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)

TGFB1I48848		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
TGFB2		ENSSSCG00000010816	10:8390284-8418277
TGFB2		location ⇒	10:11107395-11107500
TGFB2		location ⇒	10:18541027-18541131		CU466969,CH242-424N17,10:18527892-18559843 (Clone quality: bE424N17 on chr=10; Num_of_Contigs=7; )
TGFB2		location ⇒	10:22584380-22584303		CU694615,CH242-372F9,10:22556856-22588280 (Clone quality: bE372F9 on chr=10; Num_of_Contigs=14; )
TGFB2		location ⇒	10:9346766-9346669		CU855569,CH242-43A21,10:9318839-9461363 (Clone quality: bE43A21 on chr=10; Num_of_Contigs=2; )
TGFB3		ENSSSCG00000002385	7:107143961-107164189		CT737390,CH242-96M21,7:107128395-107303628 (Clone quality: bE96M21 on chr=7; Num_of_Contigs=2; )
TGFB3		location ⇒	7:107145204-107143961		CT737390,CH242-96M21,7:107128395-107303628 (Clone quality: bE96M21 on chr=7; Num_of_Contigs=2; )
TGFB3		location ⇒	7:107148560-107148390		CT737390,CH242-96M21,7:107128395-107303628 (Clone quality: bE96M21 on chr=7; Num_of_Contigs=2; )
TGFB3		location ⇒	7:107155835-107155672		CT737390,CH242-96M21,7:107128395-107303628 (Clone quality: bE96M21 on chr=7; Num_of_Contigs=2; )
TGFB3		location ⇒	7:107164189-107163577		CT737390,CH242-96M21,7:107128395-107303628 (Clone quality: bE96M21 on chr=7; Num_of_Contigs=2; )
TGFBI		ENSSSCG00000014316	2:125628407-125697256
TGFBI		location ⇒	2:125628976-125629027
TGFBI		location ⇒	2:125644883-125645048		FP089688,CH242-222D16,2:125628976-125653053 (Clone quality: bE222D16 on chr=2; Num_of_Contigs=7; )
TGFBI		location ⇒	2:125645351-125645516		FP089688,CH242-222D16,2:125628976-125653053 (Clone quality: bE222D16 on chr=2; Num_of_Contigs=7; )
TGFBI		location ⇒	2:125645734-125645882		FP089688,CH242-222D16,2:125628976-125653053 (Clone quality: bE222D16 on chr=2; Num_of_Contigs=7; )
TGFBR1		ENSSSCG00000005382	1:252432143-252486884
TGFBR2		ENSSSCG00000011226	13:14852440-14877102
TGFBR2		location ⇒	13:14874632-14874502		CU855844,CH242-252E8,13:14863795-14878235 (Clone quality: bE252E8 on chr=13; Num_of_Contigs=19; )
TGFBR2		location ⇒	13:14876796-14876282		CU855844,CH242-252E8,13:14863795-14878235 (Clone quality: bE252E8 on chr=13; Num_of_Contigs=19; )
TGFBR3		ENSSSCG00000006911	4:129336808-129506717
TGFBR3		location ⇒	4:129470715-129470904		CU179693,CH242-321I17,4:129380610-129486866 (Clone quality: bE321I17 on chr=4; Num_of_Contigs=7; )
TGFBR3		location ⇒	4:129473020-129473358		CU179693,CH242-321I17,4:129380610-129486866 (Clone quality: bE321I17 on chr=4; Num_of_Contigs=7; )
TGFBR3		location ⇒	4:129482242-129482543		CU179693,CH242-321I17,4:129380610-129486866 (Clone quality: bE321I17 on chr=4; Num_of_Contigs=7; )
TGFBR3		location ⇒	4:129543491-129543441		CU463294,CH242-380O15,4:129543404-129572109 (Clone quality: bE380O15 on chr=4; Num_of_Contigs=20; )
TGIF2		ENSSSCG00000007319	17:42129673-42140725		CU607085,CH242-137E1,17:42127348-42190090 (Clone quality: bE137E1 on chr=17; Num_of_Contigs=8; )
TGM1		ENSSSCG00000001993	7:81371208-81386082		CU019590,CH242-406B17,7:81281809-81421007 (Clone quality: bE406B17 on chr=7; Num_of_Contigs=4; )
TGM2		location ⇒	17:43400846-43401027		CU467005,CH242-240I5,17:43395287-43420738 (Clone quality: bE240I5 on chr=17; Num_of_Contigs=8; )
TGM2		location ⇒	17:43406482-43406725		CU467005,CH242-240I5,17:43395287-43420738 (Clone quality: bE240I5 on chr=17; Num_of_Contigs=8; )
TGM2		location ⇒	17:43680174-43679931		CU915723,CH242-72A24,17:43678727-43730880 (Clone quality: bE72A24 on chr=17; Num_of_Contigs=4; )
TGM2		location ⇒	17:43685810-43685629		CU915723,CH242-72A24,17:43678727-43730880 (Clone quality: bE72A24 on chr=17; Num_of_Contigs=4; )
TGM3		location ⇒	17:15122-15005		CU855955,CH242-102E13,17:11998-16751 (Clone quality: bE102E13 on chr=17; Num_of_Contigs=18; )
TGM3		location ⇒	17:25398-25487		CU855955,CH242-102E13,17:19097-28601 (Clone quality: bE102E13 on chr=17; Num_of_Contigs=18; )
TGM3		location ⇒	17:39483-39592		CU855955,CH242-102E13,17:32773-39851 (Clone quality: bE102E13 on chr=17; Num_of_Contigs=18; )
TGM3		location ⇒	17:46200-46095		CU855955,CH242-102E13,17:39952-54767 (Clone quality: bE102E13 on chr=17; Num_of_Contigs=18; )
TGM5		ENSSSCG00000004713	1:134288473-134309041	CU210852,CH242-452O20,1:134123075-134309699 (Clone quality: bE452O20 on chr=1; Num_of_Contigs=4; )
TGM6		ENSSSCG00000007177	17:34678413-34694484
TGM7		ENSSSCG00000004712	1:134261035-134276285	CU210852,CH242-452O20,1:134123075-134309699 (Clone quality: bE452O20 on chr=1; Num_of_Contigs=4; )
TGOLN2		ENSSSCG00000008236	3:54090565-54094950
TGS1		ENSSSCG00000006251	4:78808930-78839799		CU467744,CH242-37O14,4:78741713-78909653 (Clone quality: bE37O14 on chr=4; Num_of_Contigs=2; )
TH1L		ENSSSCG00000007521	17:61745937-61758361	CR956646,CH242-247L10,17:61655968-61825296 (No clone quality info on bE247L10)
THADA		ENSSSCG00000008459	3:90296319-90571026
THAP10		ENSSSCG00000004975	1:176318962-176319486		CU074280,CH242-110C4,1:176288310-176331147 (Clone quality: bE110C4 on chr=1; Num_of_Contigs=2; )
THAP11		ENSSSCG00000002769	6:12892453-12893382		FP102672,CH242-302K22,6:12890560-12904623 (Clone quality: bE302K22 on chr=6; Num_of_Contigs=5; )
THAP3		ENSSSCG00000003378	6:45765098-45937762
THAP4		ENSSSCG00000016374	15:131976319-131988704		FP017230,CH242-108B12,15:131966176-132003046 (Clone quality: bE108B12 on chr=15; Num_of_Contigs=7; )
THAP6		ENSSSCG00000008967	8:60684054-60700455		CU929705,CH242-190B8,8:60675607-60700914 (Clone quality: bE190B8 on chr=8; Num_of_Contigs=18; )
THAP7		ENSSSCG00000010098	14:51687433-51689634		CU633934,CH242-117H20,14:51553625-51738341 (Clone quality: bE117H20 on chr=14; Num_of_Contigs=1; )
THAP7		location ⇒	14:51688117-51687551		CU633934,CH242-117H20,14:51553625-51738341 (Clone quality: bE117H20 on chr=14; Num_of_Contigs=1; )
THAP7		location ⇒	14:51688434-51688291		CU633934,CH242-117H20,14:51553625-51738341 (Clone quality: bE117H20 on chr=14; 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, 1851-8

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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).