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)

SLA-9*		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-9*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-9*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-DMA		ENSSSCG00000001470	7:29509208-29513680	CU618315,CH242-254M4,7:29473579-29573903 (Clone quality: bE254M4 on chr=7; Num_of_Contigs=1; )
SLA-DMB		ENSSSCG00000001469	7:29494987-29500822	CU618315,CH242-254M4,7:29473579-29573903 (Clone quality: bE254M4 on chr=7; Num_of_Contigs=1; )
SLA-DOA		ENSSSCG00000001470	7:29509208-29513680	CU618315,CH242-254M4,7:29473579-29573903 (Clone quality: bE254M4 on chr=7; Num_of_Contigs=1; )
SLA-DOB		ENSSSCG00000001459	7:29301032-29308499	CU633196,CH242-203E5,7:29272940-29352095 (Clone quality: bE203E5 on chr=7; Num_of_Contigs=1; )
SLA-DQA		ENSSSCG00000001456	7:29224054-29229751	CU468849,CH242-213K14,7:29079506-29272939 (Clone quality: bE213K14 on chr=7; Num_of_Contigs=6; )
SLA-DQA1		ENSSSCG00000001456	7:29224054-29229751	CU468849,CH242-213K14,7:29079506-29272939 (Clone quality: bE213K14 on chr=7; Num_of_Contigs=6; )
SLA-DQB		ENSSSCG00000001457	7:29239625-29247871	CU468849,CH242-213K14,7:29079506-29272939 (Clone quality: bE213K14 on chr=7; Num_of_Contigs=6; )
SLA-DQB1		ENSSSCG00000001457	7:29239625-29247871	CU468849,CH242-213K14,7:29079506-29272939 (Clone quality: bE213K14 on chr=7; Num_of_Contigs=6; )
SLA-DRA		ENSSSCG00000001453	7:29095605-29101239	CU468849,CH242-213K14,7:29079506-29272939 (Clone quality: bE213K14 on chr=7; Num_of_Contigs=6; )
SLA-DRB		ENSSSCG00000001455	7:29171940-29184604	CU468849,CH242-213K14,7:29079506-29272939 (Clone quality: bE213K14 on chr=7; Num_of_Contigs=6; )
SLA-DRB1		ENSSSCG00000001455	7:29171940-29184604	CU468849,CH242-213K14,7:29079506-29272939 (Clone quality: bE213K14 on chr=7; Num_of_Contigs=6; )
SLA-DRB2		ENSSSCG00000001454	7:29153061-29164786	CU468849,CH242-213K14,7:29079506-29272939 (Clone quality: bE213K14 on chr=7; Num_of_Contigs=6; )
SLA-DRB2p		location ⇒	7:4236-4317		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-DRB2p		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-DRB2p		location ⇒	7:4758-4669		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-DRB2p		location ⇒	7:4758-4669		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA2		ENSSSCG00000007321	17:42164310-42187808		CU607085,CH242-137E1,17:42127348-42190090 (Clone quality: bE137E1 on chr=17; Num_of_Contigs=8; )
SLAIN2		ENSSSCG00000008821	8:32756226-32801534
SLAMF1		ENSSSCG00000006380	4:93320018-93356552		CU915315,CH242-208F9,4:93261946-93408226 (Clone quality: bE208F9 on chr=4; Num_of_Contigs=2; )
SLAMF2		ENSSSCG00000006379	4:93278346-93292708		CU915315,CH242-208F9,4:93261946-93408226 (Clone quality: bE208F9 on chr=4; Num_of_Contigs=2; )
SLAMF5		ENSSSCG00000006381	4:93381789-93570006
SLAMF6		ENSSSCG00000006382	4:93428233-93449121
SLAMF6		location ⇒	4:93428233-93428352		CU179691,CH242-251N5,4:93408227-93431947 (Clone quality: bE251N5 on chr=4; Num_of_Contigs=5; )
SLAMF6		location ⇒	4:93440192-93440525		CU179691,CH242-251N5,4:93432048-93490887 (Clone quality: bE251N5 on chr=4; Num_of_Contigs=5; )
SLAMF6		location ⇒	4:93443807-93443987		CU179691,CH242-251N5,4:93432048-93490887 (Clone quality: bE251N5 on chr=4; Num_of_Contigs=5; )
SLAMF7		ENSSSCG00000006378	4:93220455-93235041		CU606866,CH242-143J3,4:93072841-93235164 (Clone quality: bE143J3 on chr=4; Num_of_Contigs=1; )
SLAMF7		location ⇒	4:93224125-93224003		CU606866,CH242-143J3,4:93072841-93235164 (Clone quality: bE143J3 on chr=4; Num_of_Contigs=1; )
SLAMF7		location ⇒	4:93224620-93224345		CU606866,CH242-143J3,4:93072841-93235164 (Clone quality: bE143J3 on chr=4; Num_of_Contigs=1; )
SLAMF7		location ⇒	4:93226189-93225854		CU606866,CH242-143J3,4:93072841-93235164 (Clone quality: bE143J3 on chr=4; Num_of_Contigs=1; )
SLAMF7		location ⇒	4:93235041-93234964		CU606866,CH242-143J3,4:93072841-93235164 (Clone quality: bE143J3 on chr=4; Num_of_Contigs=1; )
SLAMF8		ENSSSCG00000006398	4:93983680-93994246		CU856127,CH242-86L20,4:93963235-94027316 (Clone quality: bE86L20 on chr=4; Num_of_Contigs=6; )
SLAMF8		location ⇒	4:1418879-1418996		CU693396,CH242-210M8,4:1338713-1440792 (Clone quality: bE210M8 on chr=4; Num_of_Contigs=7; )
SLAMF8		location ⇒	4:2979173-2979068		CU861599,CH242-1G3,4:2882085-3037908 (Clone quality: bE1G3 on chr=4; Num_of_Contigs=2; )
SLAMF8		location ⇒	4:5243864-5243996		CU695055,CH242-299K20,4:5241024-5272605 (Clone quality: bE299K20 on chr=4; Num_of_Contigs=6; )
SLAMF8		location ⇒	4:6105460-6105565		CU210909,CH242-479D18,4:6073872-6124287 (Clone quality: bE479D18 on chr=4; Num_of_Contigs=17; )
SLAMF9		ENSSSCG00000006400	4:94052098-94054645		CU856127,CH242-86L20,4:94027417-94074463 (Clone quality: bE86L20 on chr=4; Num_of_Contigs=6; )
SLAMF9		location ⇒	4:94052111-94052253		CU856127,CH242-86L20,4:94027417-94074463 (Clone quality: bE86L20 on chr=4; Num_of_Contigs=6; )
SLAMF9		location ⇒	4:94052691-94053035		CU856127,CH242-86L20,4:94027417-94074463 (Clone quality: bE86L20 on chr=4; Num_of_Contigs=6; )
SLAMF9		location ⇒	4:94053819-94054098		CU856127,CH242-86L20,4:94027417-94074463 (Clone quality: bE86L20 on chr=4; Num_of_Contigs=6; )
SLBP		ENSSSCG00000008676	8:168043-178763		FP102127,CH242-261D5,8:164622-185326 (Clone quality: bE261D5 on chr=8; Num_of_Contigs=8; )
SLC10A1		ENSSSCG00000002313	7:101797444-101817645	CT737423,CH242-28F9,7:101687301-101874212 (Clone quality: bE28F9 on chr=7; Num_of_Contigs=2; )
SLC10A4		ENSSSCG00000008823	8:32894761-32897840
SLC10A7		ENSSSCG00000009035	8:70855254-71049217
SLC11A1		ENSSSCG00000016190	15:113574179-113574788		CU550681,CH242-392C2,15:113574174-113576620 (Clone quality: bE392C2 on chr=15; Num_of_Contigs=23; )
SLC11A1		location ⇒	15:113573142-113573200		CU550681,CH242-392C2,15:113569015-113574073 (Clone quality: bE392C2 on chr=15; Num_of_Contigs=23; )
SLC11A1		location ⇒	15:113573302-113573863		CU550681,CH242-392C2,15:113569015-113574073 (Clone quality: bE392C2 on chr=15; Num_of_Contigs=23; )
SLC11A1		location ⇒	15:113574235-113574358		CU550681,CH242-392C2,15:113574174-113576620 (Clone quality: bE392C2 on chr=15; Num_of_Contigs=23; )

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, 2601-16

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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).