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)

CCDC6		ENSSSCG00000010211	14:65804686-65924417
CCDC60		ENSSSCG00000009842	14:33362990-33549867
CCDC61		ENSSSCG00000003100	6:36259507-36337804
CCDC62		ENSSSCG00000009787	14:30104686-30142146
CCDC62		location ⇒	14:30122926-30122839		CU468020,CH242-65H10,14:30110535-30186691 (Clone quality: bE65H10 on chr=14; Num_of_Contigs=4; )
CCDC62		location ⇒	14:30130113-30129940		CU468020,CH242-65H10,14:30110535-30186691 (Clone quality: bE65H10 on chr=14; Num_of_Contigs=4; )
CCDC62		location ⇒	14:30139041-30138845		CU468020,CH242-65H10,14:30110535-30186691 (Clone quality: bE65H10 on chr=14; Num_of_Contigs=4; )
CCDC62		location ⇒	14:30142040-30141947		CU468020,CH242-65H10,14:30110535-30186691 (Clone quality: bE65H10 on chr=14; Num_of_Contigs=4; )
CCDC63		ENSSSCG00000009829	14:32184521-32235330
CCDC64		ENSSSCG00000009896	14:40150998-40268797		CU062612,CH242-93C5,14:40150672-40322842 (Clone quality: bE93C5 on chr=14; Num_of_Contigs=2; )
CCDC65		ENSSSCG00000000179	5:13544774-13552649
CCDC68		ENSSSCG00000004534	1:107273648-107306982		CU469481,CH242-280O12,1:107132216-107314734 (Clone quality: bE280O12 on chr=1; Num_of_Contigs=1; )
CCDC70		ENSSSCG00000009383	11:16073726-16074418		CU856026,CH242-272H15,11:16072068-16078470 (Clone quality: bE272H15 on chr=11; Num_of_Contigs=15; )
CCDC71		ENSSSCG00000011378	13:26771165-26772577		CU856115,CH242-45E6,13:26748496-26786404 (Clone quality: bE45E6 on chr=13; Num_of_Contigs=7; )
CCDC72		ENSSSCG00000011351	13:26076233-26078942		FP102065,CH242-145E9,13:26070359-26088378 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CCDC75		ENSSSCG00000008497	3:96193433-96205293		CU487215,CH242-226P20,3:96159197-96242245 (Clone quality: bE226P20 on chr=3; Num_of_Contigs=5; )
CCDC76		ENSSSCG00000006869	4:122853285-122865731		CU137727,CH242-139N24,4:122852953-122865826 (Clone quality: bE139N24 on chr=4; Num_of_Contigs=16; )
CCDC77		ENSSSCG00000000751	5:63512603-63515938		FP102715,CH242-509N10,5:63512295-63521618 (Clone quality: bE509N10 on chr=5; Num_of_Contigs=14; )
CCDC80		ENSSSCG00000011928	13:109781535-109818740		CU633371,CH242-228G19,13:109724885-109839599 (Clone quality: bE228G19 on chr=13; Num_of_Contigs=4; )
CCDC81		ENSSSCG00000014917	9:20477416-20528277
CCDC82		ENSSSCG00000014972	9:28945703-28969864
CCDC83		ENSSSCG00000014912	9:20006319-20068039
CCDC84		ENSSSCG00000015102	9:44820879-44830008		CU695209,CH242-241K21,9:44763573-44853404 (Clone quality: bE241K21 on chr=9; Num_of_Contigs=5; )
CCDC85A		ENSSSCG00000008396	3:78802518-79005245
CCDC85B		ENSSSCG00000012968	2:4814406-4815014		CU928325,CH242-208C18,2:4805866-4836669 (Clone quality: bE208C18 on chr=2; Num_of_Contigs=5; )
CCDC86		ENSSSCG00000013105	2:9243698-9252370		CU861565,CH242-480L10,2:9238313-9266378 (Clone quality: bE480L10 on chr=2; Num_of_Contigs=15; )
CCDC87		ENSSSCG00000012933	2:4119142-4121715		CU928093,CH242-168G1,2:4114600-4125297 (Clone quality: bE168G1 on chr=2; Num_of_Contigs=25; )
CCDC88A		ENSSSCG00000008406	3:79937800-80024315
CCDC88B		ENSSSCG00000013042	2:6275170-6289472
CCDC88C		ENSSSCG00000002440	7:120781577-120909080
CCDC89		ENSSSCG00000014908	9:19858624-19859745		CU928672,CH242-451F17,9:19839178-19863160 (Clone quality: bE451F17 on chr=9; Num_of_Contigs=3; )
CCDC90A		ENSSSCG00000001057	7:10324292-10347927		CT841709,CH242-326P18,7:10261819-10389345 (Clone quality: bE326P18 on chr=7; Num_of_Contigs=2; )
CCDC90B		ENSSSCG00000014903	9:17524545-17554787		FP236281,CH242-190O9,9:17468362-17575805 (Clone quality: bE190O9 on chr=9; Num_of_Contigs=3; )
CCDC91		ENSSSCG00000000543	5:43791366-43941193
CCDC91		location ⇒	5:43791703-43791618		CU972370,CH242-276O14,5:43790096-43802867 (Clone quality: bE276O14 on chr=5; Num_of_Contigs=7; )
CCDC91		location ⇒	5:43792037-43791779		CU972370,CH242-276O14,5:43790096-43802867 (Clone quality: bE276O14 on chr=5; Num_of_Contigs=7; )
CCDC91		location ⇒	5:43860485-43860370		CU855763,CH242-8G15,5:43836877-43961385 (Clone quality: bE8G15 on chr=5; Num_of_Contigs=2; )
CCDC91		location ⇒	5:44025413-44025211		CU855598,CH242-334F13,5:44021914-44077347 (Clone quality: bE334F13 on chr=5; Num_of_Contigs=5; )
CCDC92		ENSSSCG00000009764	14:29178409-29193158		CU638677,CH242-254G23,14:29172666-29298652 (Clone quality: bE254G23 on chr=14; Num_of_Contigs=4; )
CCDC93		ENSSSCG00000015714	15:22189570-22286415	CU406995,CH242-505D21,15:22112976-22359365 (Clone quality: bE505D21 on chr=15; Num_of_Contigs=4; )
CCDC94		ENSSSCG00000013499	2:48423562-48439927		CU929466,CH242-60A20,2:48379010-48440195 (Clone quality: bE60A20 on chr=2; Num_of_Contigs=5; )
CCDC97		ENSSSCG00000003016	6:34081896-34089206		FP236582,CH242-238L13,6:34079127-34089697 (Clone quality: bE238L13 on chr=6; Num_of_Contigs=11; )
CCDC99		ENSSSCG00000017011	16:51573495-51592490
CCHCR1		ENSSSCG00000001391	7:27501724-27514557	CT737281,CH242-102G9,7:27394698-27581746 (Clone quality: bE102G9 on chr=7; Num_of_Contigs=3; )
CCIN		ENSSSCG00000005340	1:248111390-248113156		CU633506,CH242-257H11,1:248107578-248115549 (Clone quality: bE257H11 on chr=1; Num_of_Contigs=8; )
CCK		ENSSSCG00000001660	7:44023413-44051991
CCK		ENSSSCG00000014631	9:2721407-2831787
CCK		ENSSSCG00000011277	13:21632786-21637965
CCK		location ⇒	13:21633190-21632786		CU928734,CH242-406G23,13:21631190-21635342 (Clone quality: bE406G23 on chr=13; Num_of_Contigs=4; )
CCK		location ⇒	13:21636860-21636646		CU928734,CH242-406G23,13:21635443-21658475 (Clone quality: bE406G23 on chr=13; Num_of_Contigs=4; )

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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).