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)

AIFM2		location ⇒	14:76186453-76186615		CU633580,CH242-307B6,14:76183309-76195363 (Clone quality: bE307B6 on chr=14; Num_of_Contigs=16; )
AIFM3		ENSSSCG00000010096	14:51661019-51671982		CU633934,CH242-117H20,14:51553625-51738341 (Clone quality: bE117H20 on chr=14; Num_of_Contigs=1; )
AIG1		ENSSSCG00000004136	1:22982165-23300371
AIM1		ENSSSCG00000004372	1:76137300-76157812
AIM1		ENSSSCG00000017104	16:72710029-72749948
AIM2		location ⇒	4:94927427-94927476		CU462834,CH242-199I10,4:94881634-94956938 (Clone quality: bE199I10 on chr=4; Num_of_Contigs=5; )
AIMP2		ENSSSCG00000007591	3:4094586-4102879		FP102636,CH242-228H21,3:4070453-4106178 (Clone quality: bE228H21 on chr=3; Num_of_Contigs=5; )
AIP		ENSSSCG00000012904	2:3424123-3430150		CU633429,CH242-6G2,2:3403551-3456026 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
AK1		ENSSSCG00000005627	1:282842764-282852782		CU638853,CH242-308I15,1:282840723-282900792 (Clone quality: bE308I15 on chr=1; Num_of_Contigs=4; )
AK1		location ⇒	1:282734470-282734591		CU914182,CH242-198I10,1:282725578-282737416 (Clone quality: bE198I10 on chr=1; Num_of_Contigs=15; )
AK1		location ⇒	1:282843897-282843707		CU638853,CH242-308I15,1:282840723-282900792 (Clone quality: bE308I15 on chr=1; Num_of_Contigs=4; )
AK1		location ⇒	1:282846634-282846521		CU638853,CH242-308I15,1:282840723-282900792 (Clone quality: bE308I15 on chr=1; Num_of_Contigs=4; )
AK1		location ⇒	1:282847487-282847325		CU638853,CH242-308I15,1:282840723-282900792 (Clone quality: bE308I15 on chr=1; Num_of_Contigs=4; )
AK3		ENSSSCG00000005218	1:227339861-227361094		CU467061,CH242-40P15,1:227339625-227392310 (Clone quality: bE40P15 on chr=1; Num_of_Contigs=2; )
AK3L1		ENSSSCG00000003808	6:103670170-103745864
AK5		ENSSSCG00000003773	6:94812551-95108817
AK7		ENSSSCG00000002504	7:126547771-126604804
AKAP11		ENSSSCG00000009430	11:23674669-23693304
AKAP12		ENSSSCG00000004091	1:16023074-16133860
AKAP13		ENSSSCG00000002259	7:93862094-94026987
AKAP2		ENSSSCG00000005451	1:263872714-263904646
AKAP3		ENSSSCG00000000720	5:61534620-61558042
AKAP4		ENSSSCG00000012306	X:43223561-43232826
AKAP5		ENSSSCG00000002268	7:96814483-96815766		CU914661,CH242-30K16,7:96812121-96912476 (Clone quality: bE30K16 on chr=7; Num_of_Contigs=3; )
AKAP6		ENSSSCG00000001965	7:72886900-73175406
AKAP7		ENSSSCG00000004198	1:33648789-33649034		CU914499,CH242-19O10,1:33621234-33669466 (Clone quality: bE19O10 on chr=1; Num_of_Contigs=1; )
AKAP8		ENSSSCG00000013837	2:60289902-60308815
AKAP8L		ENSSSCG00000013838	2:60309199-60346353		CU914413,CH242-247L20,2:60301522-60353336 (Clone quality: bE247L20 on chr=2; Num_of_Contigs=8; )
AKAP9		ENSSSCG00000015310	9:67379034-67538305
AKCL2_PIG		ENSSSCG00000011150	10:62019124-62032266		CU972427,CH242-23K3,10:61914453-62050813 (Clone quality: bE23K3 on chr=10; Num_of_Contigs=1; )
AKCL2_PIG		ENSSSCG00000011150	10:62019124-62032266		CU972427,CH242-23K3,10:61914453-62050813 (Clone quality: bE23K3 on chr=10; Num_of_Contigs=1; )
AKD1		ENSSSCG00000004407	1:80288937-80307479
AKIRIN1		ENSSSCG00000003652	6:64782671-64793982	CR956385,CH242-177A17,6:64646719-64826929 (Clone quality: bE177A17 on chr=6; Num_of_Contigs=4; )
AKIRIN2		ENSSSCG00000004307	1:58764204-58786629
AKNA		ENSSSCG00000005489	1:267978420-268197604
AKR1B1		ENSSSCG00000016539	18:12977858-12996185		CU928709,CH242-57B10,18:12964676-13013079 (Clone quality: bE57B10 on chr=18; Num_of_Contigs=5; )
AKR1C2		location ⇒	10:61921557-61921640		CU972427,CH242-23K3,10:61914453-62050813 (Clone quality: bE23K3 on chr=10; Num_of_Contigs=1; )
AKR1C2		location ⇒	10:61922671-61922761		CU972427,CH242-23K3,10:61914453-62050813 (Clone quality: bE23K3 on chr=10; Num_of_Contigs=1; )
AKR1C2		location ⇒	10:61954596-61954675		CU972427,CH242-23K3,10:61914453-62050813 (Clone quality: bE23K3 on chr=10; Num_of_Contigs=1; )
AKR1C2		location ⇒	10:62223738-62223817		FP085453,CH242-523A18,10:62222583-62228435 (Clone quality: bE523A18 on chr=10; Num_of_Contigs=8; )
AKR1CL1		ENSSSCG00000011152	10:62053417-62067176		CU972427,CH242-23K3,10:62050914-62111367 (Clone quality: bE23K3 on chr=10; Num_of_Contigs=1; )
AKR1D1		ENSSSCG00000016519	18:9777485-9810772
AKR7A2		location ⇒	6:53257555-53257366		FP236131,CH242-145H9,6:53256791-53259821 (Clone quality: bE145H9 on chr=6; Num_of_Contigs=4; )
AKR7A2		location ⇒	6:53260465-53260365		FP236131,CH242-145H9,6:53259922-53265668 (Clone quality: bE145H9 on chr=6; Num_of_Contigs=4; )
AKR7A2		location ⇒	6:53261739-53261549		FP236131,CH242-145H9,6:53259922-53265668 (Clone quality: bE145H9 on chr=6; Num_of_Contigs=4; )
AKR7A2		location ⇒	6:53264832-53264658		FP236131,CH242-145H9,6:53259922-53265668 (Clone quality: bE145H9 on chr=6; Num_of_Contigs=4; )
AKT1		ENSSSCG00000003194	6:38477164-38484612		CU694867,CH242-269H19,6:38449667-38488605 (Clone quality: bE269H19 on chr=6; Num_of_Contigs=4; )
AKT1		location ⇒	X:60653452-60652851	FP015868,CH242-22N6,X:60630728-60700353 (Clone quality: bE22N6 on chr=X; Num_of_Contigs=2; )
AKT1		location ⇒	X:60765675-60766276		CU856303,CH242-152E21,X:60725698-60786270 (Clone quality: bE152E21 on chr=X; Num_of_Contigs=11; )
AKT1S1		ENSSSCG00000003194	6:38477164-38484612		CU694867,CH242-269H19,6:38449667-38488605 (Clone quality: bE269H19 on chr=6; Num_of_Contigs=4; )

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).