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)

TNKS2		location ⇒	14:108581148-108581679		CU407271,CH242-475N15,14:108479532-108605472 (Clone quality: bE475N15 on chr=14; Num_of_Contigs=1; )
TNMD		ENSSSCG00000012480	X:75611723-75635367
TNN		ENSSSCG00000015507	9:110166502-110181048		CU951453,CH242-234C7,9:110161289-110189861 (Clone quality: bE234C7 on chr=9; Num_of_Contigs=6; )
TNNC1		ENSSSCG00000011441	13:29205576-29208529		CU550676,CH242-330J9,13:29135788-29268883 (Clone quality: bE330J9 on chr=13; Num_of_Contigs=4; )
TNNC2		ENSSSCG00000007424	17:50089642-50092955		CU076086,CH242-56C16,17:49960216-50115189 (Clone quality: bE56C16 on chr=17; Num_of_Contigs=2; )
TNNC2		location ⇒	17:50090213-50090084		CU076086,CH242-56C16,17:49960216-50115189 (Clone quality: bE56C16 on chr=17; Num_of_Contigs=2; )
TNNC2		location ⇒	17:50090499-50090383		CU076086,CH242-56C16,17:49960216-50115189 (Clone quality: bE56C16 on chr=17; Num_of_Contigs=2; )
TNNC2		location ⇒	17:50090736-50090591		CU076086,CH242-56C16,17:49960216-50115189 (Clone quality: bE56C16 on chr=17; Num_of_Contigs=2; )
TNNC2		location ⇒	17:50090929-50090877		CU076086,CH242-56C16,17:49960216-50115189 (Clone quality: bE56C16 on chr=17; Num_of_Contigs=2; )
TNP1		ENSSSCG00000016179	15:112080597-112081212		CU914349,CH242-487L5,15:112073042-112094386 (Clone quality: bE487L5 on chr=15; Num_of_Contigs=9; )
TNPO2		ENSSSCG00000013726	2:55955375-55970447		CU856041,CH242-32I13,2:55919380-55991729 (Clone quality: bE32I13 on chr=2; Num_of_Contigs=2; )
TNPO3		ENSSSCG00000016572	18:17785741-17830096
TNR		ENSSSCG00000015508	9:110337587-110416513		CU694502,CH242-214B5,9:110281247-110435550 (Clone quality: bE214B5 on chr=9; Num_of_Contigs=3; )
TNR		location ⇒	9:110347576-110347479		CU694502,CH242-214B5,9:110281247-110435550 (Clone quality: bE214B5 on chr=9; Num_of_Contigs=3; )
TNR		location ⇒	9:110349125-110348968		CU694502,CH242-214B5,9:110281247-110435550 (Clone quality: bE214B5 on chr=9; Num_of_Contigs=3; )
TNR		location ⇒	9:110363857-110363722		CU694502,CH242-214B5,9:110281247-110435550 (Clone quality: bE214B5 on chr=9; Num_of_Contigs=3; )
TNR		location ⇒	9:110365159-110365028		CU694502,CH242-214B5,9:110281247-110435550 (Clone quality: bE214B5 on chr=9; Num_of_Contigs=3; )
TNRC18		ENSSSCG00000007582	3:3722522-3866012
TNRC4		ENSSSCG00000006618	4:101467904-101482265	CU457723,CH242-28L6,4:101441264-101656496 (Clone quality: bE28L6 on chr=4; Num_of_Contigs=25; )
TNRC6B		ENSSSCG00000000078	5:4332904-4376190
TNRC6B		location ⇒	5:4326896-4326838		CU639392,CH242-157D22,5:4238817-4335426 (Clone quality: bE157D22 on chr=5; Num_of_Contigs=2; )
TNRC6B		location ⇒	5:4327256-4327199		CU639392,CH242-157D22,5:4238817-4335426 (Clone quality: bE157D22 on chr=5; Num_of_Contigs=2; )
TNRC6B		location ⇒	5:4329513-4328986		CU639392,CH242-157D22,5:4238817-4335426 (Clone quality: bE157D22 on chr=5; Num_of_Contigs=2; )
TNRC6B		location ⇒	5:4332331-4332272		CU639392,CH242-157D22,5:4238817-4335426 (Clone quality: bE157D22 on chr=5; Num_of_Contigs=2; )
TNS		location ⇒	15:113145789-113145881		CU856037,CH242-30L14,15:113141667-113146340 (Clone quality: bE30L14 on chr=15; Num_of_Contigs=7; )
TNS		location ⇒	15:113148897-113149031		CU856037,CH242-30L14,15:113146441-113149652 (Clone quality: bE30L14 on chr=15; Num_of_Contigs=7; )
TNS		location ⇒	15:113204007-113204159		CU856037,CH242-30L14,15:113194957-113206662 (Clone quality: bE30L14 on chr=15; Num_of_Contigs=7; )
TNS		location ⇒	15:113209266-113209144		CU856037,CH242-30L14,15:113206763-113211986 (Clone quality: bE30L14 on chr=15; Num_of_Contigs=7; )
TNS3		ENSSSCG00000016725	18:47632833-47816403
TNS4		ENSSSCG00000017470	12:19744986-19781793
TNXB		ENSSSCG00000001429	7:27910968-27995163
TOB1		ENSSSCG00000017558	12:23906392-23910614
TOB1		location ⇒	12:23907419-23907170		CU929570,CH242-125C23,12:23864717-23908673 (Clone quality: bE125C23 on chr=12; Num_of_Contigs=4; )
TOB1		location ⇒	12:23908349-23907504		CU929570,CH242-125C23,12:23864717-23908673 (Clone quality: bE125C23 on chr=12; Num_of_Contigs=4; )
TOB1		location ⇒	12:23910594-23910335		CU929570,CH242-125C23,12:23908774-23960194 (Clone quality: bE125C23 on chr=12; Num_of_Contigs=4; )
TOE1		ENSSSCG00000003918	6:118925598-118929196		CU657926,CH242-123A1,6:118924192-118957983 (Clone quality: bE123A1 on chr=6; Num_of_Contigs=4; )
TOM1L1		ENSSSCG00000017601	12:28744823-28760307
TOMM20		ENSSSCG00000010158	14:57317608-57329790		CU407042,CH242-201M6,14:57298971-57336346 (Clone quality: bE201M6 on chr=14; Num_of_Contigs=3; )
TOMM20L		ENSSSCG00000005075	1:196470704-196481556		CU915422,CH242-435A1,1:196466510-196487429 (Clone quality: bE435A1 on chr=1; Num_of_Contigs=6; )
TOMM22		ENSSSCG00000000100	5:5675881-5677878
TOMM40		ENSSSCG00000003089	6:35898391-35907928		CU459172,CH242-480J10,6:35897337-35908067 (Clone quality: bE480J10 on chr=6; Num_of_Contigs=12; )
TOMM40L		ENSSSCG00000006354	4:92740196-92743622		CU606874,CH242-28G15,4:92698180-92745360 (Clone quality: bE28G15 on chr=4; Num_of_Contigs=6; )
TOMM5		ENSSSCG00000005351	1:249731048-249735205		CU442748,CH242-379J22,1:249648117-249741421 (Clone quality: bE379J22 on chr=1; Num_of_Contigs=5; )
TOMM7		ENSSSCG00000015384	9:85733813-85743034
TOMM70A		ENSSSCG00000011963	13:116458493-116482653
TOP1		ENSSSCG00000007355	17:45813399-45870871		CU062531,CH242-134J5,17:45795586-45881728 (Clone quality: bE134J5 on chr=17; Num_of_Contigs=2; )
TOP1		location ⇒	17:45872454-45871247		CU062531,CH242-134J5,17:45795586-45881728 (Clone quality: bE134J5 on chr=17; Num_of_Contigs=2; )
TOP1		location ⇒	17:45877993-45877877		CU062531,CH242-134J5,17:45795586-45881728 (Clone quality: bE134J5 on chr=17; Num_of_Contigs=2; )
TOP1		location ⇒	17:45880100-45879967		CU062531,CH242-134J5,17:45795586-45881728 (Clone quality: bE134J5 on chr=17; Num_of_Contigs=2; )
TOP1		location ⇒	17:45881588-45881304		CU062531,CH242-134J5,17:45795586-45881728 (Clone quality: bE134J5 on chr=17; 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, 1851-8

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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).