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)

Ccl9		location ⇒	4:114638860-114638756		CU606863,CH242-71K19,4:114596843-114641017 (Clone quality: bE71K19 on chr=4; Num_of_Contigs=8; )
Ccl9		location ⇒	4:114769163-114769059		CU570995,CH242-11B15,4:114761098-114774572 (Clone quality: bE11B15 on chr=4; Num_of_Contigs=17; )
CCM2		ENSSSCG00000016734	18:48859697-49002419
CCNA1		ENSSSCG00000009354	11:11866211-11875399		CU468057,CH242-192D12,11:11865999-11902535 (Clone quality: bE192D12 on chr=11; Num_of_Contigs=10; )
CCNA2		ENSSSCG00000009094	8:87776929-87787050
CCNB1		location ⇒	1:116809283-116809211		CU464072,CH242-235P3,1:116798393-116844561 (Clone quality: bE235P3 on chr=1; Num_of_Contigs=4; )
CCNB1IP1		ENSSSCG00000002144	7:85008453-85013405		CU571042,CH242-348N17,7:84913444-85061275 (Clone quality: bE348N17 on chr=7; Num_of_Contigs=2; )
CCNB2		ENSSSCG00000004588	1:116791570-116827208
CCNB2		location ⇒	1:2515937-2516037		FP089482,CH242-213J15,1:2514628-2517520 (Clone quality: bE213J15 on chr=1; Num_of_Contigs=5; )
CCNB2		location ⇒	1:3767419-3767346		CU481396,CH242-102H15,1:3740584-3778360 (Clone quality: bE102H15 on chr=1; Num_of_Contigs=6; )
CCNB2		location ⇒	1:844329-844402		CU633721,CH242-504P16,1:840865-950063 (Clone quality: bE504P16 on chr=1; Num_of_Contigs=3; )
CCNB2		location ⇒	1:930165-930088		CU633721,CH242-504P16,1:840865-950063 (Clone quality: bE504P16 on chr=1; Num_of_Contigs=3; )
CCNB3		ENSSSCG00000012307	X:43248153-43300124
CCNC		ENSSSCG00000004353	1:69833873-69858465
CCNC		location ⇒	1:69834133-69832880		CU041276,CH242-402K9,1:69742747-69847842 (Clone quality: bE402K9 on chr=1; Num_of_Contigs=3; )
CCNC		location ⇒	1:69843965-69843914		CU041276,CH242-402K9,1:69742747-69847842 (Clone quality: bE402K9 on chr=1; Num_of_Contigs=3; )
CCNC		location ⇒	1:69847687-69847634		CU041276,CH242-402K9,1:69742747-69847842 (Clone quality: bE402K9 on chr=1; Num_of_Contigs=3; )
CCNC		location ⇒	1:69858465-69858308		CU041276,CH242-402K9,1:69847943-69904557 (Clone quality: bE402K9 on chr=1; Num_of_Contigs=3; )
CCND1		ENSSSCG00000012873	2:1812441-1856137
CCND1		location ⇒	2:1816245-1816085		FP102526,CH242-47B2,2:1811284-1816746 (Clone quality: bE47B2 on chr=2; Num_of_Contigs=9; )
CCND1		location ⇒	2:1818220-1817801		FP102526,CH242-47B2,2:1816847-1818268 (Clone quality: bE47B2 on chr=2; Num_of_Contigs=9; )
CCND1		location ⇒	2:1855194-1855034		FP015806,CH242-82I2,2:1850231-1856438 (Clone quality: bE82I2 on chr=2; Num_of_Contigs=5; )
CCND1		location ⇒	2:1855954-1855737		FP015806,CH242-82I2,2:1850231-1856438 (Clone quality: bE82I2 on chr=2; Num_of_Contigs=5; )
CCND2		ENSSSCG00000000727	5:61964529-61981790
CCND3		ENSSSCG00000001632	7:42666183-42670750
CCND3		location ⇒	7:42666790-42666731		CU468691,CH242-161L14,7:42663535-42670478 (Clone quality: bE161L14 on chr=7; Num_of_Contigs=22; )
CCND3		location ⇒	7:42667354-42667215		CU468691,CH242-161L14,7:42663535-42670478 (Clone quality: bE161L14 on chr=7; Num_of_Contigs=22; )
CCND3		location ⇒	7:42668017-42667857		CU468691,CH242-161L14,7:42663535-42670478 (Clone quality: bE161L14 on chr=7; Num_of_Contigs=22; )
CCND3		location ⇒	7:42670750-42670579		CU468691,CH242-161L14,7:42670579-42682065 (Clone quality: bE161L14 on chr=7; Num_of_Contigs=22; )
CCNDBP1		ENSSSCG00000004715	1:134408447-134410799		CU041269,CH242-35N12,1:134381341-134411075 (Clone quality: bE35N12 on chr=1; Num_of_Contigs=12; )
CCNDBP1		location ⇒	1:134378212-134378383		CU041269,CH242-35N12,1:134370391-134381240 (Clone quality: bE35N12 on chr=1; Num_of_Contigs=12; )
CCNDBP1		location ⇒	1:134378955-134379035		CU041269,CH242-35N12,1:134370391-134381240 (Clone quality: bE35N12 on chr=1; Num_of_Contigs=12; )
CCNDBP1		location ⇒	1:134408933-134408448		CU041269,CH242-35N12,1:134381341-134411075 (Clone quality: bE35N12 on chr=1; Num_of_Contigs=12; )
CCNDBP1		location ⇒	1:134414992-134414908		CU041269,CH242-35N12,1:134413842-134418792 (Clone quality: bE35N12 on chr=1; Num_of_Contigs=12; )
CCNE1		ENSSSCG00000002855	6:27008842-27020592
CCNE1		location ⇒	10:65102210-65102852		CU928815,CH242-240P16,10:65074167-65130926 (Clone quality: bE240P16 on chr=10; Num_of_Contigs=8; )
CCNE2		ENSSSCG00000006095	4:42150042-42165730		FP085498,CH242-18C1,4:42141953-42219837 (Clone quality: bE18C1 on chr=4; Num_of_Contigs=5; )
CCNE2		location ⇒	4:42152314-42152466		FP085498,CH242-18C1,4:42141953-42219837 (Clone quality: bE18C1 on chr=4; Num_of_Contigs=5; )
CCNE2		location ⇒	4:42156969-42157118		FP085498,CH242-18C1,4:42141953-42219837 (Clone quality: bE18C1 on chr=4; Num_of_Contigs=5; )
CCNE2		location ⇒	4:42164896-42165056		FP085498,CH242-18C1,4:42141953-42219837 (Clone quality: bE18C1 on chr=4; Num_of_Contigs=5; )
CCNE2		location ⇒	4:42165484-42166967		FP085498,CH242-18C1,4:42141953-42219837 (Clone quality: bE18C1 on chr=4; Num_of_Contigs=5; )
CCNG1		ENSSSCG00000017024	16:57843248-57850733		CU694497,CH242-321D12,16:57793714-57884951 (Clone quality: bE321D12 on chr=16; Num_of_Contigs=4; )
CCNG2		ENSSSCG00000008988	8:62239553-62247659		CU915443,CH242-113L13,8:62194257-62263835 (Clone quality: bE113L13 on chr=8; Num_of_Contigs=5; )
CCNG2		location ⇒	8:62240797-62240938		CU915443,CH242-113L13,8:62194257-62263835 (Clone quality: bE113L13 on chr=8; Num_of_Contigs=5; )
CCNG2		location ⇒	8:62242236-62242489		CU915443,CH242-113L13,8:62194257-62263835 (Clone quality: bE113L13 on chr=8; Num_of_Contigs=5; )
CCNG2		location ⇒	8:62245570-62245777		CU915443,CH242-113L13,8:62194257-62263835 (Clone quality: bE113L13 on chr=8; Num_of_Contigs=5; )
CCNG2		location ⇒	8:62246942-62247515		CU915443,CH242-113L13,8:62194257-62263835 (Clone quality: bE113L13 on chr=8; Num_of_Contigs=5; )
CCNH		ENSSSCG00000014147	2:84500823-84534672		CU855959,CH242-123E22,2:84454292-84608873 (Clone quality: bE123E22 on chr=2; Num_of_Contigs=1; )
CCNI		ENSSSCG00000008987	8:62137206-62168764
CCNI2		ENSSSCG00000014284	2:122984190-122989315	CU468216,CH242-85C7,2:122831928-123020434 (Clone quality: bE85C7 on chr=2; Num_of_Contigs=1; )

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).