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)

PLD2		ENSSSCG00000017912	12:49271043-49281709		CU929524,CH242-164N17,12:49266035-49282374 (Clone quality: bE164N17 on chr=12; Num_of_Contigs=22; )
PLD4		ENSSSCG00000002554	7:133126052-133133061		CU695123,CH242-103I13,7:133119554-133156545 (Clone quality: bE103I13 on chr=7; Num_of_Contigs=13; )
PLD5		ENSSSCG00000010867	10:15353365-15364941
PLDN		ENSSSCG00000004667	1:131763860-131769732		CU012064,CH242-22G24,1:131760641-131808567 (Clone quality: bE22G24 on chr=1; Num_of_Contigs=4; )
PLDN		location ⇒	1:131770391-131770483		CU012064,CH242-22G24,1:131760641-131808567 (Clone quality: bE22G24 on chr=1; Num_of_Contigs=4; )
PLDN		location ⇒	1:131772413-131772489		CU012064,CH242-22G24,1:131760641-131808567 (Clone quality: bE22G24 on chr=1; Num_of_Contigs=4; )
PLDN		location ⇒	1:187872897-187872960		CU633502,CH242-240C20,1:187832890-187878221 (Clone quality: bE240C20 on chr=1; Num_of_Contigs=4; )
PLDN		location ⇒	1:188102010-188101947		CU606975,CH242-251A8,1:188088869-188146416 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
PLEK		ENSSSCG00000008348	3:67854564-67881271
PLEK2		ENSSSCG00000002290	7:99518891-99541547		CT967298,CH242-176H11,7:99387011-99569801 (Clone quality: bE176H11 on chr=7; Num_of_Contigs=1; )
PLEKHA1		ENSSSCG00000010702	14:138385176-138438885		CU469121,CH242-146A14,14:138306093-138465519 (Clone quality: bE146A14 on chr=14; Num_of_Contigs=3; )
PLEKHA2		ENSSSCG00000015811	15:44991886-45044229
PLEKHA4		ENSSSCG00000003137	6:37541633-37567093
PLEKHA5		ENSSSCG00000000588	5:51518327-51661551
PLEKHA6		ENSSSCG00000015281	9:62455617-62516782
PLEKHA7		ENSSSCG00000013382	2:39577038-39651269
PLEKHA9		ENSSSCG00000016682	18:41242458-41276816		CU694612,CH242-369I21,18:41219287-41305004 (Clone quality: bE369I21 on chr=18; Num_of_Contigs=4; )
PLEKHB1		ENSSSCG00000014827	9:7748335-7761706		CU638671,CH242-188E8,9:7745474-7773512 (Clone quality: bE188E8 on chr=9; Num_of_Contigs=8; )
PLEKHC1		ENSSSCG00000005042	1:191030327-191069893
PLEKHC1		location ⇒	1:190994506-190994085		CU407115,CH242-342H5,1:190778660-191001332 (Clone quality: bE342H5 on chr=1; Num_of_Contigs=1; )
PLEKHC1		location ⇒	1:191012617-191012388		CU041278,CH242-406M6,1:191001333-191027777 (Clone quality: bE406M6 on chr=1; Num_of_Contigs=6; )
PLEKHC1		location ⇒	1:191030467-191030634		CU041278,CH242-406M6,1:191030288-191036041 (Clone quality: bE406M6 on chr=1; Num_of_Contigs=6; )
PLEKHC1		location ⇒	1:191057990-191058212		CU041278,CH242-406M6,1:191040985-191070434 (Clone quality: bE406M6 on chr=1; Num_of_Contigs=6; )
PLEKHC110979		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
PLEKHF1		ENSSSCG00000002852	6:26868342-26869193		FP102582,CH242-162B21,6:26864207-26872823 (Clone quality: bE162B21 on chr=6; Num_of_Contigs=12; )
PLEKHG2		ENSSSCG00000010709	14:138683137-138691683
PLEKHG2		location ⇒	14:138685376-138685529		FP236263,CH242-159G20,14:138684424-138694872 (Clone quality: bE159G20 on chr=14; Num_of_Contigs=8; )
PLEKHG2		location ⇒	14:138685819-138685960		FP236263,CH242-159G20,14:138684424-138694872 (Clone quality: bE159G20 on chr=14; Num_of_Contigs=8; )
PLEKHG2		location ⇒	14:138686142-138686345		FP236263,CH242-159G20,14:138684424-138694872 (Clone quality: bE159G20 on chr=14; Num_of_Contigs=8; )
PLEKHG2		location ⇒	14:138686754-138686847		FP236263,CH242-159G20,14:138684424-138694872 (Clone quality: bE159G20 on chr=14; Num_of_Contigs=8; )
PLEKHG3		ENSSSCG00000002276	7:97245534-97291922
PLEKHG4		ENSSSCG00000002782	6:13282306-13290479		CU929920,CH242-351A16,6:13258514-13336829 (Clone quality: bE351A16 on chr=6; Num_of_Contigs=8; )
PLEKHG5		ENSSSCG00000003376	6:45683446-45694193		FP102449,CH242-60I1,6:45665679-45695205 (Clone quality: bE60I1 on chr=6; Num_of_Contigs=6; )
PLEKHG6		ENSSSCG00000000709	5:60350626-60367494
PLEKHH1		ENSSSCG00000002292	7:99678445-99710443
PLEKHH2		ENSSSCG00000008456	3:90049914-90079122
PLEKHH2		location ⇒	3:90043697-90043879		CU914350,CH242-523I3,3:90039731-90046289 (Clone quality: bE523I3 on chr=3; Num_of_Contigs=9; )
PLEKHH2		location ⇒	3:90053219-90053393		CU914350,CH242-523I3,3:90046390-90053733 (Clone quality: bE523I3 on chr=3; Num_of_Contigs=9; )
PLEKHH2		location ⇒	3:90188211-90188048		CU914350,CH242-523I3,3:90180240-90189913 (Clone quality: bE523I3 on chr=3; Num_of_Contigs=9; )
PLEKHH2		location ⇒	3:90198019-90197055		CU914350,CH242-523I3,3:90190014-90211361 (Clone quality: bE523I3 on chr=3; Num_of_Contigs=9; )
PLEKHH3		ENSSSCG00000017391	12:17709682-17718288		CU928483,CH242-17I6,12:17706452-17731169 (Clone quality: bE17I6 on chr=12; Num_of_Contigs=8; )
PLEKHJ1		ENSSSCG00000013453	2:47043893-47046535		CU929035,CH242-88G19,2:47043234-47050088 (Clone quality: bE88G19 on chr=2; Num_of_Contigs=27; )
PLEKHM2		ENSSSCG00000003468	6:51505946-51522784		CU457447,CH242-71A8,6:51494097-51525122 (Clone quality: bE71A8 on chr=6; Num_of_Contigs=17; )
PLEKHM3		ENSSSCG00000016141	15:103977848-104018507		CU929834,CH242-55M19,15:103961068-104027043 (Clone quality: bE55M19 on chr=15; Num_of_Contigs=4; )
PLEKHO2		ENSSSCG00000004547	1:110364178-110373868		CU582916,CH242-24C1,1:110333852-110375167 (Clone quality: bE24C1 on chr=1; Num_of_Contigs=8; )
PLF4_PIG		ENSSSCG00000000243	5:16294567-16295847		CU930049,CH242-185F9,5:16292056-16303046 (Clone quality: bE185F9 on chr=5; Num_of_Contigs=28; )
PLF4_PIG		ENSSSCG00000008955	8:59479535-59480815		CU928337,CH242-266F15,8:59474833-59511571 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
PLG		ENSSSCG00000004038	1:8079895-8127335	FP085554,CH242-84O6,1:8054542-8235565 (Clone quality: bE84O6 on chr=1; Num_of_Contigs=4; )
PLG		location ⇒	1:7899549-7899711		FP236219,CH242-342G7,1:7888437-7900388 (Clone quality: bE342G7 on chr=1; Num_of_Contigs=3; )
PLG		location ⇒	1:7910538-7910716		FP236219,CH242-342G7,1:7900489-7915252 (Clone quality: bE342G7 on chr=1; 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).