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)

KIAA0391		ENSSSCG00000001950	7:70452302-70457469		CT797470,CH242-32J12,7:70421409-70573491 (Clone quality: bE32J12 on chr=7; Num_of_Contigs=1; )
KIAA0406		ENSSSCG00000007340	17:43455607-43485186
KIAA0427		ENSSSCG00000004506	1:101379400-101610813
KIAA0467		ENSSSCG00000003941	6:120041792-120067411
KIAA0494		ENSSSCG00000003895	6:117834770-117850345
KIAA0513		ENSSSCG00000002666	6:2255862-2272049
KIAA0528		ENSSSCG00000000570	5:49408450-49435888
KIAA0556		ENSSSCG00000007814	3:17381873-17453424
KIAA0562		ENSSSCG00000003362	6:43871481-43933301
KIAA0586		ENSSSCG00000005076	1:196517133-196569662
KIAA0649		ENSSSCG00000005761	1:289881827-289883467		FP102268,CH242-95K10,1:289878419-289886139 (Clone quality: bE95K10 on chr=1; Num_of_Contigs=5; )
KIAA0652		ENSSSCG00000013257	2:14145639-14202946		FP067428,CH242-183B23,2:14139735-14217546 (Clone quality: bE183B23 on chr=2; Num_of_Contigs=2; )
KIAA0664		ENSSSCG00000017835	12:46141612-46153812
KIAA0748		ENSSSCG00000000299	5:18486835-18529196		CU457417,CH242-51K19,5:18437499-18543401 (Clone quality: bE51K19 on chr=5; Num_of_Contigs=5; )
KIAA0753		ENSSSCG00000017890	12:47975602-48039072
KIAA0774		ENSSSCG00000009323	11:5759042-5907802
KIAA0776		ENSSSCG00000004339	1:66899506-66959696
KIAA0802		ENSSSCG00000003684	6:67761947-67863475
KIAA0831		ENSSSCG00000005058	1:193284105-193324373
KIAA0895		ENSSSCG00000016659	18:36963080-37172670
KIAA0895L		ENSSSCG00000002789	6:13368273-13389141
KIAA0907		ENSSSCG00000006504	4:98044798-98062415		CU151868,CH242-286M6,4:97945564-98074701 (Clone quality: bE286M6 on chr=4; Num_of_Contigs=4; )
KIAA0913		ENSSSCG00000010309	14:79813943-79828231
KIAA0922		ENSSSCG00000009007	8:64733806-64906666
KIAA0947		ENSSSCG00000017108	16:73488379-73501262
KIAA1009		ENSSSCG00000004289	1:55627526-55733990
KIAA1012		ENSSSCG00000003728	6:80077649-80100233
KIAA1024		ENSSSCG00000001775	7:54559073-54572235
KIAA1024L		ENSSSCG00000014261	2:120266368-120279126
KIAA1033		ENSSSCG00000000840	5:74880818-74934583
KIAA1045		ENSSSCG00000005296	1:246802065-246809241		CU915495,CH242-38L5,1:246801644-246819597 (Clone quality: bE38L5 on chr=1; Num_of_Contigs=9; )
KIAA1107		ENSSSCG00000006906	4:129046915-129064487
KIAA1109		ENSSSCG00000009090	8:87182529-87420613
KIAA1128		ENSSSCG00000010351	14:89022007-89119743
KIAA1147		ENSSSCG00000016491	18:6690270-6740429
KIAA1161		ENSSSCG00000010982	10:30926039-30926641
KIAA1199		ENSSSCG00000001783	7:55854836-55926659
KIAA1210		ENSSSCG00000012628	X:96956669-96964884	CU928929,CH242-445E7,X:96956667-96981023 (Clone quality: bE445E7 on chr=X; Num_of_Contigs=7; )
KIAA1211		ENSSSCG00000008903	8:47256223-47257803		CU856166,CH242-62C23,8:47256220-47262753 (Clone quality: bE62C23 on chr=8; Num_of_Contigs=20; )
KIAA1217		ENSSSCG00000011075	10:48590855-48604229		CU694887,CH242-322E23,10:48445672-48606813 (Clone quality: bE322E23 on chr=10; Num_of_Contigs=1; )
KIAA1239		ENSSSCG00000008770	8:24150956-24416611
KIAA1244		ENSSSCG00000004152	1:27399327-27448336		CU457402,CH242-189P20,1:27348176-27448920 (Clone quality: bE189P20 on chr=1; Num_of_Contigs=3; )
KIAA1267		ENSSSCG00000017310	12:14826946-14969812
KIAA1274		ENSSSCG00000010270	14:76595303-76634042		CT737240,CH242-107C23,14:76511574-76656697 (Clone quality: bE107C23 on chr=14; Num_of_Contigs=2; )
KIAA1279		ENSSSCG00000010248	14:75218179-75244927		CT737244,CH242-205I14,14:75200455-75246574 (Clone quality: bE205I14 on chr=14; Num_of_Contigs=4; )
KIAA1324		ENSSSCG00000006836	4:115385396-115455624
KIAA1324L		ENSSSCG00000015394	9:87316672-87402750
KIAA1328		ENSSSCG00000003747	6:83873143-84114018
KIAA1370		ENSSSCG00000004617	1:123878479-123922632		CU326376,CH242-262C7,1:123788859-123940834 (Clone quality: bE262C7 on chr=1; Num_of_Contigs=2; )
KIAA1377		ENSSSCG00000014979	9:32441744-32524866

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, 551-1

Report problems to zhu

iastate.edu

$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).