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)

SELK_PIG		ENSSSCG00000011459	13:30226564-30233984		CU466421,CH242-96K10,13:30195284-30280608 (Clone quality: bE96K10 on chr=13; Num_of_Contigs=2; )
SELL		ENSSSCG00000006287	4:84394933-84415018		CU407291,CH242-513E17,4:84329694-84430611 (Clone quality: bE513E17 on chr=4; Num_of_Contigs=7; )
SELL		location ⇒	4:84397203-84397581		CU407291,CH242-513E17,4:84329694-84430611 (Clone quality: bE513E17 on chr=4; Num_of_Contigs=7; )
SELL		location ⇒	4:84401800-84401987		CU407291,CH242-513E17,4:84329694-84430611 (Clone quality: bE513E17 on chr=4; Num_of_Contigs=7; )
SELL		location ⇒	4:84413711-84414425		CU407291,CH242-513E17,4:84329694-84430611 (Clone quality: bE513E17 on chr=4; Num_of_Contigs=7; )
SELL		location ⇒	4:84414472-84414835		CU407291,CH242-513E17,4:84329694-84430611 (Clone quality: bE513E17 on chr=4; Num_of_Contigs=7; )
SELP		ENSSSCG00000006288	4:84453836-84489355	CU179726,CH242-320P15,4:84431793-84627616 (Clone quality: bE320P15 on chr=4; Num_of_Contigs=2; )
SELP		location ⇒	4:84466959-84467346	CU179726,CH242-320P15,4:84431793-84627616 (Clone quality: bE320P15 on chr=4; Num_of_Contigs=2; )
SELP		location ⇒	4:84478171-84478361	CU179726,CH242-320P15,4:84431793-84627616 (Clone quality: bE320P15 on chr=4; Num_of_Contigs=2; )
SELP		location ⇒	4:84481779-84481996	CU179726,CH242-320P15,4:84431793-84627616 (Clone quality: bE320P15 on chr=4; Num_of_Contigs=2; )
SELP		location ⇒	4:84488664-84489354	CU179726,CH242-320P15,4:84431793-84627616 (Clone quality: bE320P15 on chr=4; Num_of_Contigs=2; )
SELPLG		location ⇒	9:66846076-66846100		CU927907,CH242-402P23,9:66846025-66849417 (Clone quality: bE402P23 on chr=9; Num_of_Contigs=27; )
SELS		location ⇒	1:147569666-147569573		CU467921,CH242-97J4,1:147567760-147597783 (Clone quality: bE97J4 on chr=1; Num_of_Contigs=6; )
SELS		location ⇒	1:147572192-147572085		CU467921,CH242-97J4,1:147567760-147597783 (Clone quality: bE97J4 on chr=1; Num_of_Contigs=6; )
SELS		location ⇒	1:147574947-147574812		CU467921,CH242-97J4,1:147567760-147597783 (Clone quality: bE97J4 on chr=1; Num_of_Contigs=6; )
SELS		location ⇒	1:147575681-147575584		CU467921,CH242-97J4,1:147567760-147597783 (Clone quality: bE97J4 on chr=1; Num_of_Contigs=6; )
SEMA3A		ENSSSCG00000015398	9:89599310-89750785
SEMA3A		location ⇒	9:89599184-89599492		FP101869,CH242-30B11,9:89548536-89680533 (Clone quality: bE30B11 on chr=9; Num_of_Contigs=1; )
SEMA3A		location ⇒	9:89663496-89663560		FP101869,CH242-30B11,9:89548536-89680533 (Clone quality: bE30B11 on chr=9; Num_of_Contigs=1; )
SEMA3A		location ⇒	9:89750328-89751536		CU861995,CH242-43K11,9:89725121-89763043 (Clone quality: bE43K11 on chr=9; Num_of_Contigs=7; )
SEMA3A		location ⇒	9:89752973-89753693		CU861995,CH242-43K11,9:89725121-89763043 (Clone quality: bE43K11 on chr=9; Num_of_Contigs=7; )
SEMA3B		ENSSSCG00000011400	13:27403693-27410246		CU468071,CH242-427D1,13:27397872-27424038 (Clone quality: bE427D1 on chr=13; Num_of_Contigs=7; )
SEMA3C		ENSSSCG00000015404	9:92893449-93025709
SEMA3C		location ⇒	9:93072904-93072315		CU928116,CH242-9C18,9:93050743-93108330 (Clone quality: bE9C18 on chr=9; Num_of_Contigs=3; )
SEMA3D		ENSSSCG00000015396	9:88927566-89085644
SEMA3E		ENSSSCG00000015399	9:90294078-90375999
SEMA3F		ENSSSCG00000011398	13:27321595-27331409		CU468071,CH242-427D1,13:27313587-27382665 (Clone quality: bE427D1 on chr=13; Num_of_Contigs=7; )
SEMA3G		ENSSSCG00000011440	13:29190734-29199784		CU550676,CH242-330J9,13:29135788-29268883 (Clone quality: bE330J9 on chr=13; Num_of_Contigs=4; )
SEMA4A		ENSSSCG00000006495	4:97811658-97832266
SEMA4A		location ⇒	4:97812280-97812131		CU302298,CH242-261P14,4:97812098-97896758 (Clone quality: bE261P14 on chr=4; Num_of_Contigs=4; )
SEMA4A		location ⇒	4:97814079-97813917		CU302298,CH242-261P14,4:97812098-97896758 (Clone quality: bE261P14 on chr=4; Num_of_Contigs=4; )
SEMA4A		location ⇒	4:97814302-97814183		CU302298,CH242-261P14,4:97812098-97896758 (Clone quality: bE261P14 on chr=4; Num_of_Contigs=4; )
SEMA4A		location ⇒	4:97817051-97816884		CU302298,CH242-261P14,4:97812098-97896758 (Clone quality: bE261P14 on chr=4; Num_of_Contigs=4; )
SEMA4B		ENSSSCG00000001857	7:61322219-61327168		CU571213,CH242-243O5,7:61321368-61327805 (Clone quality: bE243O5 on chr=7; Num_of_Contigs=21; )
SEMA4C		ENSSSCG00000008197	3:52065783-52074136		FP102542,CH242-108N5,3:52055736-52099463 (Clone quality: bE108N5 on chr=3; Num_of_Contigs=4; )
SEMA4C		location ⇒	3:52074838-52074986		FP102542,CH242-108N5,3:52055736-52099463 (Clone quality: bE108N5 on chr=3; Num_of_Contigs=4; )
SEMA4C		location ⇒	3:52273989-52274137		FP102744,CH242-70H5,3:52265706-52274630 (Clone quality: bE70H5 on chr=3; Num_of_Contigs=11; )
SEMA4D		ENSSSCG00000009584	14:1167125-1208885		CU469368,CH242-181M10,14:1134838-1275802 (Clone quality: bE181M10 on chr=14; Num_of_Contigs=3; )
SEMA4D		location ⇒	14:1165997-1165697		CU469368,CH242-181M10,14:1134838-1275802 (Clone quality: bE181M10 on chr=14; Num_of_Contigs=3; )
SEMA4D		location ⇒	14:1180189-1180075		CU469368,CH242-181M10,14:1134838-1275802 (Clone quality: bE181M10 on chr=14; Num_of_Contigs=3; )
SEMA4D		location ⇒	14:1181094-1181000		CU469368,CH242-181M10,14:1134838-1275802 (Clone quality: bE181M10 on chr=14; Num_of_Contigs=3; )
SEMA4F		ENSSSCG00000008262	3:62766709-62790245		CU633183,CH242-294E8,3:62761117-62790741 (Clone quality: bE294E8 on chr=3; Num_of_Contigs=14; )
SEMA5A		ENSSSCG00000017095	16:70206088-70414206
SEMA5A		location ⇒	16:70330198-70330006		FP085582,CH242-153F4,16:70328268-70342835 (Clone quality: bE153F4 on chr=16; Num_of_Contigs=5; )
SEMA5A		location ⇒	16:70332324-70332110		FP085582,CH242-153F4,16:70328268-70342835 (Clone quality: bE153F4 on chr=16; Num_of_Contigs=5; )
SEMA5A		location ⇒	16:70411441-70411655		CU928060,CH242-267O10,16:70390058-70529885 (Clone quality: bE267O10 on chr=16; Num_of_Contigs=2; )
SEMA5A		location ⇒	16:70413567-70413759		CU928060,CH242-267O10,16:70390058-70529885 (Clone quality: bE267O10 on chr=16; Num_of_Contigs=2; )
SEMA5B		ENSSSCG00000011872	13:103604297-103624834		CU633639,CH242-157P15,13:103497865-103629124 (Clone quality: bE157P15 on chr=13; Num_of_Contigs=2; )
SEMA6A		ENSSSCG00000014224	2:109266188-109326337		CU462927,CH242-294C18,2:109191443-109407332 (Clone quality: bE294C18 on chr=2; Num_of_Contigs=1; )
SEMA6C		ENSSSCG00000006635	4:102061850-102074166	CU138569,CH242-265M12,4:101911025-102092543 (Clone quality: bE265M12 on chr=4; Num_of_Contigs=8; )

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).