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)

C20orf114		location ⇒	17:38722410-38722249		CU467098,CH242-181C3,17:38585383-38773516 (Clone quality: bE181C3 on chr=17; Num_of_Contigs=1; )
C20orf114		location ⇒	17:38729889-38729741		CU467098,CH242-181C3,17:38585383-38773516 (Clone quality: bE181C3 on chr=17; Num_of_Contigs=1; )
C20orf118		ENSSSCG00000007325	17:42404998-42413139		CU606915,CH242-133O2,17:42388106-42426177 (Clone quality: bE133O2 on chr=17; Num_of_Contigs=6; )
C20orf12		ENSSSCG00000007094	17:27394725-27461926
C20orf123		ENSSSCG00000007448	17:50812368-50818962		CU606956,CH242-160J21,17:50800293-50822443 (Clone quality: bE160J21 on chr=17; Num_of_Contigs=13; )
C20orf134		ENSSSCG00000007267	17:39089369-39091052
C20orf151		ENSSSCG00000007539	17:63996207-64003974		CU607084,CH242-119P9,17:63957573-64010144 (Clone quality: bE119P9 on chr=17; Num_of_Contigs=6; )
C20orf152		ENSSSCG00000007313	17:41401201-41454985
C20orf160		ENSSSCG00000007239	17:37715336-37733771		FP015768,CH242-273E18,17:37700535-37736005 (Clone quality: bE273E18 on chr=17; Num_of_Contigs=11; )
C20orf165		ENSSSCG00000007429	17:50143067-50144142		CU407252,CH242-441N18,17:50141076-50146604 (Clone quality: bE441N18 on chr=17; Num_of_Contigs=7; )
C20orf175		ENSSSCG00000007470	17:54283352-54316087	CR956376,CH242-7P5,17:54246817-54397383 (No clone quality info on bE7P5)
C20orf177		ENSSSCG00000007531	17:62587172-62588314		CU915385,CH242-197I13,17:62578020-62643589 (Clone quality: bE197I13 on chr=17; Num_of_Contigs=8; )
C20orf186		ENSSSCG00000007255	17:38450417-38567315
C20orf194		ENSSSCG00000007155	17:33896186-34003100
C20orf196		ENSSSCG00000007044	17:13846917-13847063		CU469266,CH242-271I11,17:13835650-13847072 (Clone quality: bE271I11 on chr=17; Num_of_Contigs=11; )
C20orf202		ENSSSCG00000007192	17:35779812-35782066		FP236274,CH242-464F3,17:35778450-35792129 (Clone quality: bE464F3 on chr=17; Num_of_Contigs=5; )
C20orf24		ENSSSCG00000007320	17:42153683-42163444		CU607085,CH242-137E1,17:42127348-42190090 (Clone quality: bE137E1 on chr=17; Num_of_Contigs=8; )
C20orf29		ENSSSCG00000007144	17:33487519-33490255
C20orf3		ENSSSCG00000007132	17:32370736-32385774		CU633263,CH242-272K17,17:32349266-32389163 (Clone quality: bE272K17 on chr=17; Num_of_Contigs=9; )
C20orf39		ENSSSCG00000007130	17:32324663-32325142		CU855486,CH242-118N5,17:32244363-32333444 (Clone quality: bE118N5 on chr=17; Num_of_Contigs=6; )
C20orf4		ENSSSCG00000007315	17:41631092-41649356		CU074399,CH242-98J17,17:41627171-41649890 (Clone quality: bE98J17 on chr=17; Num_of_Contigs=13; )
C20orf43		ENSSSCG00000007496	17:59575710-59619505	CR956640,CH242-155M9,17:59463698-59643740 (No clone quality info on bE155M9)
C20orf44		location ⇒	17:40607600-40607496		CU606930,CH242-408M19,17:40602020-40753042 (Clone quality: bE408M19 on chr=17; Num_of_Contigs=1; )
C20orf44		location ⇒	17:40944783-40944880		FP236779,CH242-109N7,17:40938405-40950217 (Clone quality: bE109N7 on chr=17; Num_of_Contigs=20; )
C20orf44		location ⇒	17:40947953-40948063		FP236779,CH242-109N7,17:40938405-40950217 (Clone quality: bE109N7 on chr=17; Num_of_Contigs=20; )
C20orf54		ENSSSCG00000007199	17:36193307-36199914
C20orf7		ENSSSCG00000007076	17:22738515-22760712
C20orf70		ENSSSCG00000007259	17:38609213-38620092		CU467098,CH242-181C3,17:38585383-38773516 (Clone quality: bE181C3 on chr=17; Num_of_Contigs=1; )
C20orf72		ENSSSCG00000007089	17:27010161-27020828
C20orf74		ENSSSCG00000007107	17:29348644-29471022
C20orf79		ENSSSCG00000007099	17:27759350-27759817		CU062516,CH242-112K11,17:27713189-27808664 (Clone quality: bE112K11 on chr=17; Num_of_Contigs=5; )
C20orf82		ENSSSCG00000007073	17:22231322-22314684
C20orf85		ENSSSCG00000007510	17:60976074-60986059	CR956359,CH242-256J18,17:60938475-61076184 (No clone quality info on bE256J18)
C20orf94		ENSSSCG00000007066	17:19543903-19617280		CU672248,CH242-357N21,17:19541741-19650833 (Clone quality: bE357N21 on chr=17; Num_of_Contigs=3; )
C20orf96		ENSSSCG00000007212	17:36827700-36877553
C21orf33		ENSSSCG00000009470	11:48037456-48040828		CU457401,CH242-185J22,11:48004963-48075214 (Clone quality: bE185J22 on chr=11; Num_of_Contigs=2; )
C21orf59		ENSSSCG00000012036	13:138719974-138735070
C21orf62		ENSSSCG00000012038	13:138826660-138827325		CU633469,CH242-211J7,13:138818322-138840852 (Clone quality: bE211J7 on chr=13; Num_of_Contigs=9; )
C21orf66		ENSSSCG00000012037	13:138776582-138792041
C21orf7		ENSSSCG00000012028	13:137032409-137048797
C22orf13		ENSSSCG00000010059	14:50651248-50661604		CU468600,CH242-236F16,14:50621163-50709737 (Clone quality: bE236F16 on chr=14; Num_of_Contigs=6; )
C22orf15		ENSSSCG00000010074	14:50938894-50940557		CU468588,CH242-282B12,14:50917167-50969731 (Clone quality: bE282B12 on chr=14; Num_of_Contigs=2; )
C22orf23		ENSSSCG00000000117	5:6471938-6478829		CU633351,CH242-161B9,5:6445792-6484454 (Clone quality: bE161B9 on chr=5; Num_of_Contigs=5; )
C22orf25		ENSSSCG00000010134	14:52706174-52717838		CT737345,CH242-178J1,14:52684022-52723015 (Clone quality: bE178J1 on chr=14; Num_of_Contigs=3; )
C22orf26		ENSSSCG00000012814	X:123488764-123755505
C22orf28		ENSSSCG00000000158	5:10762279-10789028
C22orf30		ENSSSCG00000010033	14:49240679-49294438	CU062407,CH242-82N3,14:49222813-49419557 (Clone quality: bE82N3 on chr=14; Num_of_Contigs=7; )
C22orf33		ENSSSCG00000000132	5:7043258-7054882		CU633243,CH242-20D10,5:7039128-7109453 (Clone quality: bE20D10 on chr=5; Num_of_Contigs=6; )
C22orf36		ENSSSCG00000010057	14:50623355-50626970		CU468600,CH242-236F16,14:50621163-50709737 (Clone quality: bE236F16 on chr=14; Num_of_Contigs=6; )
C22orf39		ENSSSCG00000010120	14:52220105-52223440		CU618331,CH242-323M12,14:52088643-52233728 (Clone quality: bE323M12 on chr=14; Num_of_Contigs=3; )

Go to records:
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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).