H23,9:27341017-27403279 (Clone quality: bE203H23 on chr=9; Num_of_Contigs=4; )
CWF19L1		ENSSSCG00000010550	14:116223704-116256112		CT827831,CH242-224L12,14:116210864-116263223 (Clone quality: bE224L12 on chr=14; 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).