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)

ABHD2		ENSSSCG00000001835	7:60042575-60170498
ABHD4		ENSSSCG00000002051	7:82719922-82734065		CU407030,CH242-171E18,7:82670262-82752637 (Clone quality: bE171E18 on chr=7; Num_of_Contigs=3; )
ABHD5		ENSSSCG00000011297	13:22891589-22939546		CU633675,CH242-240D16,13:22788279-22941451 (Clone quality: bE240D16 on chr=13; Num_of_Contigs=1; )
ABHD6		ENSSSCG00000011470	13:33544890-33687465
ABI1		ENSSSCG00000011062	10:46887977-46960945
ABI1		location ⇒	10:46887125-46886818		CU571224,CH242-337N1,10:46866374-46895137 (Clone quality: bE337N1 on chr=10; Num_of_Contigs=9; )
ABI1		location ⇒	10:46888533-46887631		CU571224,CH242-337N1,10:46866374-46895137 (Clone quality: bE337N1 on chr=10; Num_of_Contigs=9; )
ABI1		location ⇒	10:46961037-46960867		CU928644,CH242-496K3,10:46933147-46997826 (Clone quality: bE496K3 on chr=10; Num_of_Contigs=7; )
ABI1		location ⇒	10:47017227-47017505		CU928644,CH242-496K3,10:47009247-47023175 (Clone quality: bE496K3 on chr=10; Num_of_Contigs=7; )
ABI3BP		ENSSSCG00000011959	13:116121170-116348369
ABL1		ENSSSCG00000005706	1:286004464-286034610	FP102068,CH242-374C22,1:285992963-286044374 (Clone quality: bE374C22 on chr=1; Num_of_Contigs=5; )
ABL1		ENSSSCG00000003705	6:73661712-73753577
ABL1		ENSSSCG00000007540	17:64006676-64018123
ABL1		location ⇒	1:286016021-286015867	FP102068,CH242-374C22,1:285992963-286044374 (Clone quality: bE374C22 on chr=1; Num_of_Contigs=5; )
ABL1		location ⇒	1:286016896-286016812	FP102068,CH242-374C22,1:285992963-286044374 (Clone quality: bE374C22 on chr=1; Num_of_Contigs=5; )
ABL1		location ⇒	1:286025254-286024979	FP102068,CH242-374C22,1:285992963-286044374 (Clone quality: bE374C22 on chr=1; Num_of_Contigs=5; )
ABL1		location ⇒	1:286033578-286033281	FP102068,CH242-374C22,1:285992963-286044374 (Clone quality: bE374C22 on chr=1; Num_of_Contigs=5; )
ABL2		location ⇒	1:286015959-286015845	FP102068,CH242-374C22,1:285992963-286044374 (Clone quality: bE374C22 on chr=1; Num_of_Contigs=5; )
ABL2		location ⇒	1:286016896-286016833	FP102068,CH242-374C22,1:285992963-286044374 (Clone quality: bE374C22 on chr=1; Num_of_Contigs=5; )
ABL2		location ⇒	1:286025237-286024979	FP102068,CH242-374C22,1:285992963-286044374 (Clone quality: bE374C22 on chr=1; Num_of_Contigs=5; )
ABLIM1		ENSSSCG00000010651	14:130633369-130884957
ABLIM2		ENSSSCG00000008721	8:3328575-3421471
ABLIM3		ENSSSCG00000014430	2:135827897-135870723		CU694929,CH242-55J13,2:135825933-135930083 (Clone quality: bE55J13 on chr=2; Num_of_Contigs=3; )
ABP1		ENSSSCG00000016442	18:5244782-5248729		CU928555,CH242-184M19,18:5235311-5256667 (Clone quality: bE184M19 on chr=18; Num_of_Contigs=14; )
ABR		ENSSSCG00000017804	12:44843150-44890085
ABRA		ENSSSCG00000006036	4:30787333-30794625		CU462955,CH242-373C6,4:30733654-30853606 (Clone quality: bE373C6 on chr=4; Num_of_Contigs=7; )
ABTB2		ENSSSCG00000013303	2:25003850-25189973
ACA64		ENSSSCG00000018653	15:83204497-83204622		CU570843,CH242-321B10,15:83204369-83211359 (Clone quality: bE321B10 on chr=15; Num_of_Contigs=11; )
ACAA1		ENSSSCG00000011250	13:18896001-18906667
ACAA2		ENSSSCG00000004510	1:102229469-102256875
ACACA		ENSSSCG00000017694	12:36903467-37096675
ACACB		ENSSSCG00000009937	14:41867283-41945291
ACAD10		ENSSSCG00000009836	14:32892949-32941626		CU468489,CH242-352L7,14:32836937-32998018 (Clone quality: bE352L7 on chr=14; Num_of_Contigs=2; )
ACAD11		ENSSSCG00000011629	13:60544792-60643250
ACAD8		ENSSSCG00000015260	9:59348533-59373070
ACADL		ENSSSCG00000016156	15:106120893-106154956
ACADM		ENSSSCG00000003776	6:96130623-96164860		CU929611,CH242-276C23,6:96098364-96199408 (Clone quality: bE276C23 on chr=6; Num_of_Contigs=3; )
ACADS		ENSSSCG00000009916	14:40706674-40720741		CT737144,CH242-18L22,14:40692567-40877957 (Clone quality: bE18L22 on chr=14; Num_of_Contigs=1; )
ACADSB		ENSSSCG00000010723	14:139006971-139047603
ACADVL		ENSSSCG00000017947	12:49872036-49876082		CU681851,CH242-516E15,12:49872001-49878895 (Clone quality: bE516E15 on chr=12; Num_of_Contigs=27; )
ACAN		ENSSSCG00000001832	7:59854877-59894917
ACAP1		ENSSSCG00000017943	12:49820059-49826476
ACAP3		ENSSSCG00000003329	6:42778073-42787515
ACAT2		ENSSSCG00000004049	1:8727925-8740135
ACBD4		ENSSSCG00000017337	12:16139846-16146559		FP067380,CH242-32K16,12:15988019-16156790 (Clone quality: bE32K16 on chr=12; Num_of_Contigs=1; )
ACBD6		ENSSSCG00000015534	9:114191734-114545229
ACCN1		ENSSSCG00000017725	12:39413254-39601392
ACCN2		ENSSSCG00000000216	5:14686975-14694951
ACCN5		ENSSSCG00000008869	8:38781777-38809575		CU855637,CH242-199L13,8:38712595-38842897 (Clone quality: bE199L13 on chr=8; Num_of_Contigs=2; )
ACCS		ENSSSCG00000013282	2:16814484-16832999		CU457486,CH242-12J14,2:16813439-16854641 (Clone quality: bE12J14 on chr=2; Num_of_Contigs=7; )

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, 551-600, 601-650, 651-700, 701-750, 751-800, 801-850, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-32

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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).