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)

CLDND1		location ⇒	13:118624772-118625078		CU467089,CH242-73L22,13:118570025-118679109 (Clone quality: bE73L22 on chr=13; Num_of_Contigs=3; )
CLDND2		ENSSSCG00000003230	6:39396714-39398152		CU694842,CH242-204P3,6:39384038-39444131 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
CLEC1		ENSSSCG00000000649	5:58510388-58539023
CLEC1		location ⇒	5:58510388-58510694		CU856657,CH242-24H24,5:58487186-58529908 (Clone quality: bE24H24 on chr=5; Num_of_Contigs=4; )
CLEC1		location ⇒	5:58523901-58524002		CU856657,CH242-24H24,5:58487186-58529908 (Clone quality: bE24H24 on chr=5; Num_of_Contigs=4; )
CLEC1		location ⇒	5:58525941-58526117		CU856657,CH242-24H24,5:58487186-58529908 (Clone quality: bE24H24 on chr=5; Num_of_Contigs=4; )
CLEC1		location ⇒	5:58528595-58528749		CU856657,CH242-24H24,5:58487186-58529908 (Clone quality: bE24H24 on chr=5; Num_of_Contigs=4; )
CLEC10A		location ⇒	12:49660207-49660130		CU914703,CH242-254H21,12:49653396-49676565 (Clone quality: bE254H21 on chr=12; Num_of_Contigs=9; )
CLEC10A		location ⇒	12:49660589-49660485		CU914703,CH242-254H21,12:49653396-49676565 (Clone quality: bE254H21 on chr=12; Num_of_Contigs=9; )
CLEC10A		location ⇒	12:49661669-49661583		CU914703,CH242-254H21,12:49653396-49676565 (Clone quality: bE254H21 on chr=12; Num_of_Contigs=9; )
CLEC10A		location ⇒	12:49677767-49677722		CU914703,CH242-254H21,12:49676666-49691218 (Clone quality: bE254H21 on chr=12; Num_of_Contigs=9; )
CLEC12A		ENSSSCG00000000651	5:58570161-58577161
CLEC12A		location ⇒	5:58584843-58585049		CU633732,CH242-8P11,5:58581512-58587450 (Clone quality: bE8P11 on chr=5; Num_of_Contigs=7; )
CLEC12A		location ⇒	5:58588820-58588920		CU633732,CH242-8P11,5:58587551-58600088 (Clone quality: bE8P11 on chr=5; Num_of_Contigs=7; )
CLEC12A		location ⇒	5:58589200-58589367		CU633732,CH242-8P11,5:58587551-58600088 (Clone quality: bE8P11 on chr=5; Num_of_Contigs=7; )
CLEC12A		location ⇒	5:58590716-58590872		CU633732,CH242-8P11,5:58587551-58600088 (Clone quality: bE8P11 on chr=5; Num_of_Contigs=7; )
CLEC12B		ENSSSCG00000000651	5:58570161-58577161
CLEC17A		ENSSSCG00000013777	2:57209576-57225709
CLEC19A		ENSSSCG00000007871	3:23944206-23961556
CLEC1A		ENSSSCG00000000649	5:58510388-58539023
CLEC1B		ENSSSCG00000000650	5:58531781-58558626
CLEC2B		ENSSSCG00000000656	5:58828438-58842359		CU633551,CH242-192N12,5:58808425-58869175 (Clone quality: bE192N12 on chr=5; Num_of_Contigs=4; )
CLEC2B		location ⇒	5:58829090-58828969		CU633551,CH242-192N12,5:58808425-58869175 (Clone quality: bE192N12 on chr=5; Num_of_Contigs=4; )
CLEC2B		location ⇒	5:58836249-58836153		CU633551,CH242-192N12,5:58808425-58869175 (Clone quality: bE192N12 on chr=5; Num_of_Contigs=4; )
CLEC2B		location ⇒	5:58840215-58840054		CU633551,CH242-192N12,5:58808425-58869175 (Clone quality: bE192N12 on chr=5; Num_of_Contigs=4; )
CLEC2B		location ⇒	5:58856806-58856591		CU633551,CH242-192N12,5:58808425-58869175 (Clone quality: bE192N12 on chr=5; Num_of_Contigs=4; )
CLEC2D		ENSSSCG00000000657	5:58877403-58915787
CLEC3A		ENSSSCG00000002694	6:6969401-6977207		CU915593,CH242-277K10,6:6901316-6981448 (Clone quality: bE277K10 on chr=6; Num_of_Contigs=2; )
CLEC3B		ENSSSCG00000011299	13:23543941-23553685		CU915630,CH242-217H9,13:23481414-23584804 (Clone quality: bE217H9 on chr=13; Num_of_Contigs=4; )
CLEC4E		location ⇒	7:4654-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
CLEC4E		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
CLEC4E		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
CLEC4E		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
CLEC4F		ENSSSCG00000008320	3:65836363-65848387		CU855593,CH242-53L10,3:65814892-65863091 (Clone quality: bE53L10 on chr=3; Num_of_Contigs=46; )
CLEC4G		ENSSSCG00000013578	2:51092185-51095304		CU929919,CH242-334A8,2:51078972-51121616 (Clone quality: bE334A8 on chr=2; Num_of_Contigs=7; )
CLEC4M		location ⇒	5:2833091-2832988		CU928642,CH242-477C10,5:2827414-2839902 (Clone quality: bE477C10 on chr=5; Num_of_Contigs=6; )
CLEC4M		location ⇒	5:4483751-4483824		CU463166,CH242-381G20,5:4444980-4487814 (Clone quality: bE381G20 on chr=5; Num_of_Contigs=8; )
CLEC4M		location ⇒	5:6395798-6395859		CU633351,CH242-161B9,5:6340838-6445691 (Clone quality: bE161B9 on chr=5; Num_of_Contigs=5; )
CLEC4M		location ⇒	5:998156-998049		CU855578,CH242-90D21,5:981515-1014394 (Clone quality: bE90D21 on chr=5; Num_of_Contigs=7; )
CLEC7A		ENSSSCG00000000648	5:58494212-58507751		CU856657,CH242-24H24,5:58487186-58529908 (Clone quality: bE24H24 on chr=5; Num_of_Contigs=4; )
CLEC9A		ENSSSCG00000000638	5:58093962-58103813		CU972402,CH242-118L1,5:58047046-58140022 (Clone quality: bE118L1 on chr=5; Num_of_Contigs=3; )
CLECL1		location ⇒	5:58722545-58722579		CU633551,CH242-192N12,5:58674281-58796136 (Clone quality: bE192N12 on chr=5; Num_of_Contigs=4; )
CLECLSF9		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CLECSF1		ENSSSCG00000002694	6:6969401-6977207		CU915593,CH242-277K10,6:6901316-6981448 (Clone quality: bE277K10 on chr=6; Num_of_Contigs=2; )
CLECSF1		location ⇒	6:6969900-6969401		CU915593,CH242-277K10,6:6901316-6981448 (Clone quality: bE277K10 on chr=6; Num_of_Contigs=2; )
CLECSF1		location ⇒	6:6972488-6972403		CU915593,CH242-277K10,6:6901316-6981448 (Clone quality: bE277K10 on chr=6; Num_of_Contigs=2; )
CLECSF1		location ⇒	6:6977207-6977014		CU915593,CH242-277K10,6:6901316-6981448 (Clone quality: bE277K10 on chr=6; Num_of_Contigs=2; )
CLECSF13		ENSSSCG00000008320	3:65836363-65848387		CU855593,CH242-53L10,3:65814892-65863091 (Clone quality: bE53L10 on chr=3; Num_of_Contigs=46; )
CLECSF13		location ⇒	12:49677786-49677380		CU914703,CH242-254H21,12:49676666-49691218 (Clone quality: bE254H21 on chr=12; Num_of_Contigs=9; )
CLECSF13		location ⇒	12:49687549-49687403		CU914703,CH242-254H21,12:49676666-49691218 (Clone quality: bE254H21 on chr=12; Num_of_Contigs=9; )

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, 2601-2650, 2651-2700, 2701-2750, 2751-2800, 2801-2850, 2851-2900, 2901-2950, 2951-3000, 3001-3050, 3051-3100, 3101-3150, 3151-3200, 3201-3250, 3251-3300, 3301-3350, 3351-3400, 3401-3450, 3451-3500, 3501-3550, 3551-3600, 3601-3650, 3651-3700, 3701-3750, 3751-3800, 3801-3850, 3851-3900, 3901-12

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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).