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)

C6orf132		ENSSSCG00000001634	7:42788034-43043911
C6orf142		ENSSSCG00000001485	7:31042281-31229622
C6orf145		ENSSSCG00000001003	7:2508802-2525719		CU041347,CH242-100I6,7:2471583-2575648 (Clone quality: bE100I6 on chr=7; Num_of_Contigs=4; )
C6orf15		ENSSSCG00000001388	7:27473429-27474569	CT737281,CH242-102G9,7:27394698-27581746 (Clone quality: bE102G9 on chr=7; Num_of_Contigs=3; )
C6orf150		ENSSSCG00000004488	1:97567501-97642560
C6orf161		ENSSSCG00000012046	13:139774347-139774514		CU468438,CH242-57G7,13:139758408-139835410 (Clone quality: bE57G7 on chr=13; Num_of_Contigs=2; )
C6orf162		ENSSSCG00000004300	1:58391391-58400243		CU695028,CH242-151K16,1:58329719-58476019 (Clone quality: bE151K16 on chr=1; Num_of_Contigs=1; )
C6orf163		ENSSSCG00000004301	1:58403208-58425771		CU695028,CH242-151K16,1:58329719-58476019 (Clone quality: bE151K16 on chr=1; Num_of_Contigs=1; )
C6orf165		ENSSSCG00000004302	1:58461511-58564989
C6orf168		ENSSSCG00000004348	1:69622561-69698084
C6orf170		ENSSSCG00000004242	1:42805199-43009506
C6orf173		ENSSSCG00000004219	1:38272978-38282604		CU928284,CH242-17H23,1:38245535-38311658 (Clone quality: bE17H23 on chr=1; Num_of_Contigs=2; )
C6orf174		ENSSSCG00000004215	1:37360056-37390687
C6orf182		ENSSSCG00000004391	1:78753058-78845364
C6orf184		ENSSSCG00000004415	1:80558359-80599495		CU075452,CH242-39D23,1:80450203-80633251 (Clone quality: bE39D23 on chr=1; Num_of_Contigs=2; )
C6orf184		ENSSSCG00000004416	1:80604683-80622980		CU075452,CH242-39D23,1:80450203-80633251 (Clone quality: bE39D23 on chr=1; Num_of_Contigs=2; )
C6orf186		ENSSSCG00000004402	1:79663121-79778129
C6orf191		ENSSSCG00000004204	1:34751668-34773941		CU311188,CH242-291B3,1:34751265-34900086 (Clone quality: bE291B3 on chr=1; Num_of_Contigs=1; )
C6orf192		ENSSSCG00000004178	1:32424323-32442984		CU041311,CH242-393L4,1:32405122-32529539 (Clone quality: bE393L4 on chr=1; Num_of_Contigs=2; )
C6orf201		ENSSSCG00000001001	7:2305357-2318380
C6orf203		ENSSSCG00000004375	1:76691938-76704209		CU075351,CH242-118A22,1:76680292-76736903 (Clone quality: bE118A22 on chr=1; Num_of_Contigs=13; )
C6orf204		ENSSSCG00000004249	1:45274988-45352785
C6orf205		ENSSSCG00000001387	7:27412125-27414141	CT737281,CH242-102G9,7:27394698-27581746 (Clone quality: bE102G9 on chr=7; Num_of_Contigs=3; )
C6orf211		ENSSSCG00000004088	1:15909144-15924522		CU695031,CH242-193N5,1:15874941-15929208 (Clone quality: bE193N5 on chr=1; Num_of_Contigs=4; )
C6orf221		ENSSSCG00000004284	1:55408175-55409226		CU468562,CH242-237C6,1:55385514-55409408 (Clone quality: bE237C6 on chr=1; Num_of_Contigs=16; )
C6orf222		ENSSSCG00000001560	7:36666975-36678757
C6orf225		ENSSSCG00000004424	1:81689173-81703828		CU302401,CH242-264N18,1:81686807-81867620 (Clone quality: bE264N18 on chr=1; Num_of_Contigs=1; )
C6orf226		ENSSSCG00000001648	7:43834287-43834493	CR956379,CH242-196P11,7:43779717-43958428 (No clone quality info on bE196P11)
C6orf27		ENSSSCG00000015571	9:119435978-119436142		CU856638,CH242-162B3,9:119428496-119437666 (Clone quality: bE162B3 on chr=9; Num_of_Contigs=25; )
C6orf35		ENSSSCG00000004063	1:10597576-10647947		CU407155,CH242-209K4,1:10594123-10654860 (Clone quality: bE209K4 on chr=1; Num_of_Contigs=8; )
C6orf47		ENSSSCG00000001412	7:27733139-27734032	CU467793,CH242-60C3,7:27581747-27762222 (Clone quality: bE60C3 on chr=7; Num_of_Contigs=1; )
C6orf52		ENSSSCG00000001040	7:7838313-7845561		CU468900,CH242-267B16,7:7778252-7870334 (Clone quality: bE267B16 on chr=7; Num_of_Contigs=4; )
C6orf58		ENSSSCG00000004212	1:37111588-37255856
C6orf62		ENSSSCG00000001094	7:20520104-20532493		CU468861,CH242-123E20,7:20499469-20564207 (Clone quality: bE123E20 on chr=7; Num_of_Contigs=4; )
C6orf64		ENSSSCG00000001590	7:39509554-39509760		CU582979,CH242-382K9,7:39504393-39514192 (Clone quality: bE382K9 on chr=7; Num_of_Contigs=13; )
C6orf70		ENSSSCG00000004010	1:538051-560247
C6orf72		ENSSSCG00000004108	1:17335545-17346933
C6orf81		ENSSSCG00000001550	7:36211793-36222627		CT868716,CH242-516I1,7:36091251-36290487 (Clone quality: bE516I1 on chr=7; Num_of_Contigs=1; )
C6orf89		ENSSSCG00000001569	7:37180914-37212104
C6orf91		ENSSSCG00000004147	1:26899255-26963184		CU076042,CH242-113G19,1:26840256-26965245 (Clone quality: bE113G19 on chr=1; Num_of_Contigs=6; )
C6orf94		ENSSSCG00000004128	1:22352949-22382586
C6orf97		ENSSSCG00000004087	1:15790975-15852632
C7		ENSSSCG00000016859	16:23193261-23253423
C7		ENSSSCG00000014153	2:87185644-87213285
C7		ENSSSCG00000006682	4:103449825-103462674
C7		location ⇒	16:23195202-23195017		CU861949,CH242-227N6,16:23143041-23230906 (Clone quality: bE227N6 on chr=16; Num_of_Contigs=5; )
C7		location ⇒	16:23202553-23202362		CU861949,CH242-227N6,16:23143041-23230906 (Clone quality: bE227N6 on chr=16; Num_of_Contigs=5; )
C7		location ⇒	16:23218055-23217824		CU861949,CH242-227N6,16:23143041-23230906 (Clone quality: bE227N6 on chr=16; Num_of_Contigs=5; )
C7		location ⇒	16:23228038-23227793		CU861949,CH242-227N6,16:23143041-23230906 (Clone quality: bE227N6 on chr=16; Num_of_Contigs=5; )
C7H6orf12		ENSSSCG00000001240	7:24734685-24737354	CU607067,CH242-469P22,7:24676460-24783185 (Clone quality: bE469P22 on chr=7; Num_of_Contigs=2; )

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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).