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)

POLE3		ENSSSCG00000005478	1:266802421-266804033		FP102008,CH242-508O3,1:266799704-266845426 (Clone quality: bE508O3 on chr=1; Num_of_Contigs=5; )
POLG		ENSSSCG00000001838	7:60289662-60306310		CT943647,CH242-241C8,7:60283200-60330098 (Clone quality: bE241C8 on chr=7; Num_of_Contigs=2; )
POLG		location ⇒	7:60290183-60289697		CT943647,CH242-241C8,7:60283200-60330098 (Clone quality: bE241C8 on chr=7; Num_of_Contigs=2; )
POLG		location ⇒	7:60296596-60296513		CT943647,CH242-241C8,7:60283200-60330098 (Clone quality: bE241C8 on chr=7; Num_of_Contigs=2; )
POLG		location ⇒	7:60306166-60305692		CT943647,CH242-241C8,7:60283200-60330098 (Clone quality: bE241C8 on chr=7; Num_of_Contigs=2; )
POLG		location ⇒	7:60306463-60306193		CT943647,CH242-241C8,7:60283200-60330098 (Clone quality: bE241C8 on chr=7; Num_of_Contigs=2; )
POLH		ENSSSCG00000001683	7:44742693-44773503		CU928765,CH242-349L1,7:44716402-44811319 (Clone quality: bE349L1 on chr=7; Num_of_Contigs=5; )
POLI		ENSSSCG00000004529	1:106651863-106677716		CU694517,CH242-313D11,1:106640135-106799320 (Clone quality: bE313D11 on chr=1; Num_of_Contigs=2; )
POLK		ENSSSCG00000014082	2:73394857-73471120
POLL		ENSSSCG00000010564	14:117472402-117480990		CT737224,CH242-8E16,14:117416776-117558707 (Clone quality: bE8E16 on chr=14; Num_of_Contigs=1; )
POLM		ENSSSCG00000016755	18:49621968-49631257		CU928907,CH242-155A21,18:49598984-49712156 (Clone quality: bE155A21 on chr=18; Num_of_Contigs=2; )
POLN		ENSSSCG00000008684	8:407443-534569
POLR1A		ENSSSCG00000008226	3:53578822-53658397		CU570839,CH242-286N20,3:53540211-53717808 (Clone quality: bE286N20 on chr=3; Num_of_Contigs=1; )
POLR1B		ENSSSCG00000008098	3:39400354-39423641
POLR1D		ENSSSCG00000009310	11:4483943-4485604		CU633812,CH242-189K13,11:4472289-4485851 (Clone quality: bE189K13 on chr=11; Num_of_Contigs=14; )
POLR1E		ENSSSCG00000005347	1:249540389-249559980
POLR2B		ENSSSCG00000008895	8:46763319-46765269		CU928435,CH242-246B14,8:46750554-46766843 (Clone quality: bE246B14 on chr=8; Num_of_Contigs=16; )
POLR2F		ENSSSCG00000000116	5:6459605-6471865		CU633351,CH242-161B9,5:6445792-6484454 (Clone quality: bE161B9 on chr=5; Num_of_Contigs=5; )
POLR2I		ENSSSCG00000002925	6:30574746-30576279		CU694686,CH242-213I9,6:30551266-30589235 (Clone quality: bE213I9 on chr=6; Num_of_Contigs=4; )
POLR2J		ENSSSCG00000007688	3:8222507-8225133
POLR2J2		ENSSSCG00000003703	6:73195652-73195999		CU463086,CH242-380B10,6:73175305-73240038 (Clone quality: bE380B10 on chr=6; Num_of_Contigs=6; )
POLR2K		ENSSSCG00000009813	14:31242892-31243065		CU693466,CH242-414G9,14:31207443-31256880 (Clone quality: bE414G9 on chr=14; Num_of_Contigs=9; )
POLR2L		ENSSSCG00000000461	5:27983176-27983379		CU633380,CH242-260D22,5:27907609-28003514 (Clone quality: bE260D22 on chr=5; Num_of_Contigs=3; )
POLR3A		ENSSSCG00000010327	14:83778643-83836718		CU407090,CH242-515L11,14:83754163-83877970 (Clone quality: bE515L11 on chr=14; Num_of_Contigs=4; )
POLR3B		ENSSSCG00000000169	5:12043411-12215568
POLR3C		ENSSSCG00000006691	4:103565894-103577132		CU606940,CH242-153I6,4:103564526-103582920 (Clone quality: bE153I6 on chr=4; Num_of_Contigs=12; )
POLR3D		ENSSSCG00000009622	14:6474013-6480810		CU468634,CH242-272G24,14:6407691-6485927 (Clone quality: bE272G24 on chr=14; Num_of_Contigs=7; )
POLR3E		ENSSSCG00000007840	3:21672716-21694067		CU972409,CH242-221O18,3:21666086-21697171 (Clone quality: bE221O18 on chr=3; Num_of_Contigs=8; )
POLR3F		ENSSSCG00000007095	17:27462320-27479733		CU914246,CH242-1M4,17:27449366-27480603 (Clone quality: bE1M4 on chr=17; Num_of_Contigs=3; )
POLR3G		ENSSSCG00000014153	2:87185644-87213285
POLR3GL		ENSSSCG00000006682	4:103449825-103462674
POLR3H		ENSSSCG00000000063	5:3542222-3556797
POLR3K		ENSSSCG00000012145	X:12426341-12426658		CU463983,CH242-19L11,X:12370686-12440116 (Clone quality: bE19L11 on chr=X; Num_of_Contigs=9; )
POLS		ENSSSCG00000017102	16:72599429-72613225
POM121L2		ENSSSCG00000001162	7:22580081-22583161		CU468307,CH242-119B12,7:22568472-22710799 (Clone quality: bE119B12 on chr=7; Num_of_Contigs=3; )
POMC		location ⇒	10:19343720-19344092		CU914747,CH242-234B16,10:19339812-19348080 (Clone quality: bE234B16 on chr=10; Num_of_Contigs=16; )
POMC		location ⇒	10:19531656-19532028		CU633258,CH242-25B9,10:19511594-19619424 (Clone quality: bE25B9 on chr=10; Num_of_Contigs=2; )
POMC		location ⇒	10:19813824-19813945		FP102007,CH242-371A22,10:19715077-19885602 (Clone quality: bE371A22 on chr=10; Num_of_Contigs=1; )
POMC		location ⇒	10:19814016-19814388		FP102007,CH242-371A22,10:19715077-19885602 (Clone quality: bE371A22 on chr=10; Num_of_Contigs=1; )
POMP		location ⇒	11:5548205-5548599		CU062557,CH242-35O20,11:5547880-5553438 (Clone quality: bE35O20 on chr=11; Num_of_Contigs=14; )
POMP		location ⇒	11:5559022-5558924		CU062557,CH242-35O20,11:5556311-5560052 (Clone quality: bE35O20 on chr=11; Num_of_Contigs=14; )
POMP		location ⇒	11:5562423-5562359		CU062557,CH242-35O20,11:5560153-5571380 (Clone quality: bE35O20 on chr=11; Num_of_Contigs=14; )
POMT1		ENSSSCG00000005716	1:286831233-286846686	CU914430,CH242-421J21,1:286815524-286859256 (Clone quality: bE421J21 on chr=1; Num_of_Contigs=8; )
POMT2		ENSSSCG00000002397	7:108349235-108366918
PON1		ENSSSCG00000015332	9:70200746-70266651
PON2		ENSSSCG00000015331	9:70176701-70195601
POP1		ENSSSCG00000006078	4:38815803-38854887
POP4		ENSSSCG00000002854	6:26930676-26940826		FP102582,CH242-162B21,6:26929829-26942692 (Clone quality: bE162B21 on chr=6; Num_of_Contigs=12; )
POP5		ENSSSCG00000009912	14:40587125-40589363		CU062553,CH242-319N22,14:40577284-40626929 (Clone quality: bE319N22 on chr=14; Num_of_Contigs=5; )
POP7		ENSSSCG00000007672	3:6903969-6904391		FP102710,CH242-46P3,3:6895448-6951193 (Clone quality: bE46P3 on chr=3; Num_of_Contigs=3; )

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).