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)

SOD2		location ⇒	1:8804402-8804560		CU469098,CH242-59I11,1:8788287-8824605 (Clone quality: bE59I11 on chr=1; Num_of_Contigs=7; )
SOD2		location ⇒	1:8804465-8804572		CU469098,CH242-59I11,1:8788287-8824605 (Clone quality: bE59I11 on chr=1; Num_of_Contigs=7; )
SOD2		location ⇒	1:8808395-8808513		CU469098,CH242-59I11,1:8788287-8824605 (Clone quality: bE59I11 on chr=1; Num_of_Contigs=7; )
SOD2		location ⇒	1:8811084-8811273		CU469098,CH242-59I11,1:8788287-8824605 (Clone quality: bE59I11 on chr=1; Num_of_Contigs=7; )
SOHLH1		ENSSSCG00000005755	1:289774862-289783047
SOLH		ENSSSCG00000007993	3:35585202-35590682
SOMA_PIG		ENSSSCG00000017284	12:12638816-12640578		CU466386,CH242-271O11,12:12583385-12667411 (Clone quality: bE271O11 on chr=12; Num_of_Contigs=5; )
SON		ENSSSCG00000008478	3:94348534-94428414
SON		ENSSSCG00000005015	1:188300616-188387560		CU222525,CH242-175F12,1:188296962-188466073 (Clone quality: bE175F12 on chr=1; Num_of_Contigs=2; )
SON		location ⇒	X:109532449-109532558		CU856459,CH242-124I21,X:109501603-109629045 (Clone quality: bE124I21 on chr=X; Num_of_Contigs=4; )
SORBS1		ENSSSCG00000010494	14:111954319-112193346
SORBS2		ENSSSCG00000015797	15:43835332-44063424
SORBS3		ENSSSCG00000009626	14:6800399-6823405		CU407060,CH242-266L24,14:6787841-6832287 (Clone quality: bE266L24 on chr=14; Num_of_Contigs=5; )
SORBS3		location ⇒	14:6772755-6772872		CU469154,CH242-352D1,14:6771458-6774601 (Clone quality: bE352D1 on chr=14; Num_of_Contigs=19; )
SORBS3		location ⇒	14:6813429-6813546		CU407060,CH242-266L24,14:6787841-6832287 (Clone quality: bE266L24 on chr=14; Num_of_Contigs=5; )
SORBS3		location ⇒	14:6816455-6816583		CU407060,CH242-266L24,14:6787841-6832287 (Clone quality: bE266L24 on chr=14; Num_of_Contigs=5; )
SORBS3		location ⇒	14:6818890-6819200		CU407060,CH242-266L24,14:6787841-6832287 (Clone quality: bE266L24 on chr=14; Num_of_Contigs=5; )
SORCS1		ENSSSCG00000010619	14:122880116-123070687
SORCS1		location ⇒	14:121142497-121142549		CT737219,CH242-200A4,14:121090948-121213736 (Clone quality: bE200A4 on chr=14; Num_of_Contigs=3; )
SORCS1		location ⇒	14:121226278-121226330		CU407070,CH242-35O23,14:121213737-121271069 (Clone quality: bE35O23 on chr=14; Num_of_Contigs=9; )
SORCS1		location ⇒	14:122976614-122976539		CT737278,CH242-98O21,14:122865820-123029244 (Clone quality: bE98O21 on chr=14; Num_of_Contigs=1; )
SORCS1		location ⇒	14:123026500-123026435		CT737278,CH242-98O21,14:122865820-123029244 (Clone quality: bE98O21 on chr=14; Num_of_Contigs=1; )
SORCS3		ENSSSCG00000010617	14:120867753-121567908
SORD		ENSSSCG00000004679	1:132446719-132488622		CU459107,CH242-257E14,1:132383826-132520076 (Clone quality: bE257E14 on chr=1; Num_of_Contigs=5; )
SORL1		ENSSSCG00000015135	9:47037892-47201737
SORL1		location ⇒	9:47037831-47038169		CU633338,CH242-137B6,9:47034976-47082437 (Clone quality: bE137B6 on chr=9; Num_of_Contigs=4; )
SORL1		location ⇒	9:47157656-47157728		CU657937,CH242-281N24,9:47144106-47166023 (Clone quality: bE281N24 on chr=9; Num_of_Contigs=7; )
SORL1		location ⇒	9:47197365-47197560		CU657937,CH242-281N24,9:47166124-47202736 (Clone quality: bE281N24 on chr=9; Num_of_Contigs=7; )
SORL1		location ⇒	9:47201288-47201471		CU657937,CH242-281N24,9:47166124-47202736 (Clone quality: bE281N24 on chr=9; Num_of_Contigs=7; )
SORT1		ENSSSCG00000006831	4:115237159-115296733
SOS1		ENSSSCG00000008478	3:94348534-94428414
SOS1		location ⇒	3:94311691-94311512		CU466236,CH242-378L13,3:94311512-94313789 (Clone quality: bE378L13 on chr=3; Num_of_Contigs=5; )
SOS1		location ⇒	3:94312969-94312851		CU466236,CH242-378L13,3:94311512-94313789 (Clone quality: bE378L13 on chr=3; Num_of_Contigs=5; )
SOS1		location ⇒	3:94426377-94426495		CU694750,CH242-7I2,3:94412909-94434877 (Clone quality: bE7I2 on chr=3; Num_of_Contigs=13; )
SOS1		location ⇒	3:94427655-94428407		CU694750,CH242-7I2,3:94412909-94434877 (Clone quality: bE7I2 on chr=3; Num_of_Contigs=13; )
SOS2		ENSSSCG00000005015	1:188300616-188387560		CU222525,CH242-175F12,1:188296962-188466073 (Clone quality: bE175F12 on chr=1; Num_of_Contigs=2; )
SOST		ENSSSCG00000017375	12:17267138-17270726		CU928405,CH242-149G4,12:17230645-17278372 (Clone quality: bE149G4 on chr=12; Num_of_Contigs=4; )
SOSTDC1		ENSSSCG00000015359	9:80325128-80328448		FP102811,CH242-114K4,9:80297527-80328713 (Clone quality: bE114K4 on chr=9; Num_of_Contigs=4; )
SOX-9		ENSSSCG00000017251	12:6867870-6871241		CU640384,CH242-191B18,12:6786606-6876182 (Clone quality: bE191B18 on chr=12; Num_of_Contigs=3; )
SOX-9		location ⇒	12:6868567-6868083		CU640384,CH242-191B18,12:6786606-6876182 (Clone quality: bE191B18 on chr=12; Num_of_Contigs=3; )
SOX-9		location ⇒	12:6869028-6868692		CU640384,CH242-191B18,12:6786606-6876182 (Clone quality: bE191B18 on chr=12; Num_of_Contigs=3; )
SOX-9		location ⇒	12:6869855-6869599		CU640384,CH242-191B18,12:6786606-6876182 (Clone quality: bE191B18 on chr=12; Num_of_Contigs=3; )
SOX-9		location ⇒	12:6871241-6870808		CU640384,CH242-191B18,12:6786606-6876182 (Clone quality: bE191B18 on chr=12; Num_of_Contigs=3; )
SOX10		ENSSSCG00000000115	5:6445847-6454909		CU633351,CH242-161B9,5:6445792-6484454 (Clone quality: bE161B9 on chr=5; Num_of_Contigs=5; )
SOX11		ENSSSCG00000008649	3:119329332-119330675		FP245498,CH242-225J21,3:119313496-119331167 (Clone quality: bE225J21 on chr=3; Num_of_Contigs=5; )
SOX13		ENSSSCG00000015277	9:62319503-62329823
SOX14		ENSSSCG00000011656	13:64511819-64513028		CU855979,CH242-160B6,13:64453320-64527230 (Clone quality: bE160B6 on chr=13; Num_of_Contigs=5; )
SOX15		ENSSSCG00000017954	12:50053561-50055104	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
SOX2		ENSSSCG00000011771	13:90903394-90904353		CU928395,CH242-293K9,13:90898567-90935948 (Clone quality: bE293K9 on chr=13; Num_of_Contigs=4; )
SOX21		ENSSSCG00000009494	11:64351425-64352255		CU633813,CH242-267B4,11:64350806-64353090 (Clone quality: bE267B4 on chr=11; Num_of_Contigs=16; )

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).