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)

CTF2		ENSSSCG00000008493	3:96014184-96038392		CU695023,CH242-129E17,3:96011217-96129629 (Clone quality: bE129E17 on chr=3; Num_of_Contigs=2; )
CTGF		ENSSSCG00000004192	1:33154716-33157154		CU468353,CH242-395K18,1:33152740-33201967 (Clone quality: bE395K18 on chr=1; Num_of_Contigs=5; )
CTGF		ENSSSCG00000007379	17:48922466-48936758		FP236540,CH242-206B16,17:48921895-48938133 (Clone quality: bE206B16 on chr=17; Num_of_Contigs=10; )
CTGF		location ⇒	1:33155624-33155876		CU468353,CH242-395K18,1:33152740-33201967 (Clone quality: bE395K18 on chr=1; Num_of_Contigs=5; )
CTGF		location ⇒	1:33156011-33156223		CU468353,CH242-395K18,1:33152740-33201967 (Clone quality: bE395K18 on chr=1; Num_of_Contigs=5; )
CTGF		location ⇒	1:33156616-33157016		CU468353,CH242-395K18,1:33152740-33201967 (Clone quality: bE395K18 on chr=1; Num_of_Contigs=5; )
CTGF		location ⇒	1:33156912-33157154		CU468353,CH242-395K18,1:33152740-33201967 (Clone quality: bE395K18 on chr=1; Num_of_Contigs=5; )
CTH		ENSSSCG00000003789	6:100213217-100244856
CTHRC1		ENSSSCG00000006051	4:34133414-34150470
CTL1		ENSSSCG00000005425	1:258582618-258743259
CTLA4		ENSSSCG00000016122	15:100704141-100709270
CTLA4		location ⇒	15:100704213-100704326		CU856435,CH242-89B15,15:100689643-100705352 (Clone quality: bE89B15 on chr=15; Num_of_Contigs=3; )
CTLA4		location ⇒	15:100706973-100707322		CU856435,CH242-89B15,15:100705453-100712972 (Clone quality: bE89B15 on chr=15; Num_of_Contigs=3; )
CTLA4		location ⇒	15:100707773-100707883		CU856435,CH242-89B15,15:100705453-100712972 (Clone quality: bE89B15 on chr=15; Num_of_Contigs=3; )
CTLA4		location ⇒	15:100709165-100709272		CU856435,CH242-89B15,15:100705453-100712972 (Clone quality: bE89B15 on chr=15; Num_of_Contigs=3; )
CTNNA1		ENSSSCG00000014339	2:127747557-127840081
CTNNA1		location ⇒	2:127839866-127840070		CU463907,CH242-154P16,2:127833066-127842729 (Clone quality: bE154P16 on chr=2; Num_of_Contigs=13; )
CTNNA1		location ⇒	2:127891932-127890821		CU463907,CH242-154P16,2:127890491-127895025 (Clone quality: bE154P16 on chr=2; Num_of_Contigs=13; )
CTNNA1		location ⇒	2:127894448-127894266		CU463907,CH242-154P16,2:127890491-127895025 (Clone quality: bE154P16 on chr=2; Num_of_Contigs=13; )
CTNNA1		location ⇒	2:127923787-127923631		CU463907,CH242-154P16,2:127922194-127926934 (Clone quality: bE154P16 on chr=2; Num_of_Contigs=13; )
CTNNA2		ENSSSCG00000008250	3:57482883-57597557
CTNNA2		location ⇒	3:57596928-57597239		CU695026,CH242-141I7,3:57588537-57622113 (Clone quality: bE141I7 on chr=3; Num_of_Contigs=3; )
CTNNA2		location ⇒	3:57597290-57597557		CU695026,CH242-141I7,3:57588537-57622113 (Clone quality: bE141I7 on chr=3; Num_of_Contigs=3; )
CTNNA3		ENSSSCG00000010230	14:72322151-73160656
CTNNA3		location ⇒	14:72322436-72322259		CT827950,CH242-277L5,14:72214230-72366915 (Clone quality: bE277L5 on chr=14; Num_of_Contigs=1; )
CTNNA3		location ⇒	14:72385670-72385534		CU329694,CH242-281J17,14:72366916-72537141 (Clone quality: bE281J17 on chr=14; Num_of_Contigs=1; )
CTNNA3		location ⇒	14:72398896-72398787		CU329694,CH242-281J17,14:72366916-72537141 (Clone quality: bE281J17 on chr=14; Num_of_Contigs=1; )
CTNNA3		location ⇒	14:72475217-72475033		CU329694,CH242-281J17,14:72366916-72537141 (Clone quality: bE281J17 on chr=14; Num_of_Contigs=1; )
CTNNAL1		ENSSSCG00000005443	1:262760613-262814114
CTNNAL1		location ⇒	1:262761085-262761009		CU442740,CH242-321N10,1:262654894-262770561 (Clone quality: bE321N10 on chr=1; Num_of_Contigs=3; )
CTNNAL1		location ⇒	1:262762091-262761991		CU442740,CH242-321N10,1:262654894-262770561 (Clone quality: bE321N10 on chr=1; Num_of_Contigs=3; )
CTNNAL1		location ⇒	1:262769836-262769679		CU442740,CH242-321N10,1:262654894-262770561 (Clone quality: bE321N10 on chr=1; Num_of_Contigs=3; )
CTNNAL1		location ⇒	1:262782352-262782198		CU442740,CH242-321N10,1:262770662-262788247 (Clone quality: bE321N10 on chr=1; Num_of_Contigs=3; )
CTNNB1		ENSSSCG00000015386	9:85935030-85951631		FP102348,CH242-188H10,9:85931672-85957896 (Clone quality: bE188H10 on chr=9; Num_of_Contigs=13; )
CTNNB1		ENSSSCG00000011274	13:20905977-20950024		CU861524,CH242-156J19,13:20905383-20993819 (Clone quality: bE156J19 on chr=13; Num_of_Contigs=6; )
CTNNB1		location ⇒	13:20942104-20942445		CU861524,CH242-156J19,13:20905383-20993819 (Clone quality: bE156J19 on chr=13; Num_of_Contigs=6; )
CTNNB1		location ⇒	13:20942104-20942445		CU861524,CH242-156J19,13:20905383-20993819 (Clone quality: bE156J19 on chr=13; Num_of_Contigs=6; )
CTNNB1		location ⇒	13:20949409-20950022		CU861524,CH242-156J19,13:20905383-20993819 (Clone quality: bE156J19 on chr=13; Num_of_Contigs=6; )
CTNNB1		location ⇒	13:20949409-20950022		CU861524,CH242-156J19,13:20905383-20993819 (Clone quality: bE156J19 on chr=13; Num_of_Contigs=6; )
CTNNBL1		ENSSSCG00000007337	17:43302744-43347401
CTNND1		ENSSSCG00000013174	2:11163152-11188015		CU464011,CH242-383N23,2:11069163-11208431 (Clone quality: bE383N23 on chr=2; Num_of_Contigs=2; )
CTNND1		location ⇒	2:11172933-11173020		CU464011,CH242-383N23,2:11069163-11208431 (Clone quality: bE383N23 on chr=2; Num_of_Contigs=2; )
CTNND1		location ⇒	2:11175031-11175188		CU464011,CH242-383N23,2:11069163-11208431 (Clone quality: bE383N23 on chr=2; Num_of_Contigs=2; )
CTNND1		location ⇒	2:11176121-11176240		CU464011,CH242-383N23,2:11069163-11208431 (Clone quality: bE383N23 on chr=2; Num_of_Contigs=2; )
CTNND1		location ⇒	2:11177337-11177522		CU464011,CH242-383N23,2:11069163-11208431 (Clone quality: bE383N23 on chr=2; Num_of_Contigs=2; )
CTNND2		ENSSSCG00000016780	16:218938-583660
CTNND2		location ⇒	16:219035-218957		CU972434,CH242-383P22,16:210835-311990 (Clone quality: bE383P22 on chr=16; Num_of_Contigs=2; )
CTNND2		location ⇒	16:225229-225096		CU972434,CH242-383P22,16:210835-311990 (Clone quality: bE383P22 on chr=16; Num_of_Contigs=2; )
CTNND2		location ⇒	16:230206-230118		CU972434,CH242-383P22,16:210835-311990 (Clone quality: bE383P22 on chr=16; Num_of_Contigs=2; )
CTNS		ENSSSCG00000017865	12:47026848-47046510

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).