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)

PRSS2		location ⇒	18:6343476-6343269		CU655925,CH242-295C16,18:6335980-6357590 (Clone quality: bE295C16 on chr=18; Num_of_Contigs=15; )
PRSS2		location ⇒	18:6343865-6343727		CU655925,CH242-295C16,18:6335980-6357590 (Clone quality: bE295C16 on chr=18; Num_of_Contigs=15; )
PRSS2		location ⇒	18:6344575-6344320		CU655925,CH242-295C16,18:6335980-6357590 (Clone quality: bE295C16 on chr=18; Num_of_Contigs=15; )
PRSS2		location ⇒	18:6345610-6345450		CU655925,CH242-295C16,18:6335980-6357590 (Clone quality: bE295C16 on chr=18; Num_of_Contigs=15; )
PRSS21		ENSSSCG00000008063	3:37130636-37134958
PRSS22		ENSSSCG00000008062	3:37096171-37147278
PRSS23		ENSSSCG00000004452	1:86787658-86788893		CU407112,CH242-322O1,1:86776107-86939727 (Clone quality: bE322O1 on chr=1; Num_of_Contigs=4; )
PRSS23		location ⇒	9:20996689-20996291		FP102391,CH242-358A3,9:20995946-20999003 (Clone quality: bE358A3 on chr=9; Num_of_Contigs=7; )
PRSS23		location ⇒	9:20997537-20997453		FP102391,CH242-358A3,9:20995946-20999003 (Clone quality: bE358A3 on chr=9; Num_of_Contigs=7; )
PRSS23		location ⇒	9:20998488-20997640		FP102391,CH242-358A3,9:20995946-20999003 (Clone quality: bE358A3 on chr=9; Num_of_Contigs=7; )
PRSS23		location ⇒	9:20998788-20998511		FP102391,CH242-358A3,9:20995946-20999003 (Clone quality: bE358A3 on chr=9; Num_of_Contigs=7; )
PRSS27		ENSSSCG00000008059	3:36981166-37007501
PRSS36		ENSSSCG00000007760	3:15851071-15859242		CU464163,CH242-418M3,3:15802333-15893853 (Clone quality: bE418M3 on chr=3; Num_of_Contigs=3; )
PRSS42		ENSSSCG00000011324	13:24707421-24710422		CU856704,CH242-520E7,13:24707034-24734208 (Clone quality: bE520E7 on chr=13; Num_of_Contigs=12; )
PRSS48		ENSSSCG00000009017	8:66805744-66813276
PRSS7		ENSSSCG00000012019	13:131807103-131950631
PRSS7		location ⇒	13:131807314-131806792		CU856297,CH242-341M2,13:131786447-131943091 (Clone quality: bE341M2 on chr=13; Num_of_Contigs=1; )
PRSS7		location ⇒	13:131815925-131815743		CU856297,CH242-341M2,13:131786447-131943091 (Clone quality: bE341M2 on chr=13; Num_of_Contigs=1; )
PRSS7		location ⇒	13:131838148-131837987		CU856297,CH242-341M2,13:131786447-131943091 (Clone quality: bE341M2 on chr=13; Num_of_Contigs=1; )
PRSS7		location ⇒	13:131838375-131838324		CU856297,CH242-341M2,13:131786447-131943091 (Clone quality: bE341M2 on chr=13; Num_of_Contigs=1; )
PRSS8		ENSSSCG00000007761	3:15864504-15866364		CU464163,CH242-418M3,3:15802333-15893853 (Clone quality: bE418M3 on chr=3; Num_of_Contigs=3; )
PRTFDC1		ENSSSCG00000011072	10:48240678-48260978		CU915555,CH242-310M24,10:48230654-48267950 (Clone quality: bE310M24 on chr=10; Num_of_Contigs=9; )
PRTG		ENSSSCG00000004606	1:120861234-120997544
PRTG		location ⇒	1:23474057-23473956		CU469471,CH242-174E21,1:23461531-23496599 (Clone quality: bE174E21 on chr=1; Num_of_Contigs=10; )
PRTG		location ⇒	1:27217093-27217194		CU570706,CH242-141M11,1:27161262-27289909 (Clone quality: bE141M11 on chr=1; Num_of_Contigs=4; )
PRTG		location ⇒	1:28815767-28815872		CU407212,CH242-362N8,1:28813112-28816419 (Clone quality: bE362N8 on chr=1; Num_of_Contigs=15; )
PRTG		location ⇒	1:7153535-7153438		CU639475,CH242-203N1,1:7060696-7195267 (Clone quality: bE203N1 on chr=1; Num_of_Contigs=2; )
PRTN3		ENSSSCG00000013417	2:46134366-46137464		FP015903,CH242-504E7,2:46128360-46188530 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
PRTN3		location ⇒	2:46135343-46135206		FP015903,CH242-504E7,2:46128360-46188530 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
PRTN3		location ⇒	2:46135827-46135686		FP015903,CH242-504E7,2:46128360-46188530 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
PRTN3		location ⇒	2:46136697-46136464		FP015903,CH242-504E7,2:46128360-46188530 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
PRTN3		location ⇒	2:46137460-46137149		FP015903,CH242-504E7,2:46128360-46188530 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
PRUNE		ENSSSCG00000006641	4:102150133-102172237
PRUNE2		ENSSSCG00000005278	1:240104079-240176692		CU302442,CH242-506H7,1:240042666-240259276 (Clone quality: bE506H7 on chr=1; Num_of_Contigs=5; )
PRV1		location ⇒	6:34833255-34833397		FP102750,CH242-80G20,6:34829257-34836463 (Clone quality: bE80G20 on chr=6; Num_of_Contigs=9; )
PRV1		location ⇒	6:34833696-34833880		FP102750,CH242-80G20,6:34829257-34836463 (Clone quality: bE80G20 on chr=6; Num_of_Contigs=9; )
PRV1		location ⇒	6:34834559-34834678		FP102750,CH242-80G20,6:34829257-34836463 (Clone quality: bE80G20 on chr=6; Num_of_Contigs=9; )
PRV1		location ⇒	6:34859001-34859144		FP102750,CH242-80G20,6:34855493-34859260 (Clone quality: bE80G20 on chr=6; Num_of_Contigs=9; )
PSAP		ENSSSCG00000010281	14:77916826-77951788		CU468981,CH242-208A14,14:77877009-77954292 (Clone quality: bE208A14 on chr=14; Num_of_Contigs=3; )
PSAPL1		ENSSSCG00000008714	8:2715252-2716787		FP101952,CH242-222L22,8:2711862-2724110 (Clone quality: bE222L22 on chr=8; Num_of_Contigs=16; )
PSAT1		ENSSSCG00000005287	1:241888185-241917558
PSCD1		ENSSSCG00000017167	12:1975893-2044159	CU942393,CH242-200M2,12:1864056-2044534 (Clone quality: bE200M2 on chr=14; Num_of_Contigs=6; )
PSCD1		location ⇒	12:2044107-2044160	CU942393,CH242-200M2,12:1864056-2044534 (Clone quality: bE200M2 on chr=14; Num_of_Contigs=6; )
PSCD2L		location ⇒	6:37498145-37498285		FP102301,CH242-20J11,6:37475901-37499164 (Clone quality: bE20J11 on chr=6; Note=In Finishing;)
PSCD2L		location ⇒	6:37502362-37502513		FP102301,CH242-20J11,6:37499265-37520560 (Clone quality: bE20J11 on chr=6; Note=In Finishing;)
PSCD2L		location ⇒	6:37506210-37506365		FP102301,CH242-20J11,6:37499265-37520560 (Clone quality: bE20J11 on chr=6; Note=In Finishing;)
PSCD2L		location ⇒	6:37506455-37506715		FP102301,CH242-20J11,6:37499265-37520560 (Clone quality: bE20J11 on chr=6; Note=In Finishing;)
PSD2		ENSSSCG00000014359	2:128755467-128830369
PSD3		ENSSSCG00000007034	17:12349228-12669723
PSEN1		ENSSSCG00000002340	7:104515793-104559907		CU914658,CH242-289F14,7:104499973-104562452 (Clone quality: bE289F14 on chr=7; Num_of_Contigs=6; )

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, 2201-21

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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).