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)

CASP1		location ⇒	9:34958330-34958070		CU855956,CH242-116E23,9:34933346-35042600 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP10		ENSSSCG00000015934	15:71377171-71407147
CASP12		location ⇒	9:34919975-34919800		CU855956,CH242-116E23,9:34904888-34921749 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP12		location ⇒	9:34920463-34920381		CU855956,CH242-116E23,9:34904888-34921749 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP12		location ⇒	9:34924157-34924030		CU855956,CH242-116E23,9:34921850-34933245 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP12		location ⇒	9:34929344-34929239		CU855956,CH242-116E23,9:34921850-34933245 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP14		ENSSSCG00000013835	2:60189732-60192718		CU915718,CH242-156C19,2:60173510-60199107 (Clone quality: bE156C19 on chr=2; Num_of_Contigs=6; )
CASP14		location ⇒	2:60191072-60191221		CU915718,CH242-156C19,2:60173510-60199107 (Clone quality: bE156C19 on chr=2; Num_of_Contigs=6; )
CASP15		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CASP2		ENSSSCG00000016464	18:5944416-5964015		CU928380,CH242-107B19,18:5868328-5998133 (Clone quality: bE107B19 on chr=18; Num_of_Contigs=4; )
CASP2		location ⇒	18:5851047-5850852		CU929961,CH242-59I9,18:5825279-5863758 (Clone quality: bE59I9 on chr=18; Num_of_Contigs=6; )
CASP2		location ⇒	18:5854498-5854336		CU929961,CH242-59I9,18:5825279-5863758 (Clone quality: bE59I9 on chr=18; Num_of_Contigs=6; )
CASP2		location ⇒	18:5960564-5960369		CU928380,CH242-107B19,18:5868328-5998133 (Clone quality: bE107B19 on chr=18; Num_of_Contigs=4; )
CASP2		location ⇒	18:5964015-5963853		CU928380,CH242-107B19,18:5868328-5998133 (Clone quality: bE107B19 on chr=18; Num_of_Contigs=4; )
CASP3		ENSSSCG00000015783	15:42806968-42815526
CASP3		location ⇒	15:22215-22304		FP236224,CH242-441A13,15:15069-25523 (Clone quality: bE441A13 on chr=15; Num_of_Contigs=3; )
CASP3		location ⇒	15:32526-32421		FP236224,CH242-441A13,15:25624-50693 (Clone quality: bE441A13 on chr=15; Num_of_Contigs=3; )
CASP3		location ⇒	15:43099-43204		FP236224,CH242-441A13,15:25624-50693 (Clone quality: bE441A13 on chr=15; Num_of_Contigs=3; )
CASP3		location ⇒	15:46839-46687		FP236224,CH242-441A13,15:25624-50693 (Clone quality: bE441A13 on chr=15; Num_of_Contigs=3; )
CASP4		ENSSSCG00000014997	9:34926978-34959053
CASP4		location ⇒	9:34918584-34918525		CU855956,CH242-116E23,9:34904888-34921749 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP4		location ⇒	9:34929344-34929244		CU855956,CH242-116E23,9:34921850-34933245 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP4		location ⇒	9:34934180-34933984		CU855956,CH242-116E23,9:34933346-35042600 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP4		location ⇒	9:34950993-34950917		CU855956,CH242-116E23,9:34933346-35042600 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP5		ENSSSCG00000014997	9:34926978-34959053
CASP5		location ⇒	9:34927552-34926730		CU855956,CH242-116E23,9:34921850-34933245 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP5		location ⇒	9:34934220-34933984		CU855956,CH242-116E23,9:34933346-35042600 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP5		location ⇒	9:34935819-34935668		CU855956,CH242-116E23,9:34933346-35042600 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP5		location ⇒	9:34941212-34940977		CU855956,CH242-116E23,9:34933346-35042600 (Clone quality: bE116E23 on chr=9; Num_of_Contigs=6; )
CASP6		ENSSSCG00000009140	8:96724720-96731855
CASP6		location ⇒	8:96725285-96725435		CU694741,CH242-514C2,8:96712621-96726662 (Clone quality: bE514C2 on chr=8; Num_of_Contigs=10; )
CASP6		location ⇒	8:96727505-96727682		CU694741,CH242-514C2,8:96726763-96744196 (Clone quality: bE514C2 on chr=8; Num_of_Contigs=10; )
CASP6		location ⇒	8:96730957-96731121		CU694741,CH242-514C2,8:96726763-96744196 (Clone quality: bE514C2 on chr=8; Num_of_Contigs=10; )
CASP6		location ⇒	8:96734898-96735107		CU694741,CH242-514C2,8:96726763-96744196 (Clone quality: bE514C2 on chr=8; Num_of_Contigs=10; )
CASP7		ENSSSCG00000010642	14:129889934-129921308		CU012038,CH242-328H13,14:129818796-130012065 (Clone quality: bE328H13 on chr=14; Num_of_Contigs=2; )
CASP7		location ⇒	14:129913429-129913566		CU012038,CH242-328H13,14:129818796-130012065 (Clone quality: bE328H13 on chr=14; Num_of_Contigs=2; )
CASP7		location ⇒	14:129913972-129914104		CU012038,CH242-328H13,14:129818796-130012065 (Clone quality: bE328H13 on chr=14; Num_of_Contigs=2; )
CASP7		location ⇒	14:129917043-129917221		CU012038,CH242-328H13,14:129818796-130012065 (Clone quality: bE328H13 on chr=14; Num_of_Contigs=2; )
CASP7		location ⇒	14:129919882-129921492		CU012038,CH242-328H13,14:129818796-130012065 (Clone quality: bE328H13 on chr=14; Num_of_Contigs=2; )
CASP8		ENSSSCG00000016106	15:98741656-98744520		CU928282,CH242-38C15,15:98737786-98744766 (Clone quality: bE38C15 on chr=15; Num_of_Contigs=9; )
CASP8		ENSSSCG00000004331	1:60927081-60946661		CU468058,CH242-196P17,1:60913615-60954877 (Clone quality: bE196P17 on chr=1; Num_of_Contigs=13; )
CASP8		location ⇒	15:98741658-98742163		CU928282,CH242-38C15,15:98737786-98744766 (Clone quality: bE38C15 on chr=15; Num_of_Contigs=9; )
CASP8		location ⇒	15:98744119-98744450		CU928282,CH242-38C15,15:98737786-98744766 (Clone quality: bE38C15 on chr=15; Num_of_Contigs=9; )
CASP8		location ⇒	15:98744515-98744738		CU928282,CH242-38C15,15:98737786-98744766 (Clone quality: bE38C15 on chr=15; Num_of_Contigs=9; )
CASP8		location ⇒	15:98744905-98745391		CU928282,CH242-38C15,15:98744867-98755436 (Clone quality: bE38C15 on chr=15; Num_of_Contigs=9; )
CASP8AP2		location ⇒	1:3270953-3270868		CU234145,CH242-273F9,1:3262080-3295091 (Clone quality: bE273F9 on chr=1; Num_of_Contigs=3; )
CASP8AP2		location ⇒	1:3659489-3659574		CU468589,CH242-314O11,1:3649098-3660336 (Clone quality: bE314O11 on chr=1; Num_of_Contigs=7; )
CASP8AP2		location ⇒	1:3763670-3763747		CU481396,CH242-102H15,1:3740584-3778360 (Clone quality: bE102H15 on chr=1; Num_of_Contigs=6; )
CASP8AP2		location ⇒	1:3931856-3931933		CU914228,CH242-145N21,1:3908171-3944858 (Clone quality: bE145N21 on chr=1; Num_of_Contigs=7; )
CASP9		ENSSSCG00000003460	6:51246493-51268853

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).