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)

PPRC1		ENSSSCG00000010575	14:118117579-118133378		CT737175,CH242-202A24,14:118086409-118163897 (Clone quality: bE202A24 on chr=14; Num_of_Contigs=4; )
PPT1		ENSSSCG00000003671	6:66044461-66063462	CR974432,PigE-204L22,6:65914672-66073853 (No clone quality info on bT204L22)
PPT2		ENSSSCG00000001433	7:28027719-28040084	CT954269,CH242-404E7,7:27953077-28153182 (Clone quality: bE404E7 on chr=7; Num_of_Contigs=12; )
PPTC7		ENSSSCG00000009825	14:31936053-31973788
PPTC7		location ⇒	14:31936818-31936637		CT737176,CH242-22G23,14:31924275-31959444 (Clone quality: bE22G23 on chr=14; Num_of_Contigs=3; )
PPTC7		location ⇒	14:31938719-31938587		CT737176,CH242-22G23,14:31924275-31959444 (Clone quality: bE22G23 on chr=14; Num_of_Contigs=3; )
PPTC7		location ⇒	14:31943669-31943470		CT737176,CH242-22G23,14:31924275-31959444 (Clone quality: bE22G23 on chr=14; Num_of_Contigs=3; )
PPTC7		location ⇒	14:31949139-31948973		CT737176,CH242-22G23,14:31924275-31959444 (Clone quality: bE22G23 on chr=14; Num_of_Contigs=3; )
PPWD1		location ⇒	16:41393260-41393070		CU570838,CH242-27G12,16:41378006-41457782 (Clone quality: bE27G12 on chr=16; Num_of_Contigs=3; )
PPWD1		location ⇒	16:41396169-41395722		CU570838,CH242-27G12,16:41378006-41457782 (Clone quality: bE27G12 on chr=16; Num_of_Contigs=3; )
PPWD1		location ⇒	16:41460252-41460699		CU856268,CH242-30E20,16:41457783-41623625 (Clone quality: bE30E20 on chr=16; Num_of_Contigs=2; )
PPWD1		location ⇒	16:41463161-41463351		CU856268,CH242-30E20,16:41457783-41623625 (Clone quality: bE30E20 on chr=16; Num_of_Contigs=2; )
PPY		ENSSSCG00000017368	12:17132651-17133285		CU914436,CH242-507H4,12:17130148-17144522 (Clone quality: bE507H4 on chr=12; Num_of_Contigs=9; )
PPYR1		ENSSSCG00000010369	14:92000565-92002360		CU633482,CH242-183G20,14:91954577-92014278 (Clone quality: bE183G20 on chr=14; Num_of_Contigs=5; )
PQLC1		ENSSSCG00000005779	1:291035927-291092499		CU041273,CH242-39O17,1:291029585-291098409 (Clone quality: bE39O17 on chr=1; Num_of_Contigs=4; )
PQLC2		ENSSSCG00000003492	6:53265230-53280778
PQLC3		ENSSSCG00000008631	3:116314872-116326912		CU915597,CH242-518I17,3:116314671-116336502 (Clone quality: bE518I17 on chr=3; Num_of_Contigs=9; )
PR39		location ⇒	13:26044977-26044870		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PR39		location ⇒	13:26044977-26044870		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PR39		location ⇒	13:26045596-26045381		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PR39		location ⇒	13:26045596-26045381		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PRAF2		ENSSSCG00000012289	X:42583896-42586466		FP067404,CH242-247J8,X:42575088-42641365 (Clone quality: bE247J8 on chr=X; Num_of_Contigs=5; )
PRAM1		location ⇒	2:51762032-51761884		FP090904,CH242-212F1,2:51700191-51798128 (Clone quality: bE212F1 on chr=2; Num_of_Contigs=2; )
PRAM1		location ⇒	2:51762554-51762390		FP090904,CH242-212F1,2:51700191-51798128 (Clone quality: bE212F1 on chr=2; Num_of_Contigs=2; )
PRAM1		location ⇒	2:51762806-51762698		FP090904,CH242-212F1,2:51700191-51798128 (Clone quality: bE212F1 on chr=2; Num_of_Contigs=2; )
PRAM1		location ⇒	2:51765511-51765435		FP090904,CH242-212F1,2:51700191-51798128 (Clone quality: bE212F1 on chr=2; Num_of_Contigs=2; )
PRAME		ENSSSCG00000010043	14:49864292-49867589		CU467669,CH242-141B5,14:49851532-49926359 (Clone quality: bE141B5 on chr=14; Num_of_Contigs=7; )
PRAP1		ENSSSCG00000010792	14:148503108-148506987		CU570809,CH242-121F20,14:148499673-148510138 (Clone quality: bE121F20 on chr=14; Num_of_Contigs=15; )
PRC1		ENSSSCG00000010883	10:18785448-18794334
PRC1		location ⇒	10:18791271-18791191		CU914644,CH242-234J22,10:18787457-18795069 (Clone quality: bE234J22 on chr=10; Num_of_Contigs=14; )
PRC1		location ⇒	10:18791933-18791773		CU914644,CH242-234J22,10:18787457-18795069 (Clone quality: bE234J22 on chr=10; Num_of_Contigs=14; )
PRC1		location ⇒	10:18792244-18792019		CU914644,CH242-234J22,10:18787457-18795069 (Clone quality: bE234J22 on chr=10; Num_of_Contigs=14; )
PRCC		ENSSSCG00000006467	4:96990577-97017676
PRCP		ENSSSCG00000014899	9:17122742-17157369		CU929487,CH242-68O18,9:17122524-17168610 (Clone quality: bE68O18 on chr=9; Num_of_Contigs=8; )
PRDM1		ENSSSCG00000004369	1:75734444-75755436		CU041281,CH242-47G3,1:75697101-75818068 (Clone quality: bE47G3 on chr=1; Num_of_Contigs=2; )
PRDM1		location ⇒	1:75754004-75753843		CU041281,CH242-47G3,1:75697101-75818068 (Clone quality: bE47G3 on chr=1; Num_of_Contigs=2; )
PRDM1		location ⇒	1:75754503-75754371		CU041281,CH242-47G3,1:75697101-75818068 (Clone quality: bE47G3 on chr=1; Num_of_Contigs=2; )
PRDM1		location ⇒	1:75755040-75754862		CU041281,CH242-47G3,1:75697101-75818068 (Clone quality: bE47G3 on chr=1; Num_of_Contigs=2; )
PRDM10		ENSSSCG00000015243	9:55082193-55171542
PRDM10		location ⇒	9:55120337-55120047		CU694643,CH242-72G13,9:55091073-55216680 (Clone quality: bE72G13 on chr=9; Num_of_Contigs=4; )
PRDM10		location ⇒	9:55122000-55121757		CU694643,CH242-72G13,9:55091073-55216680 (Clone quality: bE72G13 on chr=9; Num_of_Contigs=4; )
PRDM10		location ⇒	9:55141698-55141531		CU694643,CH242-72G13,9:55091073-55216680 (Clone quality: bE72G13 on chr=9; Num_of_Contigs=4; )
PRDM10		location ⇒	9:55144458-55144272		CU694643,CH242-72G13,9:55091073-55216680 (Clone quality: bE72G13 on chr=9; Num_of_Contigs=4; )
PRDM11		ENSSSCG00000013276	2:15601504-15646859
PRDM12		ENSSSCG00000005703	1:285905408-285921415
PRDM13		ENSSSCG00000004354	1:69898485-69905990
PRDM14		ENSSSCG00000006195	4:67454450-67475663
PRDM15		ENSSSCG00000012084	13:144758647-144800621
PRDM2		ENSSSCG00000003453	6:50485172-50499719		CU694706,CH242-284G6,6:50484583-50503630 (Clone quality: bE284G6 on chr=6; Num_of_Contigs=12; )
PRDM4		ENSSSCG00000000160	5:10821167-10849747

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).