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)

SLC38A11		ENSSSCG00000015903	15:66699517-66805310
SLC38A5		ENSSSCG00000011397	13:27284676-27360380
SLC38A6		ENSSSCG00000005092	1:198767132-198997120
SLC38A7		ENSSSCG00000002798	6:19161086-19167134		FP103045,CH242-261E8,6:19158775-19167395 (Clone quality: bE261E8 on chr=6; Num_of_Contigs=12; )
SLC38A8		ENSSSCG00000002683	6:3147432-3158701
SLC38A9		ENSSSCG00000016914	16:32502823-32524980
SLC39A1		ENSSSCG00000006561	4:99770504-99961017
SLC39A11		ENSSSCG00000017250	12:5949691-6369897
SLC39A12		ENSSSCG00000011039	10:42402676-42482357		CU466345,CH242-21O2,10:42375729-42509794 (Clone quality: bE21O2 on chr=10; Num_of_Contigs=6; )
SLC39A13		ENSSSCG00000013238	2:13279591-13287617		CU856312,CH242-38I7,2:13257671-13307229 (Clone quality: bE38I7 on chr=2; Num_of_Contigs=10; )
SLC39A14		ENSSSCG00000009623	14:6592445-6636672
SLC39A3		ENSSSCG00000013466	2:47374804-47378801		CU972376,CH242-107L7,2:47367584-47461889 (Clone quality: bE107L7 on chr=2; Num_of_Contigs=6; )
SLC39A5		ENSSSCG00000000385	5:20553964-20559810
SLC39A5		location ⇒	5:20555248-20555538		CU694915,CH242-453C18,5:20555037-20579943 (Clone quality: bE453C18 on chr=5; Num_of_Contigs=10; )
SLC39A5		location ⇒	5:20559099-20559290		CU694915,CH242-453C18,5:20555037-20579943 (Clone quality: bE453C18 on chr=5; Num_of_Contigs=10; )
SLC39A5		location ⇒	5:20661399-20661208		CU498845,CH242-111P13,5:20651482-20663322 (Clone quality: bE111P13 on chr=5; Num_of_Contigs=18; )
SLC39A5		location ⇒	5:20663322-20663222		CU498845,CH242-111P13,5:20651482-20663322 (Clone quality: bE111P13 on chr=5; Num_of_Contigs=18; )
SLC39A7		ENSSSCG00000001475	7:29618573-29623114	CT737383,CH242-215D15,7:29573904-29764538 (Clone quality: bE215D15 on chr=7; Num_of_Contigs=3; )
SLC39A8		ENSSSCG00000009169	8:101810629-101881059
SLC39A9		ENSSSCG00000002308	7:101480589-101534040
SLC41A2		ENSSSCG00000000838	5:74641792-74753405
SLC41A3		ENSSSCG00000001825	7:59213778-59236583	CT868688,CH242-510G16,7:59026976-59242142 (Clone quality: bE510G16 on chr=7; Num_of_Contigs=3; )
SLC44A1		ENSSSCG00000005425	1:258582618-258743259
SLC44A2		ENSSSCG00000013639	2:52870113-52884576		CU993813,CH242-86K24,2:52867551-52887632 (Clone quality: bE86K24 on chr=2; Num_of_Contigs=13; )
SLC44A3		ENSSSCG00000006888	4:127222668-127250529		CU639441,CH242-134D14,4:127222495-127252056 (Clone quality: bE134D14 on chr=4; Num_of_Contigs=7; )
SLC44A4		ENSSSCG00000001419	7:27780863-27799469	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
SLC44A5		ENSSSCG00000003777	6:96184582-96587176
SLC45A1		ENSSSCG00000003388	6:46557968-46567233
SLC45A2		ENSSSCG00000016821	16:17474432-17515063
SLC45A4		ENSSSCG00000005930	4:1504395-1512140		CU407190,CH242-272D18,4:1451678-1513192 (Clone quality: bE272D18 on chr=4; Num_of_Contigs=7; )
SLC46A2		ENSSSCG00000005472	1:266470013-266480023		CU041260,CH242-55A14,1:266438281-266562122 (Clone quality: bE55A14 on chr=1; Num_of_Contigs=9; )
SLC46A3		ENSSSCG00000009322	11:5500231-5512141
SLC47A2		ENSSSCG00000018042	12:56543310-56558075		FP003595,CH242-47E22,12:56532412-56616940 (Clone quality: bE47E22 on chr=12; Num_of_Contigs=5; )
SLC4A1		ENSSSCG00000017358	12:16859433-16871908		CU468984,CH242-216D12,12:16857125-16875764 (Clone quality: bE216D12 on chr=12; Num_of_Contigs=22; )
SLC4A1		location ⇒	12:16859899-16859842		CU468984,CH242-216D12,12:16857125-16875764 (Clone quality: bE216D12 on chr=12; Num_of_Contigs=22; )
SLC4A1		location ⇒	12:16860633-16860456		CU468984,CH242-216D12,12:16857125-16875764 (Clone quality: bE216D12 on chr=12; Num_of_Contigs=22; )
SLC4A1		location ⇒	12:16860896-16860724		CU468984,CH242-216D12,12:16857125-16875764 (Clone quality: bE216D12 on chr=12; Num_of_Contigs=22; )
SLC4A1		location ⇒	12:16862502-16862279		CU468984,CH242-216D12,12:16857125-16875764 (Clone quality: bE216D12 on chr=12; Num_of_Contigs=22; )
SLC4A10		ENSSSCG00000015893	15:63699776-63849448
SLC4A11		ENSSSCG00000007157	17:34036888-34039016		CU468064,CH242-324C22,17:34036789-34040301 (Clone quality: bE324C22 on chr=17; Num_of_Contigs=12; )
SLC4A1AP		ENSSSCG00000008549	3:104219266-104246958
SLC4A4		ENSSSCG00000008943	8:57822775-57933935
SLC4A7		ENSSSCG00000011218	13:11801566-11867043		CU914223,CH242-127D6,13:11796471-11874648 (Clone quality: bE127D6 on chr=13; Num_of_Contigs=9; )
Slc4a8		location ⇒	5:15598166-15598245		CU856685,CH242-158H5,5:15580149-15608044 (Clone quality: bE158H5 on chr=5; Num_of_Contigs=11; )
Slc4a8		location ⇒	5:15612965-15613017		CU914420,CH242-302G7,5:15608045-15615764 (Clone quality: bE302G7 on chr=5; Num_of_Contigs=10; )
Slc4a8		location ⇒	5:15760353-15760299		CU914420,CH242-302G7,5:15752758-15768307 (Clone quality: bE302G7 on chr=5; Num_of_Contigs=10; )
Slc4a8		location ⇒	5:15764177-15763924		CU914420,CH242-302G7,5:15752758-15768307 (Clone quality: bE302G7 on chr=5; Num_of_Contigs=10; )
SLC4A9		ENSSSCG00000014363	2:129139579-129148110		CU466537,CH242-391J6,2:129139556-129188804 (Clone quality: bE391J6 on chr=2; Num_of_Contigs=9; )
SLC5A10		ENSSSCG00000018048	12:56737097-56752276		FP074851,CH242-203F20,12:56719312-56755196 (Clone quality: bE203F20 on chr=12; Num_of_Contigs=16; )
SLC5A11		ENSSSCG00000007828	3:20063518-20068150		FP236382,CH242-23G12,3:20061719-20069971 (Clone quality: bE23G12 on chr=3; Num_of_Contigs=30; )

Go to records:
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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).