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)

PTGS2		ENSSSCG00000015579	9:120143783-120152326		CU640376,CH242-149O22,9:120036039-120178014 (Clone quality: bE149O22 on chr=9; Num_of_Contigs=1; )
PTGS2		location ⇒	9:38808394-38808300		CU657951,CH242-322L21,9:38781851-38831276 (Clone quality: bE322L21 on chr=9; Num_of_Contigs=9; )
PTGS2		location ⇒	9:41191347-41191264		CU861591,CH242-180C16,9:41180276-41261213 (Clone quality: bE180C16 on chr=9; Num_of_Contigs=10; )
PTGS2		location ⇒	9:50620057-50620153		CU656002,CH242-314J3,9:50466714-50627914 (Clone quality: bE314J3 on chr=9; Num_of_Contigs=1; )
PTGS2		location ⇒	9:7286667-7286563		FP102302,CH242-226L8,9:7278176-7325511 (Clone quality: bE226L8 on chr=9; Num_of_Contigs=9; )
PTH		ENSSSCG00000013394	2:42712290-42715312		FP067371,CH242-200E20,2:42683050-42718299 (Clone quality: bE200E20 on chr=2; Num_of_Contigs=7; )
PTH		location ⇒	2:42712290-42712380		FP067371,CH242-200E20,2:42683050-42718299 (Clone quality: bE200E20 on chr=2; Num_of_Contigs=7; )
PTH		location ⇒	2:42714327-42714419		FP067371,CH242-200E20,2:42683050-42718299 (Clone quality: bE200E20 on chr=2; Num_of_Contigs=7; )
PTH		location ⇒	2:42714797-42715312		FP067371,CH242-200E20,2:42683050-42718299 (Clone quality: bE200E20 on chr=2; Num_of_Contigs=7; )
PTH		location ⇒	2:42907673-42907583		CU914667,CH242-359F2,2:42905877-42919887 (Clone quality: bE359F2 on chr=2; Num_of_Contigs=8; )
PTH1R		ENSSSCG00000011326	13:24757645-24783308
PTH2		ENSSSCG00000003171	6:38037835-38038710
PTH2R		ENSSSCG00000016148	15:104467991-104527478
PTHLH		ENSSSCG00000000544	5:44375746-44387876
PTHLH		location ⇒	5:44375745-44376042		CU633308,CH242-523H4,5:44375352-44382077 (Clone quality: bE523H4 on chr=5; Num_of_Contigs=8; )
PTHLH		location ⇒	5:44376216-44376338		CU633308,CH242-523H4,5:44375352-44382077 (Clone quality: bE523H4 on chr=5; Num_of_Contigs=8; )
PTHLH		location ⇒	5:44382376-44382799		CU633308,CH242-523H4,5:44382178-44394003 (Clone quality: bE523H4 on chr=5; Num_of_Contigs=8; )
PTHLH		location ⇒	5:44387404-44387869		CU633308,CH242-523H4,5:44382178-44394003 (Clone quality: bE523H4 on chr=5; Num_of_Contigs=8; )
PTHR1		location ⇒	13:24778438-24778636		CU856704,CH242-520E7,13:24777004-24783451 (Clone quality: bE520E7 on chr=13; Num_of_Contigs=12; )
PTHR1		location ⇒	13:24779113-24779268		CU856704,CH242-520E7,13:24777004-24783451 (Clone quality: bE520E7 on chr=13; Num_of_Contigs=12; )
PTHR1		location ⇒	13:24782783-24782932		CU856704,CH242-520E7,13:24777004-24783451 (Clone quality: bE520E7 on chr=13; Num_of_Contigs=12; )
PTHR1		location ⇒	13:24783001-24783271		CU856704,CH242-520E7,13:24777004-24783451 (Clone quality: bE520E7 on chr=13; Num_of_Contigs=12; )
PTK2		ENSSSCG00000005931	4:1573343-1582321
PTK2		location ⇒	4:1641262-1641344		CU570940,CH242-286B11,4:1641014-1643048 (Clone quality: bE286B11 on chr=4; Num_of_Contigs=25; )
PTK2		location ⇒	4:1642604-1642818		CU570940,CH242-286B11,4:1641014-1643048 (Clone quality: bE286B11 on chr=4; Num_of_Contigs=25; )
PTK2		location ⇒	4:1642904-1643034		CU570940,CH242-286B11,4:1641014-1643048 (Clone quality: bE286B11 on chr=4; Num_of_Contigs=25; )
PTK2		location ⇒	4:1647334-1647445		CU570940,CH242-286B11,4:1645330-1648273 (Clone quality: bE286B11 on chr=4; Num_of_Contigs=25; )
PTK2B		ENSSSCG00000009664	14:11248055-11313269
PTK2B		location ⇒	14:11307808-11307884		CU633626,CH242-119C13,14:11303101-11316588 (Clone quality: bE119C13 on chr=14; Num_of_Contigs=3; )
PTK2B		location ⇒	14:11310510-11310650		CU633626,CH242-119C13,14:11303101-11316588 (Clone quality: bE119C13 on chr=14; Num_of_Contigs=3; )
PTK7		ENSSSCG00000001660	7:44023413-44051991
PTK7		location ⇒	7:44037426-44037631	CR956433,CH242-96L23,7:43958429-44038128 (No clone quality info on bE96L23)
PTK7		location ⇒	7:44038371-44038528	CR974479,PigE-150P18,7:44038129-44188858 (Clone quality: bT150P18 on chr=7; Num_of_Contigs=4; )
PTK7		location ⇒	7:44459253-44459458		CU633197,CH242-208A12,7:44458779-44468827 (Clone quality: bE208A12 on chr=7; Num_of_Contigs=8; )
PTK7		location ⇒	7:44460198-44460355		CU633197,CH242-208A12,7:44458779-44468827 (Clone quality: bE208A12 on chr=7; Num_of_Contigs=8; )
PTMA		location ⇒	6:117326456-117326540		CU463219,CH242-378M22,6:117299904-117343890 (Clone quality: bE378M22 on chr=6; Num_of_Contigs=7; )
PTMA		location ⇒	6:248284-248083		FP102614,CH242-198I21,6:246706-249719 (Clone quality: bE198I21 on chr=6; Num_of_Contigs=22; )
PTMA		location ⇒	6:248706-248370		FP102614,CH242-198I21,6:246706-249719 (Clone quality: bE198I21 on chr=6; Num_of_Contigs=22; )
PTMA		location ⇒	6:42258681-42258738		FP102419,CH242-106M5,6:42251006-42262139 (Clone quality: bE106M5 on chr=6; Num_of_Contigs=4; )
PTMS		ENSSSCG00000000689	5:59974471-59977966
PTMS		location ⇒	5:59977897-59977732		CU457492,CH242-370K21,5:59976993-59980590 (Clone quality: bE370K21 on chr=5; Num_of_Contigs=10; )
PTN		ENSSSCG00000016522	18:10629256-10718361
PTOV1		ENSSSCG00000003196	6:38493509-38501623		CU694867,CH242-269H19,6:38488706-38576788 (Clone quality: bE269H19 on chr=6; Num_of_Contigs=4; )
PTP4A2		ENSSSCG00000003605	6:60649606-60660132
PTP4A2		location ⇒	6:60649376-60649176		CU861549,CH242-250B15,6:60644530-60652680 (Clone quality: bE250B15 on chr=6; Num_of_Contigs=23; )
PTP4A2		location ⇒	6:60649710-60649460		CU861549,CH242-250B15,6:60644530-60652680 (Clone quality: bE250B15 on chr=6; Num_of_Contigs=23; )
PTP4A2		location ⇒	6:60656999-60656905		CU861549,CH242-250B15,6:60652781-60662778 (Clone quality: bE250B15 on chr=6; Num_of_Contigs=23; )
PTP4A2		location ⇒	6:60660740-60660036		CU861549,CH242-250B15,6:60652781-60662778 (Clone quality: bE250B15 on chr=6; Num_of_Contigs=23; )
PTPDC1		ENSSSCG00000008083	3:38401323-38495784
PTPLA		ENSSSCG00000011035	10:42118966-42191896

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).