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)

PCTK2		location ⇒	10:66454682-66456213		CT841523,CH242-158A13,10:66421507-66520400 (Clone quality: bE158A13 on chr=10; Num_of_Contigs=4; )
PCTK2		location ⇒	10:66456744-66457559		CT841523,CH242-158A13,10:66421507-66520400 (Clone quality: bE158A13 on chr=10; Num_of_Contigs=4; )
PCTK3		ENSSSCG00000015290	9:63236256-63239434		FP102849,CH242-21K8,9:63234146-63239626 (Clone quality: bE21K8 on chr=9; Num_of_Contigs=13; )
PCTP		ENSSSCG00000017608	12:29655525-29826571
PCYOX1		ENSSSCG00000008330	3:66282292-66284976		CU929337,CH242-249L10,3:66281660-66288737 (Clone quality: bE249L10 on chr=3; Num_of_Contigs=18; )
PCYOX1L		ENSSSCG00000014433	2:135978102-135989151		CU694929,CH242-55J13,2:135975430-136052686 (Clone quality: bE55J13 on chr=2; Num_of_Contigs=3; )
PCYT1A		ENSSSCG00000011845	13:100603224-100649430	CU695181,CH242-182C12,13:100594044-100802412 (Clone quality: bE182C12 on chr=13; Num_of_Contigs=21; )
PCYT1B		ENSSSCG00000012182	X:19488914-19596445
PDC		ENSSSCG00000015578	9:119945639-119952560		CU657929,CH242-301H1,9:119854087-120036038 (Clone quality: bE301H1 on chr=9; Num_of_Contigs=1; )
PDCD1		location ⇒	15:120762284-120762306		CU640386,CH242-196G10,15:120753642-120792119 (Clone quality: bE196G10 on chr=15; Num_of_Contigs=4; )
PDCD1		location ⇒	2:104727590-104727616		CU657942,CH242-425E13,2:104659438-104797123 (Clone quality: bE425E13 on chr=2; Num_of_Contigs=2; )
PDCD10		ENSSSCG00000011739	13:81556006-81596704
PDCD10		location ⇒	13:81532872-81533248
PDCD10		location ⇒	13:81556493-81556011		CU469054,CH242-68P3,13:81532872-81586465 (Clone quality: bE68P3 on chr=13; Num_of_Contigs=4; )
PDCD10		location ⇒	13:81580639-81580428		CU469054,CH242-68P3,13:81532872-81586465 (Clone quality: bE68P3 on chr=13; Num_of_Contigs=4; )
PDCD10		location ⇒	13:81596701-81596559		CU469054,CH242-68P3,13:81586566-81627091 (Clone quality: bE68P3 on chr=13; Num_of_Contigs=4; )
PDCD1LG2		ENSSSCG00000005210	1:226477241-226503352
PDCD1LG2		location ⇒	1:226477295-226477244		CU457399,CH242-185B23,1:226461602-226481555 (Clone quality: bE185B23 on chr=1; Num_of_Contigs=9; )
PDCD1LG2		location ⇒	1:226482017-226481878		CU457399,CH242-185B23,1:226481656-226508279 (Clone quality: bE185B23 on chr=1; Num_of_Contigs=9; )
PDCD1LG2		location ⇒	1:226488266-226487996		CU457399,CH242-185B23,1:226481656-226508279 (Clone quality: bE185B23 on chr=1; Num_of_Contigs=9; )
PDCD1LG2		location ⇒	1:226503002-226502694		CU457399,CH242-185B23,1:226481656-226508279 (Clone quality: bE185B23 on chr=1; Num_of_Contigs=9; )
PDCD2		location ⇒	12:34254201-34254080		CU463348,CH242-175J3,12:34165606-34300471 (Clone quality: bE175J3 on chr=12; Num_of_Contigs=1; )
PDCD2		location ⇒	12:34255216-34254237		CU463348,CH242-175J3,12:34165606-34300471 (Clone quality: bE175J3 on chr=12; Num_of_Contigs=1; )
PDCD2L		ENSSSCG00000002875	6:29459641-29482601		CU929776,CH242-347I7,6:29450852-29482800 (Clone quality: bE347I7 on chr=6; Num_of_Contigs=4; )
PDCD4		ENSSSCG00000010627	14:126902476-126931666		CT737336,CH242-143P15,14:126897173-127111088 (Clone quality: bE143P15 on chr=14; Num_of_Contigs=1; )
PDCD4		location ⇒	14:126919644-126919446		CT737336,CH242-143P15,14:126897173-127111088 (Clone quality: bE143P15 on chr=14; Num_of_Contigs=1; )
PDCD4		location ⇒	14:126922599-126922482		CT737336,CH242-143P15,14:126897173-127111088 (Clone quality: bE143P15 on chr=14; Num_of_Contigs=1; )
PDCD4		location ⇒	14:126926564-126926454		CT737336,CH242-143P15,14:126897173-127111088 (Clone quality: bE143P15 on chr=14; Num_of_Contigs=1; )
PDCD4		location ⇒	14:126926911-126926800		CT737336,CH242-143P15,14:126897173-127111088 (Clone quality: bE143P15 on chr=14; Num_of_Contigs=1; )
PDCD5		ENSSSCG00000002860	6:28513318-28521227		FP102642,CH242-236J21,6:28490537-28523128 (Clone quality: bE236J21 on chr=6; Num_of_Contigs=9; )
PDCD6IP		location ⇒	13:16601366-16601590		CU928095,CH242-177L19,13:16600845-16667490 (Clone quality: bE177L19 on chr=13; Num_of_Contigs=8; )
PDCD6IP		location ⇒	13:16619812-16620064		CU928095,CH242-177L19,13:16600845-16667490 (Clone quality: bE177L19 on chr=13; Num_of_Contigs=8; )
PDCD6IP		location ⇒	13:16634424-16634474		CU928095,CH242-177L19,13:16600845-16667490 (Clone quality: bE177L19 on chr=13; Num_of_Contigs=8; )
PDCD6IP		location ⇒	13:16792901-16792851		CU915600,CH242-8A11,13:16780132-16795932 (Clone quality: bE8A11 on chr=13; Num_of_Contigs=7; )
PDCD7		ENSSSCG00000004926	1:170190008-170202756		CU856492,CH242-206L6,1:170178720-170216975 (Clone quality: bE206L6 on chr=1; Num_of_Contigs=2; )
PDCD7		location ⇒	1:170190631-170190422		CU856492,CH242-206L6,1:170178720-170216975 (Clone quality: bE206L6 on chr=1; Num_of_Contigs=2; )
PDCD7		location ⇒	1:170193200-170193144		CU856492,CH242-206L6,1:170178720-170216975 (Clone quality: bE206L6 on chr=1; Num_of_Contigs=2; )
PDCD7		location ⇒	1:170193391-170193295		CU856492,CH242-206L6,1:170178720-170216975 (Clone quality: bE206L6 on chr=1; Num_of_Contigs=2; )
PDCD7		location ⇒	1:170199463-170199323		CU856492,CH242-206L6,1:170178720-170216975 (Clone quality: bE206L6 on chr=1; Num_of_Contigs=2; )
PDCL		ENSSSCG00000005574	1:278246472-278256325		CU075436,CH242-173A3,1:278242304-278277447 (Clone quality: bE173A3 on chr=1; Num_of_Contigs=10; )
PDCL2		ENSSSCG00000008908	8:47695056-47727197		CU861936,CH242-17G22,8:47684923-47735424 (Clone quality: bE17G22 on chr=8; Num_of_Contigs=6; )
PDCL3		ENSSSCG00000008172	3:49433796-49444341
PDDC1		ENSSSCG00000012846	2:185919-191739		FP015900,CH242-40P17,2:170992-201722 (Clone quality: bE40P17 on chr=2; Num_of_Contigs=6; )
PDE10A		ENSSSCG00000004027	1:3953692-4177717
PDE11A		ENSSSCG00000015995	15:78480014-78700357
PDE12		ENSSSCG00000011465	13:32979127-32982436		CU467952,CH242-20F23,13:32971201-32987153 (Clone quality: bE20F23 on chr=13; Num_of_Contigs=11; )
PDE1B		ENSSSCG00000000297	5:18292784-18318461
PDE1C		ENSSSCG00000016668	18:39685792-39728417		CU468582,CH242-180I1,18:39664209-39729139 (Clone quality: bE180I1 on chr=18; Num_of_Contigs=4; )
PDE2A		ENSSSCG00000014816	9:6767590-6795745
PDE3A		ENSSSCG00000000586	5:50415643-50469193

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).