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)

PDGFRL		location ⇒	17:5121194-5121490		CU682348,CH242-166L11,17:5095201-5121917 (Clone quality: bE166L11 on chr=17; Num_of_Contigs=5; )
PDGFRL		location ⇒	17:5186171-5186772		CU606969,CH242-163K19,17:5183877-5272411 (Clone quality: bE163K19 on chr=17; Num_of_Contigs=5; )
PDGFRL		location ⇒	17:5274445-5274743		CU606969,CH242-163K19,17:5272512-5280465 (Clone quality: bE163K19 on chr=17; Num_of_Contigs=5; )
PDHX		ENSSSCG00000013298	2:24440038-24519462
PDIA2		ENSSSCG00000007983	3:35373368-35374861		FP102907,CH242-215K19,3:35373346-35375394 (Clone quality: bE215K19 on chr=3; Num_of_Contigs=7; )
PDIA3		ENSSSCG00000004700	1:133861462-133890030
PDIA3		location ⇒	1:133867690-133867574	CU062440,CH242-140A18,1:133801433-133876483 (Clone quality: bE140A18 on chr=1; Num_of_Contigs=11; )
PDIA3		location ⇒	1:133869851-133869720	CU062440,CH242-140A18,1:133801433-133876483 (Clone quality: bE140A18 on chr=1; Num_of_Contigs=11; )
PDIA3		location ⇒	1:133879510-133879391		CU861634,CH242-463N18,1:133876484-133885169 (Clone quality: bE463N18 on chr=1; Num_of_Contigs=7; )
PDIA3		location ⇒	1:133889957-133889686		CU861634,CH242-463N18,1:133885270-133939793 (Clone quality: bE463N18 on chr=1; Num_of_Contigs=7; )
PDIA4		ENSSSCG00000015453	9:101857057-101875916
PDIA5		ENSSSCG00000011870	13:103339909-103357650
PDIA6		ENSSSCG00000008633	3:116578644-116601790
PDILT		ENSSSCG00000007860	3:23046506-23070700
PDK1		ENSSSCG00000008060	3:37050515-37069536
PDK1		ENSSSCG00000015957	15:73568651-73576378
PDK1		location ⇒	15:106164301-106164034		CU694911,CH242-42I19,15:106161918-106186670 (Clone quality: bE42I19 on chr=15; Num_of_Contigs=2; )
PDK1		location ⇒	15:106165494-106165055		CU694911,CH242-42I19,15:106161918-106186670 (Clone quality: bE42I19 on chr=15; Num_of_Contigs=2; )
PDK1		location ⇒	15:73575570-73575786		CU469224,CH242-428F9,15:73572245-73583289 (Clone quality: bE428F9 on chr=15; Num_of_Contigs=15; )
PDK1		location ⇒	15:73611759-73611943		CU469224,CH242-428F9,15:73609541-73612133 (Clone quality: bE428F9 on chr=15; Num_of_Contigs=15; )
PDK3		ENSSSCG00000012181	X:19401655-19471675		CU207272,CH242-227G20,X:19315864-19481708 (Clone quality: bE227G20 on chr=X; Num_of_Contigs=2; )
PDK4		ENSSSCG00000015334	9:70465829-70477355		CU633220,CH242-147O16,9:70459550-70626938 (Clone quality: bE147O16 on chr=9; Num_of_Contigs=1; )
PDL1		ENSSSCG00000005211	1:226573119-226592640		CU457399,CH242-185B23,1:226537240-226608332 (Clone quality: bE185B23 on chr=1; Num_of_Contigs=9; )
PDLIM1		ENSSSCG00000010493	14:111799609-111828760
PDLIM2		ENSSSCG00000009625	14:6782366-6841003
PDLIM3		ENSSSCG00000015796	15:43764259-43794626
PDLIM4		ENSSSCG00000014274	2:122341491-122355933	CU372899,CH242-156J20,2:122331474-122542304 (Clone quality: bE156J20 on chr=2; Num_of_Contigs=2; )
PDLIM5		ENSSSCG00000009192	8:107127204-107340415
PDP1		ENSSSCG00000006107	4:43377017-43378630	CU179672,CH242-371G3,4:43234569-43424391 (Clone quality: bE371G3 on chr=4; Num_of_Contigs=2; )
PDPK1		ENSSSCG00000008060	3:37050515-37069536
PDPN		ENSSSCG00000003451	6:50299906-50308519		FP236409,CH242-139N22,6:50299882-50316412 (Clone quality: bE139N22 on chr=6; Num_of_Contigs=12; )
PDPR		ENSSSCG00000002721	6:9634339-9651203
PDRG1		ENSSSCG00000007237	17:37654582-37660722		CU694986,CH242-170L12,17:37609131-37681341 (Clone quality: bE170L12 on chr=17; Num_of_Contigs=5; )
PDS5B		ENSSSCG00000009345	11:8582224-8907912
PDSS1		ENSSSCG00000011061	10:46835913-46886624
PDYN		ENSSSCG00000007180	17:35038893-35055061		CU076083,CH242-165N9,17:35002939-35058589 (Clone quality: bE165N9 on chr=17; Num_of_Contigs=11; )
PDYN		location ⇒	17:35049968-35050118		CU076083,CH242-165N9,17:35002939-35058589 (Clone quality: bE165N9 on chr=17; Num_of_Contigs=11; )
PDYN		location ⇒	17:35052884-35053927		CU076083,CH242-165N9,17:35002939-35058589 (Clone quality: bE165N9 on chr=17; Num_of_Contigs=11; )
PDYN		location ⇒	17:35053968-35054738		CU076083,CH242-165N9,17:35002939-35058589 (Clone quality: bE165N9 on chr=17; Num_of_Contigs=11; )
PDYN		location ⇒	17:35054774-35055061		CU076083,CH242-165N9,17:35002939-35058589 (Clone quality: bE165N9 on chr=17; Num_of_Contigs=11; )
PDZD11		ENSSSCG00000012378	X:54910416-54913557	CU463005,CH242-411O22,X:54745943-54944013 (Clone quality: bE411O22 on chr=X; Num_of_Contigs=1; )
PDZD2		ENSSSCG00000016810	16:16012742-16127043		CU570817,CH242-136M15,16:16010401-16139008 (Clone quality: bE136M15 on chr=16; Num_of_Contigs=5; )
PDZD2		location ⇒	16:15853507-15853937		CU855706,CH242-278I11,16:15803335-15885217 (Clone quality: bE278I11 on chr=16; Num_of_Contigs=4; )
PDZD2		location ⇒	16:16012741-16012941		CU570817,CH242-136M15,16:16010401-16139008 (Clone quality: bE136M15 on chr=16; Num_of_Contigs=5; )
PDZD4		ENSSSCG00000012785	X:122657107-122679349		CU915581,CH242-139K22,X:122611684-122679782 (Clone quality: bE139K22 on chr=X; Num_of_Contigs=13; )
PDZD7		ENSSSCG00000010559	14:116940201-116944276		CU062549,CH242-28G23,14:116935216-116944308 (Clone quality: bE28G23 on chr=14; Num_of_Contigs=16; )
PDZD8		ENSSSCG00000010669	14:133261862-133414015
PDZK1		ENSSSCG00000006693	4:103708512-103740596		CU467072,CH242-100P4,4:103582921-103758989 (Clone quality: bE100P4 on chr=4; Num_of_Contigs=2; )
PDZK1IP1		ENSSSCG00000003753	6:88676320-88682035		CU467007,CH242-257B4,6:88671282-88779821 (Clone quality: bE257B4 on chr=6; Num_of_Contigs=2; )
PDZK3		ENSSSCG00000016810	16:16012742-16127043		CU570817,CH242-136M15,16:16010401-16139008 (Clone quality: bE136M15 on chr=16; Num_of_Contigs=5; )

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).