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)

TLR10		location ⇒	8:44501-44388		FP102972,CH242-47L5,8:43508-48739 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
TLR10		location ⇒	8:7304-7417		FP102972,CH242-47L5,8:6630-11538 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
TLR10		location ⇒	8:7417-7304		FP102972,CH242-47L5,8:6630-11538 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
TLR11		location ⇒	13:18909988-18910127		CU464076,CH242-481B9,13:18898351-18944492 (Clone quality: bE481B9 on chr=13; Num_of_Contigs=5; )
TLR11		location ⇒	13:18910343-18910426		CU464076,CH242-481B9,13:18898351-18944492 (Clone quality: bE481B9 on chr=13; Num_of_Contigs=5; )
TLR11		location ⇒	13:18910694-18910851		CU464076,CH242-481B9,13:18898351-18944492 (Clone quality: bE481B9 on chr=13; Num_of_Contigs=5; )
TLR2		ENSSSCG00000009002	8:64387243-64397290		FP086612,CH242-215B19,8:64380629-64492930 (Clone quality: bE215B19 on chr=8; Num_of_Contigs=1; )
TLR2		location ⇒	8:64394727-64397279		FP086612,CH242-215B19,8:64380629-64492930 (Clone quality: bE215B19 on chr=8; Num_of_Contigs=1; )
TLR2		location ⇒	8:64394727-64397279		FP086612,CH242-215B19,8:64380629-64492930 (Clone quality: bE215B19 on chr=8; Num_of_Contigs=1; )
TLR2		location ⇒	8:64671614-64669063		FP089697,CH242-452I24,8:64641403-64678489 (Clone quality: bE452I24 on chr=8; Num_of_Contigs=5; )
TLR2		location ⇒	8:64671614-64669063		FP089697,CH242-452I24,8:64641403-64678489 (Clone quality: bE452I24 on chr=8; Num_of_Contigs=5; )
TLR3		ENSSSCG00000015801	15:44284517-44293098
TLR3		location ⇒	15:44281752-44281805		CU466336,CH242-451P14,15:44280501-44284753 (Clone quality: bE451P14 on chr=15; Num_of_Contigs=7; )
TLR3		location ⇒	15:44284507-44284753
TLR3		location ⇒	15:44290786-44292640		CU466336,CH242-451P14,15:44284854-44301107 (Clone quality: bE451P14 on chr=15; Num_of_Contigs=7; )
TLR3		location ⇒	15:44292868-44293268		CU466336,CH242-451P14,15:44284854-44301107 (Clone quality: bE451P14 on chr=15; Num_of_Contigs=7; )
TLR4		ENSSSCG00000005503	1:271621935-271631702	CR938718,CH242-2F11,1:271517643-271688227 (No clone quality info on bE2F11)
TLR4		location ⇒	1:150748011-150747896		CU074324,CH242-154G8,1:150701054-150778730 (Clone quality: bE154G8 on chr=1; Num_of_Contigs=13; )
TLR4		location ⇒	1:150844432-150844317		CU466499,CH242-508L4,1:150835536-150848679 (Clone quality: bE508L4 on chr=1; Num_of_Contigs=19; )
TLR4		location ⇒	1:266030421-266030317		CU468167,CH242-273J14,1:266015765-266032580 (Clone quality: bE273J14 on chr=1; Num_of_Contigs=10; )
TLR4		location ⇒	1:72445195-72445272		CU210895,CH242-184D2,1:72353057-72524232 (Clone quality: bE184D2 on chr=1; Num_of_Contigs=1; )
TLR5		location ⇒	10:18905151-18905646		CU914644,CH242-234J22,10:18890404-18921255 (Clone quality: bE234J22 on chr=10; Num_of_Contigs=14; )
TLR6		location ⇒	8:25567055-25569443		FP089508,CH242-63B6,8:25543927-25603877 (Clone quality: bE63B6 on chr=8; Num_of_Contigs=4; )
TLR6		location ⇒	8:25582668-25583699		FP089508,CH242-63B6,8:25543927-25603877 (Clone quality: bE63B6 on chr=8; Num_of_Contigs=4; )
TLR6		location ⇒	8:25709987-25708956		CU694791,CH242-295G5,8:25655285-25835574 (Clone quality: bE295G5 on chr=8; Num_of_Contigs=1; )
TLR6		location ⇒	8:25725600-25723212		CU694791,CH242-295G5,8:25655285-25835574 (Clone quality: bE295G5 on chr=8; Num_of_Contigs=1; )
TLR7		ENSSSCG00000012117	X:8503790-8529729
TLR7		location ⇒	X:8504219-8504326		FP236647,CH242-248C8,X:8407987-8522808 (Clone quality: bE248C8 on chr=X; Num_of_Contigs=1; )
TLR7		location ⇒	X:8525987-8529570	FP102063,CH242-76E20,X:8522809-8545557 (Clone quality: bE76E20 on chr=X; Num_of_Contigs=2; )
TLR8		ENSSSCG00000012118	X:8553177-8729326
TLR8		location ⇒	X:8553189-8553362	FP102063,CH242-76E20,X:8545658-8722254 (Clone quality: bE76E20 on chr=X; Num_of_Contigs=2; )
TLR8		location ⇒	X:8556063-8556185	FP102063,CH242-76E20,X:8545658-8722254 (Clone quality: bE76E20 on chr=X; Num_of_Contigs=2; )
TLR8		location ⇒	X:8562105-8565252	FP102063,CH242-76E20,X:8545658-8722254 (Clone quality: bE76E20 on chr=X; Num_of_Contigs=2; )
TLR8		location ⇒	X:8726177-8729324	FP085461,CH242-524I24,X:8722255-8912483 (Clone quality: bE524I24 on chr=X; Num_of_Contigs=2; )
TLR9		ENSSSCG00000011436	13:29049282-29052128		CU915558,CH242-407L22,13:29047015-29052186 (Clone quality: bE407L22 on chr=13; Num_of_Contigs=4; )
TLR9		location ⇒	13:28826746-28824365		CU914695,CH242-195P19,13:28772257-28826761 (Clone quality: bE195P19 on chr=13; Num_of_Contigs=14; )
TLR9		location ⇒	13:28832867-28832924		CU914695,CH242-195P19,13:28830492-28833577 (Clone quality: bE195P19 on chr=13; Num_of_Contigs=14; )
TLR9		location ⇒	13:29049281-29052165		CU915558,CH242-407L22,13:29047015-29052186 (Clone quality: bE407L22 on chr=13; Num_of_Contigs=4; )
TLR9		location ⇒	13:29052287-29052461
TLX		ENSSSCG00000004384	1:77851596-77871232		CU469092,CH242-73E11,1:77831921-77891718 (Clone quality: bE73E11 on chr=1; Num_of_Contigs=6; )
TLX1		ENSSSCG00000010561	14:117047982-117050934
TLX1		location ⇒	16:49904760-49904672		CU915526,CH242-84K24,16:49903103-49905970 (Clone quality: bE84K24 on chr=16; Num_of_Contigs=2; )
TLX1		location ⇒	16:49905864-49905632		CU915526,CH242-84K24,16:49903103-49905970 (Clone quality: bE84K24 on chr=16; Num_of_Contigs=2; )
TLX3		ENSSSCG00000016999	16:49904552-49905865		CU915526,CH242-84K24,16:49903103-49905970 (Clone quality: bE84K24 on chr=16; Num_of_Contigs=2; )
TM2D1		ENSSSCG00000003822	6:106603924-106610430		FP015935,CH242-309J8,6:106595699-106612331 (Clone quality: bE309J8 on chr=6; Num_of_Contigs=4; )
TM2D2		ENSSSCG00000015809	15:44964565-44971596		CU469515,CH242-238L24,15:44884786-44988021 (Clone quality: bE238L24 on chr=15; Num_of_Contigs=5; )
TM2D3		ENSSSCG00000005782	1:291920369-291931818		CU914575,CH242-143N16,1:291876315-291952153 (Clone quality: bE143N16 on chr=1; Num_of_Contigs=3; )
TM4SF1		ENSSSCG00000011702	13:72908421-72915617
TM4SF18		ENSSSCG00000011701	13:72829511-73033820
TM4SF2		location ⇒	X:34084345-34084534		FP102385,CH242-81B3,X:34005128-34178208 (Clone quality: bE81B3 on chr=X; 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).