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)

SEMA6D		ENSSSCG00000004663	1:129294663-129346064
SEMA7A		location ⇒	13:27406896-27406923		CU468071,CH242-427D1,13:27397872-27424038 (Clone quality: bE427D1 on chr=13; Num_of_Contigs=7; )
SENP1		ENSSSCG00000000816	5:73700816-73746157
SENP2		ENSSSCG00000011794	13:93417739-93455241
SENP3		ENSSSCG00000017958	12:50070390-50071993	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
SENP3		location ⇒	12:50071470-50071419	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
SENP3		location ⇒	12:50071670-50071585	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
SENP3		location ⇒	12:50071991-50071854	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
SENP5		ENSSSCG00000011841	13:100446380-100498924
SENP6		location ⇒	1:95220209-95220117		CU076095,CH242-35C20,1:95175376-95222006 (Clone quality: bE35C20 on chr=1; Num_of_Contigs=6; )
SENP6		location ⇒	1:95230669-95230724		CU076095,CH242-35C20,1:95223972-95249018 (Clone quality: bE35C20 on chr=1; Num_of_Contigs=6; )
SENP6		location ⇒	1:95270068-95269996		CU062587,CH242-59G16,1:95255721-95276676 (Clone quality: bE59G16 on chr=1; Num_of_Contigs=5; )
SENP6		location ⇒	1:95299274-95299219		CU062587,CH242-59G16,1:95276777-95331572 (Clone quality: bE59G16 on chr=1; Num_of_Contigs=5; )
SEPHS1		ENSSSCG00000015704	15:16228120-16229541		FP085441,CH242-167G2,15:16191472-16269000 (Clone quality: bE167G2 on chr=15; Num_of_Contigs=4; )
SEPHS2		ENSSSCG00000007795	3:16468561-16469553		CU928725,CH242-25P12,3:16465919-16471589 (Clone quality: bE25P12 on chr=3; Num_of_Contigs=8; )
SEPN1		ENSSSCG00000003554	6:57441970-57446196		CU457419,CH242-59A10,6:57441576-57446992 (Clone quality: bE59A10 on chr=6; Num_of_Contigs=10; )
SEPT1		ENSSSCG00000007800	3:16564317-16577660		CU928725,CH242-25P12,3:16542593-16582945 (Clone quality: bE25P12 on chr=3; Num_of_Contigs=8; )
SEPT11		ENSSSCG00000008986	8:62038051-62129100
SEPT12		ENSSSCG00000007933	3:33639567-33650324
SEPT14		ENSSSCG00000007751	3:15520771-15556962
SEPT2		ENSSSCG00000016370	15:131877142-131900710
SEPT3		ENSSSCG00000000040	5:2913843-2935092	BX296515,PigE-121D21,5:2907737-3087427 (Clone quality: bT121D21 on chr=5; Num_of_Contigs=8; )
SEPT4		ENSSSCG00000017643	12:32791235-32803524
SEPT6		ENSSSCG00000012619	X:96520019-96589576
SEPT7		ENSSSCG00000016661	18:37357791-37458294
SEPT8		ENSSSCG00000014285	2:122988354-123014360	CU468216,CH242-85C7,2:122831928-123020434 (Clone quality: bE85C7 on chr=2; Num_of_Contigs=1; )
SEPT8		location ⇒	2:122992843-122992785	CU468216,CH242-85C7,2:122831928-123020434 (Clone quality: bE85C7 on chr=2; Num_of_Contigs=1; )
SEPT8		location ⇒	2:122995055-122994148	CU468216,CH242-85C7,2:122831928-123020434 (Clone quality: bE85C7 on chr=2; Num_of_Contigs=1; )
SEPT8		location ⇒	2:122998179-122997987	CU468216,CH242-85C7,2:122831928-123020434 (Clone quality: bE85C7 on chr=2; Num_of_Contigs=1; )
SEPT8		location ⇒	2:123014410-123014230	CU468216,CH242-85C7,2:122831928-123020434 (Clone quality: bE85C7 on chr=2; Num_of_Contigs=1; )
SEPW1		ENSSSCG00000002986	6:33376815-33377609		FP102547,CH242-120H3,6:33375907-33395729 (Clone quality: bE120H3 on chr=6; Num_of_Contigs=3; )
SERAC1		ENSSSCG00000012314	X:44226287-44278461
SERBP1		ENSSSCG00000003798	6:102195509-102208960		CU442704,CH242-111N2,6:102164133-102241390 (Clone quality: bE111N2 on chr=6; Num_of_Contigs=4; )
SERGEF		ENSSSCG00000013373	2:38357273-38643387
SERINC1		ENSSSCG00000004237	1:41690242-41731303
SERINC1		location ⇒	1:41730662-41730949		CU972418,CH242-148G13,1:41714631-41769833 (Clone quality: bE148G13 on chr=1; Num_of_Contigs=6; )
SERINC1		location ⇒	1:41732216-41732306		CU972418,CH242-148G13,1:41714631-41769833 (Clone quality: bE148G13 on chr=1; Num_of_Contigs=6; )
SERINC1		location ⇒	1:41862829-41862739		FP104538,CH242-44E9,1:41861018-41867427 (Clone quality: bE44E9 on chr=1; Num_of_Contigs=16; )
SERINC1		location ⇒	1:41864383-41864096		FP104538,CH242-44E9,1:41861018-41867427 (Clone quality: bE44E9 on chr=1; Num_of_Contigs=16; )
SERINC2		ENSSSCG00000003595	6:60181171-60184609		FP103091,CH242-129P15,6:60174748-60185608 (Clone quality: bE129P15 on chr=6; Num_of_Contigs=20; )
SERINC3		ENSSSCG00000007375	17:48708150-48713336
SERINC4		ENSSSCG00000004698	1:133835904-133840398	CU062440,CH242-140A18,1:133801433-133876483 (Clone quality: bE140A18 on chr=1; Num_of_Contigs=11; )
SERP1		ENSSSCG00000011709	13:73742886-73745334		CU928694,CH242-282O4,13:73739690-73754868 (Clone quality: bE282O4 on chr=13; Num_of_Contigs=4; )
SERP2		ENSSSCG00000009423	11:21600874-21629114
SERPINA1		ENSSSCG00000002476	7:124003262-124013640		CU302423,CH242-194J4,7:123950058-124030402 (Clone quality: bE194J4 on chr=7; Num_of_Contigs=6; )
SERPINA1		location ⇒	7:124003547-124003277		CU302423,CH242-194J4,7:123950058-124030402 (Clone quality: bE194J4 on chr=7; Num_of_Contigs=6; )
SERPINA1		location ⇒	7:124004827-124004677		CU302423,CH242-194J4,7:123950058-124030402 (Clone quality: bE194J4 on chr=7; Num_of_Contigs=6; )
SERPINA1		location ⇒	7:124006264-124005992		CU302423,CH242-194J4,7:123950058-124030402 (Clone quality: bE194J4 on chr=7; Num_of_Contigs=6; )
SERPINA1		location ⇒	7:124008712-124008053		CU302423,CH242-194J4,7:123950058-124030402 (Clone quality: bE194J4 on chr=7; Num_of_Contigs=6; )
SERPINA11		ENSSSCG00000002479	7:124279537-124295079		CU633316,CH242-69M9,7:124252539-124319088 (Clone quality: bE69M9 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).