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)

CDK2		ENSSSCG00000005047	1:192401013-192415532
CDK2		ENSSSCG00000009775	14:29587767-29593976		CU462966,CH242-408L13,14:29576419-29594527 (Clone quality: bE408L13 on chr=14; Num_of_Contigs=11; )
CDK2		ENSSSCG00000012902	2:3406772-3408962		CU633429,CH242-6G2,2:3403551-3456026 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
CDK2		ENSSSCG00000016835	16:18868174-18905906	CU856110,CH242-36H10,16:18824515-19007053 (Clone quality: bE36H10 on chr=16; Num_of_Contigs=2; )
CDK2		location ⇒	5:20332627-20332869
CDK2		location ⇒	5:20335148-20335323		CU457395,CH242-13B13,5:20332627-20335712 (Clone quality: bE13B13 on chr=5; Num_of_Contigs=23; )
CDK2		location ⇒	5:20337338-20337542		CU457395,CH242-13B13,5:20335813-20343473 (Clone quality: bE13B13 on chr=5; Num_of_Contigs=23; )
CDK2		location ⇒	5:20337819-20338189		CU457395,CH242-13B13,5:20335813-20343473 (Clone quality: bE13B13 on chr=5; Num_of_Contigs=23; )
CDK2AP1		ENSSSCG00000009775	14:29587767-29593976		CU462966,CH242-408L13,14:29576419-29594527 (Clone quality: bE408L13 on chr=14; Num_of_Contigs=11; )
CDK2AP2		ENSSSCG00000012902	2:3406772-3408962		CU633429,CH242-6G2,2:3403551-3456026 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
CDK3		ENSSSCG00000003705	6:73661712-73753577
CDK3		ENSSSCG00000007540	17:64006676-64018123
CDK3		ENSSSCG00000017193	12:3785816-3789490		CU928029,CH242-304M1,12:3750666-3894443 (Clone quality: bE304M1 on chr=12; Num_of_Contigs=9; )
CDK3		location ⇒	12:3787274-3787070		CU928029,CH242-304M1,12:3750666-3894443 (Clone quality: bE304M1 on chr=12; Num_of_Contigs=9; )
CDK3		location ⇒	12:3787666-3787561		CU928029,CH242-304M1,12:3750666-3894443 (Clone quality: bE304M1 on chr=12; Num_of_Contigs=9; )
CDK3		location ⇒	12:3787922-3787748		CU928029,CH242-304M1,12:3750666-3894443 (Clone quality: bE304M1 on chr=12; Num_of_Contigs=9; )
CDK4		ENSSSCG00000000445	5:21901907-21902707		CU914582,CH242-235E14,5:21901770-21904026 (Clone quality: bE235E14 on chr=5; Num_of_Contigs=33; )
CDK4		ENSSSCG00000005132	1:209499306-209529714
CDK4		location ⇒	5:21902079-21901908		CU914582,CH242-235E14,5:21901770-21904026 (Clone quality: bE235E14 on chr=5; Num_of_Contigs=33; )
CDK4		location ⇒	5:21902728-21902489		CU914582,CH242-235E14,5:21901770-21904026 (Clone quality: bE235E14 on chr=5; Num_of_Contigs=33; )
CDK4		location ⇒	5:21903388-21903171		CU914582,CH242-235E14,5:21901770-21904026 (Clone quality: bE235E14 on chr=5; Num_of_Contigs=33; )
CDK4		location ⇒	5:21967108-21967503		CU914582,CH242-235E14,5:21966566-21968744 (Clone quality: bE235E14 on chr=5; Num_of_Contigs=33; )
CDK5		ENSSSCG00000003705	6:73661712-73753577
CDK5		ENSSSCG00000001080	7:16620234-17280446
CDK5		ENSSSCG00000005505	1:273948158-273990224
CDK5R1		ENSSSCG00000017730	12:40183369-40184292		CU695029,CH242-169J22,12:40003526-40192006 (Clone quality: bE169J22 on chr=12; Num_of_Contigs=1; )
CDK5RAP1		ENSSSCG00000007264	17:38797699-38831219
CDK5RAP2		ENSSSCG00000005505	1:273948158-273990224
CDK5RAP3		ENSSSCG00000017524	12:21680618-21683032		CU681834,CH242-505F23,12:21678954-21683281 (Clone quality: bE505F23 on chr=12; Num_of_Contigs=26; )
CDK6		ENSSSCG00000015318	9:67905086-68226459
CDK6		location ⇒	9:67904995-67904759		FP102994,CH242-279H20,9:67872880-67942919 (Clone quality: bE279H20 on chr=9; Num_of_Contigs=1; )
CDK6		location ⇒	9:67905604-67905251		FP102994,CH242-279H20,9:67872880-67942919 (Clone quality: bE279H20 on chr=9; Num_of_Contigs=1; )
CDK6		location ⇒	9:68223467-68223223		CU856662,CH242-305E15,9:68222853-68225091 (Clone quality: bE305E15 on chr=9; Num_of_Contigs=5; )
CDK6		location ⇒	9:68223823-68223532		CU856662,CH242-305E15,9:68222853-68225091 (Clone quality: bE305E15 on chr=9; Num_of_Contigs=5; )
CDK7		ENSSSCG00000005090	1:198435585-198751937
CDK7		ENSSSCG00000016961	16:44731126-44757008
CDK7		location ⇒	16:44731322-44731132		FP085444,CH242-185P14,16:44727312-44749875 (Clone quality: bE185P14 on chr=16; Num_of_Contigs=5; )
CDK7		location ⇒	16:44731846-44731696		FP085444,CH242-185P14,16:44727312-44749875 (Clone quality: bE185P14 on chr=16; Num_of_Contigs=5; )
CDK7		location ⇒	16:44734729-44734579		FP085444,CH242-185P14,16:44727312-44749875 (Clone quality: bE185P14 on chr=16; Num_of_Contigs=5; )
CDK7		location ⇒	16:44756998-44756821		FP085444,CH242-185P14,16:44749976-44763467 (Clone quality: bE185P14 on chr=16; Num_of_Contigs=5; )
CDK8		ENSSSCG00000009298	11:3128530-3237839
CDK9		ENSSSCG00000005621	1:282627917-282639414
CDKAL1		ENSSSCG00000001080	7:16620234-17280446
CDKL1		ENSSSCG00000005018	1:188456686-188471840
CDKL2		ENSSSCG00000008970	8:60746412-60763868
CDKL3		ENSSSCG00000014299	2:124364378-124383298
CDKL4		ENSSSCG00000008477	3:94143560-94216572
CDKL5		ENSSSCG00000012156	X:14571908-14656656		FP085429,CH242-362P2,X:14496883-14657415 (Clone quality: bE362P2 on chr=X; Num_of_Contigs=3; )
CDKN1A		ENSSSCG00000001565	7:36987622-36995484	CU326356,CH242-61G11,7:36975834-37183903 (Clone quality: bE61G11 on chr=7; Num_of_Contigs=4; )
CDKN1A		ENSSSCG00000005640	1:283255579-283275705

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).