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)

TCRDV3.1		location ⇒	7:83051605-83051311		CU468882,CH242-63B2,7:83001624-83076399 (Clone quality: bE63B2 on chr=7; Num_of_Contigs=5; )
TCRDV3.1		location ⇒	7:83051911-83051790		CU468882,CH242-63B2,7:83001624-83076399 (Clone quality: bE63B2 on chr=7; Num_of_Contigs=5; )
TCRDV3.1		location ⇒	7:83179301-83179007		CU571294,CH242-414N2,7:83105900-83181462 (Clone quality: bE414N2 on chr=7; Num_of_Contigs=4; )
TCRDV3.1		location ⇒	7:83179607-83179486		CU571294,CH242-414N2,7:83105900-83181462 (Clone quality: bE414N2 on chr=7; Num_of_Contigs=4; )
TCRDV4		location ⇒	7:82911459-82911163		CU468882,CH242-63B2,7:82906348-82953449 (Clone quality: bE63B2 on chr=7; Num_of_Contigs=5; )
TCRDV5.1		location ⇒	7:82760857-82760807		CU469449,CH242-94J9,7:82757638-82766225 (Clone quality: bE94J9 on chr=7; Num_of_Contigs=2; )
TCRVB12		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
TCRVB4		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
TCRVB5		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
TCRVB7		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
TCTE1		ENSSSCG00000001705	7:45798260-45821014	CT009542,CH242-272H8,7:45714746-45890644 (Clone quality: bE272H8 on chr=7; Num_of_Contigs=13; )
TCTE3		ENSSSCG00000004009	1:440195-666100
TCTEL1		location ⇒	1:9618333-9618267		CU498836,CH242-100E21,1:9618267-9651855 (Clone quality: bE100E21 on chr=1; Num_of_Contigs=11; )
TCTEL1		location ⇒	1:9618693-9618614		CU498836,CH242-100E21,1:9618267-9651855 (Clone quality: bE100E21 on chr=1; Num_of_Contigs=11; )
TCTEL1		location ⇒	1:9619150-9619025		CU498836,CH242-100E21,1:9618267-9651855 (Clone quality: bE100E21 on chr=1; Num_of_Contigs=11; )
TCTEL1		location ⇒	1:9622111-9622067		CU498836,CH242-100E21,1:9618267-9651855 (Clone quality: bE100E21 on chr=1; Num_of_Contigs=11; )
TCTEX1D4		ENSSSCG00000003927	6:119349673-119351182		CU928738,CH242-6J15,6:119339955-119396828 (Clone quality: bE6J15 on chr=6; Num_of_Contigs=6; )
TCTN1		ENSSSCG00000009826	14:32003878-32034906		CT737176,CH242-22G23,14:31959545-32075293 (Clone quality: bE22G23 on chr=14; Num_of_Contigs=3; )
TCTN2		ENSSSCG00000009768	14:29413023-29443364		CU468658,CH242-245F7,14:29355652-29557150 (Clone quality: bE245F7 on chr=14; Num_of_Contigs=1; )
TCTN3		ENSSSCG00000010496	14:112287720-112319413		CT737262,CH242-169I8,14:112174454-112352511 (Clone quality: bE169I8 on chr=14; Num_of_Contigs=1; )
TCTP		ENSSSCG00000000207	5:14445093-14445604		CU633424,CH242-4O24,5:14435312-14464184 (Clone quality: bE4O24 on chr=5; Num_of_Contigs=4; )
TCTP		ENSSSCG00000000622	5:57210433-57210965		CU459114,CH242-375L4,5:57201915-57248947 (Clone quality: bE375L4 on chr=5; Num_of_Contigs=4; )
TCTP		location ⇒	5:14445696-14444929		CU633424,CH242-4O24,5:14435312-14464184 (Clone quality: bE4O24 on chr=5; Num_of_Contigs=4; )
TCTP		location ⇒	5:57210374-57211091		CU459114,CH242-375L4,5:57201915-57248947 (Clone quality: bE375L4 on chr=5; Num_of_Contigs=4; )
TDG		ENSSSCG00000000847	5:75576905-75594208		CU457468,CH242-236A7,5:75565013-75608068 (Clone quality: bE236A7 on chr=5; Num_of_Contigs=7; )
TDO2		ENSSSCG00000008868	8:38730384-38747596		CU855637,CH242-199L13,8:38712595-38842897 (Clone quality: bE199L13 on chr=8; Num_of_Contigs=2; )
TDP1		ENSSSCG00000002431	7:119621566-119707343
TDRD10		ENSSSCG00000006546	4:99298295-99351527	CU469085,CH242-42I4,4:99200352-99380372 (Clone quality: bE42I4 on chr=4; Num_of_Contigs=1; )
TDRD12		ENSSSCG00000002857	6:28400165-28427876
TDRD3		ENSSSCG00000009449	11:32057724-32161615
TDRD5		ENSSSCG00000015527	9:113648574-113801096
TDRD6		ENSSSCG00000001721	7:48872778-48873380		CU607063,CH242-261A14,7:48866108-48898664 (Clone quality: bE261A14 on chr=7; Num_of_Contigs=10; )
TDRD7		ENSSSCG00000005364	1:250807805-250875573		CU407125,CH242-372M9,1:250708340-250913158 (Clone quality: bE372M9 on chr=1; Num_of_Contigs=1; )
TDRD9		ENSSSCG00000002552	7:133006420-133086612
TEAD1		ENSSSCG00000013399	2:43216440-43252882
TEAD3		location ⇒	7:35862132-35862069		CU571051,CH242-525J6,7:35852280-35867399 (Clone quality: bE525J6 on chr=7; Num_of_Contigs=14; )
TEAD3		location ⇒	7:35927363-35927300		CU467978,CH242-397F5,7:35872400-35952461 (Clone quality: bE397F5 on chr=7; Num_of_Contigs=4; )
TEAD3		location ⇒	7:35938819-35938563		CU467978,CH242-397F5,7:35872400-35952461 (Clone quality: bE397F5 on chr=7; Num_of_Contigs=4; )
TEAD3		location ⇒	7:36014908-36014751		CU424481,CH242-125B19,7:36010211-36015288 (Clone quality: bE125B19 on chr=7; Num_of_Contigs=28; )
TEAD4		ENSSSCG00000000736	5:63007626-63070628
TEC		ENSSSCG00000008820	8:32570872-32701620
TEC		location ⇒	8:32571546-32570925		FP016039,CH242-161I20,8:32560945-32628146 (Clone quality: bE161I20 on chr=8; Num_of_Contigs=4; )
TEC		location ⇒	8:32573351-32573193		FP016039,CH242-161I20,8:32560945-32628146 (Clone quality: bE161I20 on chr=8; Num_of_Contigs=4; )
TEC		location ⇒	8:32573540-32573445		FP016039,CH242-161I20,8:32560945-32628146 (Clone quality: bE161I20 on chr=8; Num_of_Contigs=4; )
TECPR1		ENSSSCG00000007601	3:4623551-4646491
TECPR2		ENSSSCG00000002528	7:131310827-131575430
TECR		ENSSSCG00000013780	2:57264339-57266343		FP103015,CH242-135B13,2:57262602-57266612 (Clone quality: bE135B13 on chr=2; Num_of_Contigs=14; )
TECTA		ENSSSCG00000015132	9:46681929-46874964
TECTB		ENSSSCG00000010632	14:128281910-128300508	CT737200,CH242-13L11,14:128170000-128387926 (Clone quality: bE13L11 on chr=14; Num_of_Contigs=1; )
TEDDM1		ENSSSCG00000015546	9:116127003-116127779		CU855743,CH242-470F20,9:116099941-116165911 (Clone quality: bE470F20 on chr=9; Num_of_Contigs=8; )

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).