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)

C12orf50		ENSSSCG00000000924	5:90203371-90233836
C12orf51		ENSSSCG00000009885	14:39468945-39520006
C12orf52		ENSSSCG00000009878	14:39072718-39077182		CU694784,CH242-25E24,14:39068759-39084260 (Clone quality: bE25E24 on chr=14; Num_of_Contigs=11; )
C12orf53		ENSSSCG00000000692	5:60032014-60152075
C12orf56		ENSSSCG00000000464	5:28613031-28689037
C12orf60		ENSSSCG00000000609	5:55041656-55042351		CU463008,CH242-511E2,5:55026707-55063558 (Clone quality: bE511E2 on chr=5; Num_of_Contigs=3; )
C12orf63		ENSSSCG00000000889	5:82317371-82318441		CU896549,CH242-102O23,5:82283330-82320429 (Clone quality: bE102O23 on chr=5; Num_of_Contigs=5; )
C12orf64		ENSSSCG00000000943	5:95661092-95698781		CU861561,CH242-366N21,5:95637273-95706528 (Clone quality: bE366N21 on chr=5; Num_of_Contigs=1; )
C12orf65		ENSSSCG00000009774	14:29570340-29584262
C12orf66		ENSSSCG00000000465	5:28726677-28745861		CU855647,CH242-276J18,5:28678881-28748090 (Clone quality: bE276J18 on chr=5; Num_of_Contigs=6; )
C12orf69		ENSSSCG00000000610	5:55053257-55053934		CU463008,CH242-511E2,5:55026707-55063558 (Clone quality: bE511E2 on chr=5; Num_of_Contigs=3; )
C12orf70		ENSSSCG00000000550	5:44781532-44799632		CU633729,CH242-7N4,5:44779925-44807509 (Clone quality: bE7N4 on chr=5; Num_of_Contigs=9; )
C12orf76		ENSSSCG00000009923	14:41109275-41109427		CU467935,CH242-88C19,14:41101390-41125413 (Clone quality: bE88C19 on chr=14; Num_of_Contigs=7; )
C13orf1		ENSSSCG00000009390	11:17744988-17766252		CU062582,CH242-56C13,11:17739187-17770954 (Clone quality: bE56C13 on chr=11; Num_of_Contigs=8; )
C13orf15		ENSSSCG00000009434	11:24448858-24448989		CU424441,CH242-487M5,11:24447326-24449542 (Clone quality: bE487M5 on chr=11; Num_of_Contigs=11; )
C13orf18		ENSSSCG00000009410	11:20402330-20419821
C13orf23		ENSSSCG00000009367	11:13879572-13881262		CU633806,CH242-181G7,11:13875841-13881304 (Clone quality: bE181G7 on chr=11; Num_of_Contigs=20; )
C13orf27		ENSSSCG00000009531	11:71931794-71939079
C13orf30		ENSSSCG00000009428	11:23177327-23185533		CU639473,CH242-156N10,11:23157743-23203373 (Clone quality: bE156N10 on chr=11; Num_of_Contigs=4; )
C13orf31		ENSSSCG00000009425	11:22268960-22277640
C13orf33		ENSSSCG00000009331	11:6936035-6952817
C13orf36		ENSSSCG00000009355	11:12055587-12055910		CU606927,CH242-319N3,11:12054274-12069090 (Clone quality: bE319N3 on chr=11; Num_of_Contigs=4; )
C13orf37		ENSSSCG00000009459	11:44217359-44233478
C13orf39		ENSSSCG00000009529	11:71866046-71872206		CU915499,CH242-3J3,11:71857643-71879946 (Clone quality: bE3J3 on chr=11; Num_of_Contigs=4; )
C14orf101		ENSSSCG00000005062	1:194402567-194509042
C14orf102		ENSSSCG00000002434	7:119898655-119947154
C14orf104		ENSSSCG00000005007	1:187905794-187907020		CU633502,CH242-240C20,1:187883994-187931470 (Clone quality: bE240C20 on chr=1; Num_of_Contigs=4; )
C14orf105		ENSSSCG00000005067	1:195208443-195244022
C14orf106		ENSSSCG00000004999	1:183798730-183820683		CU570961,CH242-89I4,1:183793786-183899389 (Clone quality: bE89I4 on chr=1; Num_of_Contigs=2; )
C14orf109		ENSSSCG00000002458	7:122793174-122794882	CT737384,CH242-22E21,7:122753757-122927074 (Clone quality: bE22E21 on chr=7; Num_of_Contigs=2; )
C14orf115		ENSSSCG00000002364	7:105854978-105857074		CU682356,CH242-154M12,7:105845054-105945783 (Clone quality: bE154M12 on chr=7; Num_of_Contigs=2; )
C14orf118		ENSSSCG00000002387	7:107338418-107381296		CU329678,CH242-143K5,7:107303629-107395791 (Clone quality: bE143K5 on chr=7; Num_of_Contigs=3; )
C14orf119		ENSSSCG00000002035	7:82358403-82358828		CU468526,CH242-14D10,7:82320563-82367321 (Clone quality: bE14D10 on chr=7; Num_of_Contigs=8; )
C14orf126		ENSSSCG00000001969	7:74188390-74210719
C14orf129		ENSSSCG00000002503	7:126524436-126543961		CU633930,CH242-67N6,7:126414601-126572725 (Clone quality: bE67N6 on chr=7; Num_of_Contigs=2; )
C14orf129		location ⇒	7:126540180-126540443		CU633930,CH242-67N6,7:126414601-126572725 (Clone quality: bE67N6 on chr=7; Num_of_Contigs=2; )
C14orf133		ENSSSCG00000002403	7:108622644-108630968
C14orf135		ENSSSCG00000005082	1:197841769-197871367
C14orf138		ENSSSCG00000005014	1:188279413-188280600		CU062586,CH242-59F9,1:188278728-188282993 (Clone quality: bE59F9 on chr=1; Num_of_Contigs=15; )
C14orf142		ENSSSCG00000002459	7:122804995-122809152	CT737384,CH242-22E21,7:122753757-122927074 (Clone quality: bE22E21 on chr=7; Num_of_Contigs=2; )
C14orf143		ENSSSCG00000002430	7:119454062-119620290
C14orf145		ENSSSCG00000002410	7:111203881-111354950
C14orf147		ENSSSCG00000001962	7:71090536-71113034		CU304973,CH242-141J19,7:71046495-71136465 (Clone quality: bE141J19 on chr=7; Num_of_Contigs=5; )
C14orf153		ENSSSCG00000002547	7:132839376-132888001
C14orf159		ENSSSCG00000002438	7:120695617-120734716	CT737342,CH242-172F13,7:120694979-120886569 (Clone quality: bE172F13 on chr=7; Num_of_Contigs=3; )
C14orf166		ENSSSCG00000005029	1:189940772-189958405
C14orf166B		ENSSSCG00000002391	7:107969729-107996864		CU062448,CH242-200H14,7:107965357-108017790 (Clone quality: bE200H14 on chr=7; Num_of_Contigs=5; )
C14orf174		ENSSSCG00000002400	7:108423088-108426491		CU468241,CH242-271B5,7:108423068-108427161 (Clone quality: bE271B5 on chr=7; Num_of_Contigs=18; )
C14orf179		ENSSSCG00000002386	7:107168980-107264764		CT737390,CH242-96M21,7:107128395-107303628 (Clone quality: bE96M21 on chr=7; Num_of_Contigs=2; )
C14orf181		ENSSSCG00000002301	7:101012085-101012393		CU683824,CH242-124P13,7:101006661-101044236 (Clone quality: bE124P13 on chr=7; 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).