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)

KCNK10		ENSSSCG00000002423	7:117989535-118066148
KCNK12		ENSSSCG00000008427	3:86239888-86290224		FP102206,CH242-144B3,3:86204847-86374841 (Clone quality: bE144B3 on chr=3; Num_of_Contigs=1; )
KCNK13		ENSSSCG00000002432	7:119721824-119835158
KCNK15		ENSSSCG00000007377	17:48770015-48774721
KCNK17		ENSSSCG00000001592	7:39670205-39690728
KCNK18		ENSSSCG00000010667	14:133207021-133215984		CU468444,CH242-75D17,14:133196126-133216586 (Clone quality: bE75D17 on chr=14; Num_of_Contigs=6; )
KCNK3		ENSSSCG00000008563	3:104833103-104932491
KCNK4		ENSSSCG00000013031	2:6207011-6210977		CU861533,CH242-1H13,2:6206722-6217704 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
KCNK6		ENSSSCG00000002951	6:32394337-32400985		FP236590,CH242-507G2,6:32388919-32407185 (Clone quality: bE507G2 on chr=6; Num_of_Contigs=4; )
KCNK7		ENSSSCG00000012986	2:5129202-5132389		CU914305,CH242-95H15,2:5125545-5133216 (Clone quality: bE95H15 on chr=2; Num_of_Contigs=19; )
KCNK9		ENSSSCG00000005936	4:2493438-2566091
KCNMA1		ENSSSCG00000010325	14:82619610-82911574
KCNMB1		ENSSSCG00000017005	16:50909790-50921249		CU915479,CH242-305G16,16:50908137-50928441 (Clone quality: bE305G16 on chr=16; Num_of_Contigs=5; )
KCNMB2		ENSSSCG00000011761	13:89166152-89194414		CU861526,CH242-176C20,13:89122556-89208208 (Clone quality: bE176C20 on chr=13; Num_of_Contigs=4; )
KCNMB4		ENSSSCG00000000503	5:33431373-33500800
KCNN1		ENSSSCG00000013892	2:62209573-62230615		CU463003,CH242-317A24,2:62151810-62279750 (Clone quality: bE317A24 on chr=2; Num_of_Contigs=2; )
KCNN2		ENSSSCG00000014213	2:107409591-107558117
KCNN3		ENSSSCG00000006542	4:98997267-99168980
KCNQ3		ENSSSCG00000005953	4:7860915-7912417
KCNQ4		ENSSSCG00000003975	6:121743215-121797250
KCNQ5		ENSSSCG00000004281	1:55211285-55347570	CU041280,CH242-45J18,1:55200094-55385513 (Clone quality: bE45J18 on chr=1; Num_of_Contigs=8; )
KCNRG		ENSSSCG00000009388	11:17634131-17639350		CU062573,CH242-415L14,11:17628495-17647998 (Clone quality: bE415L14 on chr=11; Num_of_Contigs=7; )
KCNS3		ENSSSCG00000008609	3:111276141-111278001
KCNT1		ENSSSCG00000005762	1:289886318-289907691
KCNT2		ENSSSCG00000010892	10:20569161-20770732
KCNV1		ENSSSCG00000006021	4:27347685-27353374		CU179723,CH242-243F14,4:27336730-27398367 (Clone quality: bE243F14 on chr=4; Num_of_Contigs=7; )
KCNV2		ENSSSCG00000005228	1:229264085-229276539		CU062572,CH242-412G21,1:229197616-229293366 (Clone quality: bE412G21 on chr=1; Num_of_Contigs=2; )
KCTD1		ENSSSCG00000003719	6:76595333-76693500
KCTD10		ENSSSCG00000009934	14:41671712-41696531		CU638684,CH242-434M9,14:41660146-41771253 (Clone quality: bE434M9 on chr=14; Num_of_Contigs=2; )
KCTD11		ENSSSCG00000017944	12:49827968-49828666		CU681851,CH242-516E15,12:49824922-49829536 (Clone quality: bE516E15 on chr=12; Num_of_Contigs=27; )
KCTD12		ENSSSCG00000009468	11:47976064-47977044		CT956058,CH242-156P24,11:47940321-47985298 (Clone quality: bE156P24 on chr=11; Num_of_Contigs=6; )
KCTD14		ENSSSCG00000014885	9:12289929-12290582		FP089552,CH242-519A4,9:12250415-12290971 (Clone quality: bE519A4 on chr=9; Num_of_Contigs=6; )
KCTD17		ENSSSCG00000000135	5:7100429-7111159
KCTD18		ENSSSCG00000016091	15:97819567-97846368		CU915540,CH242-160L13,15:97806887-97896803 (Clone quality: bE160L13 on chr=15; Num_of_Contigs=3; )
KCTD19		ENSSSCG00000002781	6:13248220-13281398
KCTD2		ENSSSCG00000017217	12:4412205-4422785		CU640421,CH242-384L19,12:4390867-4423921 (Clone quality: bE384L19 on chr=12; Num_of_Contigs=8; )
KCTD20		ENSSSCG00000001562	7:36776187-36822278		CT842148,CH242-261F2,7:36742296-36863465 (Clone quality: bE261F2 on chr=7; Num_of_Contigs=4; )
KCTD3		ENSSSCG00000010811	10:5896103-5956153
KCTD6		ENSSSCG00000011476	13:33848823-33851079		CU927912,CH242-524I3,13:33839842-33907683 (Clone quality: bE524I3 on chr=13; Num_of_Contigs=9; )
KCTD7		ENSSSCG00000007734	3:14567570-14575256		CU467678,CH242-176C17,3:14562037-14582493 (Clone quality: bE176C17 on chr=3; Num_of_Contigs=8; )
KCTD8		ENSSSCG00000008805	8:29592481-29592951		CU856071,CH242-93P24,8:29589969-29595543 (Clone quality: bE93P24 on chr=8; Num_of_Contigs=8; )
KCTD9		ENSSSCG00000009652	14:9572666-9635445
KCTD9P2		ENSSSCG00000012545	X:84381760-84449091
KDELC1		ENSSSCG00000009532	11:71949339-71960538
KDELC2		ENSSSCG00000015009	9:36116123-36137959		CU464170,CH242-497A10,9:36081529-36163451 (Clone quality: bE497A10 on chr=9; Num_of_Contigs=4; )
KDELR1		ENSSSCG00000003132	6:37424318-37432364		FP102301,CH242-20J11,6:37418263-37433567 (Clone quality: bE20J11 on chr=6; Note=In Finishing;)
KDELR3		ENSSSCG00000000105	5:5866182-5876316
KDM2A		ENSSSCG00000012923	2:3810209-3815557		CU915632,CH242-307O16,2:3796797-3836586 (Clone quality: bE307O16 on chr=2; Num_of_Contigs=9; )
KDM3A		ENSSSCG00000008221	3:53192637-53244610
KDM3B		ENSSSCG00000014331	2:127323352-127393028

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

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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).