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)

SLC11A1		location ⇒	15:113574669-113574788		CU550681,CH242-392C2,15:113574174-113576620 (Clone quality: bE392C2 on chr=15; Num_of_Contigs=23; )
SLC11A24891		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
SLC12A1		ENSSSCG00000004659	1:128781933-128870974
SLC12A2		ENSSSCG00000014255	2:118727614-118817356
SLC12A4		location ⇒	17:50277211-50277319		CU407252,CH242-441N18,17:50275599-50277699 (Clone quality: bE441N18 on chr=17; Num_of_Contigs=7; )
SLC12A5		ENSSSCG00000007437	17:50254030-50287590
SLC12A6		ENSSSCG00000002243	7:88011136-88037300		CU407046,CH242-221M18,7:87977656-88060858 (Clone quality: bE221M18 on chr=7; Num_of_Contigs=3; )
SLC12A8		ENSSSCG00000011860	13:101661653-101678573		CU633365,CH242-203M21,13:101647226-101685321 (Clone quality: bE203M21 on chr=13; Num_of_Contigs=7; )
SLC13A1		ENSSSCG00000016609	18:22306552-22364907	CU457413,CH242-454C22,18:22286896-22481750 (Clone quality: bE454C22 on chr=18; Num_of_Contigs=3; )
SLC13A2		ENSSSCG00000017763	12:42546442-42567505
SLC13A3		ENSSSCG00000007449	17:50826218-50899885
SLC13A4		ENSSSCG00000016527	18:11960808-12001684		CU694894,CH242-34G1,18:11899902-12006322 (Clone quality: bE34G1 on chr=18; Num_of_Contigs=4; )
SLC13A5		ENSSSCG00000017888	12:47927418-47952186
SLC14A1		ENSSSCG00000004492	1:99161725-99183172
SLC14A2		ENSSSCG00000004491	1:99064230-99123148		CU467546,CH242-261D4,1:99033807-99138531 (Clone quality: bE261D4 on chr=1; Num_of_Contigs=4; )
SLC15A1		ENSSSCG00000009513	11:68619739-68654635
SLC15A1		location ⇒	11:68619885-68619576		CT962496,CH242-406G19,11:68613860-68629247 (Clone quality: bE406G19 on chr=11; Num_of_Contigs=3; )
SLC15A1		location ⇒	11:68620331-68619921		CT962496,CH242-406G19,11:68613860-68629247 (Clone quality: bE406G19 on chr=11; Num_of_Contigs=3; )
SLC15A1		location ⇒	11:68623792-68623646		CT962496,CH242-406G19,11:68613860-68629247 (Clone quality: bE406G19 on chr=11; Num_of_Contigs=3; )
SLC15A1		location ⇒	11:68633054-68632904		CT962496,CH242-406G19,11:68629348-68633305 (Clone quality: bE406G19 on chr=11; Num_of_Contigs=3; )
SLC15A2		ENSSSCG00000011879	13:104164595-104167897		CU694714,CH242-321J16,13:104162781-104205409 (Clone quality: bE321J16 on chr=13; Num_of_Contigs=1; )
SLC15A5		ENSSSCG00000000598	5:53856973-53925760
SLC16A1		ENSSSCG00000006769	4:111879347-111914029
SLC16A1		location ⇒	4:111911582-111912453		CU463248,CH242-400P6,4:111906000-111962256 (Clone quality: bE400P6 on chr=4; Num_of_Contigs=4; )
SLC16A1		location ⇒	4:111913623-111914138		CU463248,CH242-400P6,4:111906000-111962256 (Clone quality: bE400P6 on chr=4; Num_of_Contigs=4; )
SLC16A1		location ⇒	4:111914172-111915528		CU463248,CH242-400P6,4:111906000-111962256 (Clone quality: bE400P6 on chr=4; Num_of_Contigs=4; )
SLC16A1		location ⇒	4:112001131-112002001		CU463248,CH242-400P6,4:111962357-112002340 (Clone quality: bE400P6 on chr=4; Num_of_Contigs=4; )
SLC16A10		ENSSSCG00000004417	1:80652904-80667986		FP102400,CH242-288J22,1:80652287-80683720 (Clone quality: bE288J22 on chr=1; Num_of_Contigs=3; )
SLC16A11		ENSSSCG00000017925	12:49555132-49557519
SLC16A12		ENSSSCG00000010455	14:106177734-106268713
SLC16A13		ENSSSCG00000017926	12:49558540-49561985		CU914703,CH242-254H21,12:49555381-49564490 (Clone quality: bE254H21 on chr=12; Num_of_Contigs=9; )
SLC16A14		ENSSSCG00000016260	15:123490304-123491614		CU607086,CH242-147K21,15:123489499-123492358 (Clone quality: bE147K21 on chr=15; Num_of_Contigs=26; )
SLC16A2		ENSSSCG00000012418	X:58961778-58973445		CU856210,CH242-133C8,X:58941620-58992669 (Clone quality: bE133C8 on chr=X; Num_of_Contigs=8; )
SLC16A4		ENSSSCG00000006808	4:114204503-114214126		CU915404,CH242-292M23,4:114190001-114215484 (Clone quality: bE292M23 on chr=4; Num_of_Contigs=12; )
SLC16A5		ENSSSCG00000017215	12:4367895-4378941	CU928896,CH242-521B23,12:4294467-4388657 (Clone quality: bE521B23 on chr=12; Num_of_Contigs=4; )
SLC16A6		ENSSSCG00000017262	12:10144812-10153995
SLC16A7		ENSSSCG00000000456	5:23885870-24040302
SLC16A7		location ⇒	5:23985825-23986010		CU855554,CH242-111C21,5:23870416-24006402 (Clone quality: bE111C21 on chr=5; Num_of_Contigs=3; )
SLC16A7		location ⇒	5:24035700-24036209		CU694880,CH242-30O16,5:24027928-24090745 (Clone quality: bE30O16 on chr=5; Num_of_Contigs=3; )
SLC16A7		location ⇒	5:24040152-24040214		CU694880,CH242-30O16,5:24027928-24090745 (Clone quality: bE30O16 on chr=5; Num_of_Contigs=3; )
SLC16A7		location ⇒	5:24041546-24041643		CU694880,CH242-30O16,5:24027928-24090745 (Clone quality: bE30O16 on chr=5; Num_of_Contigs=3; )
SLC16A8		ENSSSCG00000000113	5:6357460-6359833		CU633351,CH242-161B9,5:6340838-6445691 (Clone quality: bE161B9 on chr=5; Num_of_Contigs=5; )
SLC16A9		ENSSSCG00000010210	14:65653558-65733698
SLC16A9		location ⇒	14:65653734-65653561		CU407028,CH242-160D19,14:65550168-65663306 (Clone quality: bE160D19 on chr=14; Num_of_Contigs=2; )
SLC16A9		location ⇒	14:65655350-65654429		CU407028,CH242-160D19,14:65550168-65663306 (Clone quality: bE160D19 on chr=14; Num_of_Contigs=2; )
SLC16A9		location ⇒	14:65674187-65674042		CU407028,CH242-160D19,14:65663407-65685359 (Clone quality: bE160D19 on chr=14; Num_of_Contigs=2; )
SLC16A9		location ⇒	14:65694832-65694630		CT954248,CH242-508D22,14:65685360-65905326 (Clone quality: bE508D22 on chr=14; Num_of_Contigs=1; )
SLC17A1		ENSSSCG00000001107	7:21752380-21769511		CU234127,CH242-38G11,7:21744013-21771050 (Clone quality: bE38G11 on chr=7; Num_of_Contigs=4; )
SLC17A2		ENSSSCG00000001109	7:21834099-21851446		CT797471,CH242-54M14,7:21795511-21989531 (Clone quality: bE54M14 on chr=7; Num_of_Contigs=1; )
SLC17A4		ENSSSCG00000001106	7:21679541-21701649		CU234127,CH242-38G11,7:21615284-21708972 (Clone quality: bE38G11 on chr=7; Num_of_Contigs=4; )

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).