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)

CD80		location ⇒	13:25591699-25591834		CU929897,CH242-249I18,13:25551483-25594846 (Clone quality: bE249I18 on chr=13; Num_of_Contigs=19; )
CD80		location ⇒	13:36675956-36675839		CU481219,CH242-178J21,13:36662916-36742112 (Clone quality: bE178J21 on chr=13; Num_of_Contigs=5; )
CD81		location ⇒	5:60413132-60413195		CU856072,CH242-98O22,5:60384645-60418659 (Clone quality: bE98O22 on chr=5; Num_of_Contigs=6; )
CD82		ENSSSCG00000013279	2:16274761-16458005
CD83		ENSSSCG00000001059	7:10571782-10589831
CD83		location ⇒	7:10571933-10572041		CT827871,CH242-258D4,7:10519229-10573708 (Clone quality: bE258D4 on chr=7; Num_of_Contigs=3; )
CD83		location ⇒	7:10585235-10585448		CU467769,CH242-445O1,7:10573709-10725481 (Clone quality: bE445O1 on chr=7; Num_of_Contigs=3; )
CD83		location ⇒	7:10587554-10587662		CU467769,CH242-445O1,7:10573709-10725481 (Clone quality: bE445O1 on chr=7; Num_of_Contigs=3; )
CD83		location ⇒	7:10589507-10589817		CU467769,CH242-445O1,7:10573709-10725481 (Clone quality: bE445O1 on chr=7; Num_of_Contigs=3; )
CD84		ENSSSCG00000006381	4:93381789-93570006
CD84		ENSSSCG00000006400	4:94052098-94054645		CU856127,CH242-86L20,4:94027417-94074463 (Clone quality: bE86L20 on chr=4; Num_of_Contigs=6; )
CD84		location ⇒	4:203292-203199		CU468612,CH242-60P12,4:201536-229042 (Clone quality: bE60P12 on chr=4; Num_of_Contigs=10; )
CD84		location ⇒	4:2509224-2509305		CU467694,CH242-219C15,4:2504896-2511333 (Clone quality: bE219C15 on chr=4; Num_of_Contigs=16; )
CD84		location ⇒	4:2519373-2519292		CU407255,CH242-450I4,4:2518196-2523045 (Clone quality: bE450I4 on chr=4; Num_of_Contigs=9; )
CD84		location ⇒	4:898586-898513		FP085471,CH242-106F14,4:880399-899643 (Clone quality: bE106F14 on chr=4; Num_of_Contigs=12; )
CD86		ENSSSCG00000011877	13:103961666-103995796		CU694886,CH242-322E12,13:103947006-104157780 (Clone quality: bE322E12 on chr=13; Num_of_Contigs=1; )
CD86		location ⇒	13:103973503-103973839		CU694886,CH242-322E12,13:103947006-104157780 (Clone quality: bE322E12 on chr=13; Num_of_Contigs=1; )
CD86		location ⇒	13:103975391-103975697		CU694886,CH242-322E12,13:103947006-104157780 (Clone quality: bE322E12 on chr=13; Num_of_Contigs=1; )
CD86		location ⇒	13:103978417-103978572		CU694886,CH242-322E12,13:103947006-104157780 (Clone quality: bE322E12 on chr=13; Num_of_Contigs=1; )
CD86		location ⇒	13:103994879-103994988		CU694886,CH242-322E12,13:103947006-104157780 (Clone quality: bE322E12 on chr=13; Num_of_Contigs=1; )
CD87		ENSSSCG00000003065	6:35092325-35107861
CD89		ENSSSCG00000003284	6:41064930-41074740
CD8A		ENSSSCG00000008217	3:52919378-52926379		CU467723,CH242-297H15,3:52893862-52927344 (Clone quality: bE297H15 on chr=3; Num_of_Contigs=13; )
CD8A		location ⇒	3:52920724-52919378		CU467723,CH242-297H15,3:52893862-52927344 (Clone quality: bE297H15 on chr=3; Num_of_Contigs=13; )
CD8A		location ⇒	3:52925123-52925013		CU467723,CH242-297H15,3:52893862-52927344 (Clone quality: bE297H15 on chr=3; Num_of_Contigs=13; )
CD8A		location ⇒	3:52926056-52925694		CU467723,CH242-297H15,3:52893862-52927344 (Clone quality: bE297H15 on chr=3; Num_of_Contigs=13; )
CD8A		location ⇒	3:52926379-52926166		CU467723,CH242-297H15,3:52893862-52927344 (Clone quality: bE297H15 on chr=3; Num_of_Contigs=13; )
CD8B		location ⇒	3:52719317-52719673		CU856068,CH242-8G4,3:52707259-52723736 (Clone quality: bE8G4 on chr=3; Num_of_Contigs=15; )
CD8B		location ⇒	3:52812691-52812782		CU856068,CH242-8G4,3:52811535-52813844 (Clone quality: bE8G4 on chr=3; Num_of_Contigs=15; )
CD8B		location ⇒	3:52818968-52819194		CU856068,CH242-8G4,3:52816320-52820822 (Clone quality: bE8G4 on chr=3; Num_of_Contigs=15; )
CD8B		location ⇒	3:52821198-52821907		CU856068,CH242-8G4,3:52820923-52827796 (Clone quality: bE8G4 on chr=3; Num_of_Contigs=15; )
CD8BB		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CD9		ENSSSCG00000000710	5:60379256-60418644
CD9		location ⇒	5:60379326-60379478		CU856072,CH242-98O22,5:60378801-60384544 (Clone quality: bE98O22 on chr=5; Num_of_Contigs=6; )
CD9		location ⇒	5:60415514-60415611		CU856072,CH242-98O22,5:60384645-60418659 (Clone quality: bE98O22 on chr=5; Num_of_Contigs=6; )
CD9		location ⇒	5:60418531-60418634		CU856072,CH242-98O22,5:60384645-60418659 (Clone quality: bE98O22 on chr=5; Num_of_Contigs=6; )
CD9		location ⇒	5:60418760-60418958
CD90		ENSSSCG00000015122	9:45309364-45310847		CU951455,CH242-416J8,9:45293029-45311092 (Clone quality: bE416J8 on chr=9; Num_of_Contigs=2; )
CD91		ENSSSCG00000000423	5:21397928-21413617		CU633428,CH242-524E23,5:21392304-21414238 (Clone quality: bE524E23 on chr=5; Num_of_Contigs=9; )
CD92		ENSSSCG00000005425	1:258582618-258743259
CD93		ENSSSCG00000007116	17:31744235-31746961		CU606974,CH242-23K16,17:31739767-31793889 (Clone quality: bE23K16 on chr=17; Num_of_Contigs=5; )
CD94		ENSSSCG00000000642	5:58220196-58224166		CU856203,CH242-259K19,5:58140023-58263158 (Clone quality: bE259K19 on chr=5; Num_of_Contigs=4; )
CD95		ENSSSCG00000010448	14:105826565-105852532		CT737322,CH242-203A14,14:105756080-105909175 (Clone quality: bE203A14 on chr=14; Num_of_Contigs=1; )
CD96		ENSSSCG00000011935	13:111588741-111625422
CD96		location ⇒	13:111499939-111499543		CU550693,CH242-88C11,13:111491563-111503449 (Clone quality: bE88C11 on chr=13; Num_of_Contigs=23; )
CD96		location ⇒	13:111597448-111597661		CU550693,CH242-88C11,13:111596236-111603792 (Clone quality: bE88C11 on chr=13; Num_of_Contigs=23; )
CD96		location ⇒	13:111608862-111608703		CU550693,CH242-88C11,13:111608703-111612123 (Clone quality: bE88C11 on chr=13; Num_of_Contigs=23; )
CD96		location ⇒	13:111615285-111615476		CU550693,CH242-88C11,13:111612224-111629388 (Clone quality: bE88C11 on chr=13; Num_of_Contigs=23; )
CD97		ENSSSCG00000013775	2:57169360-57186527
CD97		location ⇒	2:57172765-57172816		FP103015,CH242-135B13,2:57166941-57184281 (Clone quality: bE135B13 on chr=2; Num_of_Contigs=14; )

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).