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)

PTPRB		location ⇒	5:33536891-33537028		CU463092,CH242-445F23,5:33506486-33585419 (Clone quality: bE445F23 on chr=5; Num_of_Contigs=4; )
PTPRB		location ⇒	5:33538661-33538824		CU463092,CH242-445F23,5:33506486-33585419 (Clone quality: bE445F23 on chr=5; Num_of_Contigs=4; )
PTPRC		ENSSSCG00000010908	10:22721069-22743562		FP067416,CH242-483G3,10:22720837-22744862 (Clone quality: bE483G3 on chr=10; Num_of_Contigs=5; )
PTPRC		ENSSSCG00000012909	2:3468942-3469568		CU633429,CH242-6G2,2:3468458-3486670 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
PTPRC		location ⇒	10:22726101-22726198		FP067416,CH242-483G3,10:22720837-22744862 (Clone quality: bE483G3 on chr=10; Num_of_Contigs=5; )
PTPRC		location ⇒	10:22731084-22731235		FP067416,CH242-483G3,10:22720837-22744862 (Clone quality: bE483G3 on chr=10; Num_of_Contigs=5; )
PTPRC		location ⇒	10:22736626-22736771		FP067416,CH242-483G3,10:22720837-22744862 (Clone quality: bE483G3 on chr=10; Num_of_Contigs=5; )
PTPRC		location ⇒	10:22738973-22739090		FP067416,CH242-483G3,10:22720837-22744862 (Clone quality: bE483G3 on chr=10; Num_of_Contigs=5; )
PTPRCAP		ENSSSCG00000012909	2:3468942-3469568		CU633429,CH242-6G2,2:3468458-3486670 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
PTPRCAP		location ⇒	2:3467660-3467724		CU633429,CH242-6G2,2:3461790-3468357 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
PTPRCAP		location ⇒	2:3468944-3469048		CU633429,CH242-6G2,2:3468458-3486670 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
PTPRCAP		location ⇒	2:3469102-3469746		CU633429,CH242-6G2,2:3468458-3486670 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
PTPRD		ENSSSCG00000005194	1:223065120-223220583		CU633291,CH242-39J23,1:223061699-223239324 (Clone quality: bE39J23 on chr=1; Num_of_Contigs=1; )
PTPRD		location ⇒	1:223368426-223368291		CU896533,CH242-140D8,1:223339832-223369808 (Clone quality: bE140D8 on chr=1; Num_of_Contigs=8; )
PTPRD		location ⇒	1:223461566-223461411		FP017288,CH242-250J6,1:223458033-223484131 (Clone quality: bE250J6 on chr=1; Num_of_Contigs=1; )
PTPRD		location ⇒	1:223464588-223464449		FP017288,CH242-250J6,1:223458033-223484131 (Clone quality: bE250J6 on chr=1; Num_of_Contigs=1; )
PTPRD		location ⇒	1:223466874-223466667		FP017288,CH242-250J6,1:223458033-223484131 (Clone quality: bE250J6 on chr=1; Num_of_Contigs=1; )
PTPRF		ENSSSCG00000003938	6:119905206-119951284
PTPRF		ENSSSCG00000000549	5:44608561-44658126
PTPRF		ENSSSCG00000000940	5:94410183-94547079		CU633642,CH242-167I17,5:94386592-94554001 (Clone quality: bE167I17 on chr=5; Num_of_Contigs=1; )
PTPRF		ENSSSCG00000012866	2:1411757-1420165
PTPRF		ENSSSCG00000014598	9:1352429-1460845
PTPRF		ENSSSCG00000015474	9:106759290-106794554
PTPRF		ENSSSCG00000016781	16:2980222-3204046
PTPRF		location ⇒	6:119897652-119898354		CU463920,CH242-310K18,6:119897631-119904088 (Clone quality: bE310K18 on chr=6; Num_of_Contigs=10; )
PTPRG		ENSSSCG00000011485	13:36945056-37093057
PTPRH		ENSSSCG00000013220	2:12585454-12608690
PTPRJ		location ⇒	2:1447739-1447674		CU469203,CH242-236K15,2:1447674-1451688 (Clone quality: bE236K15 on chr=2; Num_of_Contigs=23; )
PTPRJ		location ⇒	2:1522815-1522892		FP085516,CH242-270C7,2:1489714-1536776 (Clone quality: bE270C7 on chr=2; Num_of_Contigs=5; )
PTPRJ		location ⇒	2:276522-276643		FP015900,CH242-40P17,2:266769-291575 (Clone quality: bE40P17 on chr=2; Num_of_Contigs=6; )
PTPRJ		location ⇒	2:774358-774443		FP102714,CH242-507P14,2:768400-788007 (Clone quality: bE507P14 on chr=2; Num_of_Contigs=19; )
PTPRK		ENSSSCG00000004209	1:36404866-36761816
PTPRN		ENSSSCG00000016218	15:114325915-114345774		CU457453,CH242-470M7,15:114314554-114348461 (Clone quality: bE470M7 on chr=15; Num_of_Contigs=11; )
PTPRO		ENSSSCG00000000601	5:54469066-54516196		CU655983,CH242-226N9,5:54333462-54523626 (Clone quality: bE226N9 on chr=5; Num_of_Contigs=1; )
PTPRU		ENSSSCG00000003590	6:59035952-59100679
PTPRU		location ⇒	6:59088059-59088214		CU638838,CH242-209O13,6:59072089-59088928 (Clone quality: bE209O13 on chr=6; Num_of_Contigs=12; )
PTPRU		location ⇒	6:59090147-59090286		CU638838,CH242-209O13,6:59089029-59092129 (Clone quality: bE209O13 on chr=6; Num_of_Contigs=12; )
PTPRU		location ⇒	6:59090803-59090954		CU638838,CH242-209O13,6:59089029-59092129 (Clone quality: bE209O13 on chr=6; Num_of_Contigs=12; )
PTPRU		location ⇒	6:59092408-59092583		CU638838,CH242-209O13,6:59092230-59104984 (Clone quality: bE209O13 on chr=6; Num_of_Contigs=12; )
PTPRZ1		ENSSSCG00000016614	18:23204383-23291497	CU463080,CH242-269N20,18:23159073-23362655 (Clone quality: bE269N20 on chr=18; Num_of_Contigs=11; )
PTRF		ENSSSCG00000017404	12:18032859-18045443		CU914191,CH242-236G5,12:18025552-18052509 (Clone quality: bE236G5 on chr=12; Num_of_Contigs=14; )
PTRF		location ⇒	12:18031276-18031118		CU914191,CH242-236G5,12:18025552-18052509 (Clone quality: bE236G5 on chr=12; Num_of_Contigs=14; )
PTRF		location ⇒	12:18031434-18031344		CU914191,CH242-236G5,12:18025552-18052509 (Clone quality: bE236G5 on chr=12; Num_of_Contigs=14; )
PTRF		location ⇒	12:18033562-18033004		CU914191,CH242-236G5,12:18025552-18052509 (Clone quality: bE236G5 on chr=12; Num_of_Contigs=14; )
PTRF		location ⇒	12:18045473-18044963		CU914191,CH242-236G5,12:18025552-18052509 (Clone quality: bE236G5 on chr=12; Num_of_Contigs=14; )
PTRH2		ENSSSCG00000017667	12:34060420-34060959		CU639474,CH242-173P3,12:34030800-34165605 (Clone quality: bE173P3 on chr=12; Num_of_Contigs=2; )
PTS		ENSSSCG00000015040	9:38870948-38878481		CU657951,CH242-322L21,9:38838246-38903616 (Clone quality: bE322L21 on chr=9; Num_of_Contigs=9; )
PTTG1_PIG		ENSSSCG00000017032	16:60571623-60579247		CU928350,CH242-226E17,16:60563924-60593473 (Clone quality: bE226E17 on chr=16; Num_of_Contigs=6; )
PTX3		ENSSSCG00000011727	13:77150724-77156269		CU633549,CH242-178L15,13:77122444-77202872 (Clone quality: bE178L15 on chr=13; Num_of_Contigs=4; )
PTX3		location ⇒	13:77150965-77151162		CU633549,CH242-178L15,13:77122444-77202872 (Clone quality: bE178L15 on chr=13; Num_of_Contigs=4; )

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).