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)

FAM71F1		ENSSSCG00000016582	18:18109762-18124275		CU861972,CH242-288G22,18:18062282-18138680 (Clone quality: bE288G22 on chr=18; Num_of_Contigs=5; )
FAM71F2		ENSSSCG00000016583	18:18145291-18158367		CU861972,CH242-288G22,18:18138781-18167275 (Clone quality: bE288G22 on chr=18; Num_of_Contigs=5; )
FAM73A		ENSSSCG00000003770	6:94485878-94560069
FAM73B		ENSSSCG00000005669	1:284012467-284036737	CU076102,CH242-68C14,1:283855073-284074390 (Clone quality: bE68C14 on chr=1; Num_of_Contigs=6; )
FAM76B		ENSSSCG00000014967	9:28276582-28296164		CU640454,CH242-260F8,9:28229458-28311889 (Clone quality: bE260F8 on chr=9; Num_of_Contigs=8; )
FAM78B		ENSSSCG00000006321	4:87782046-88038916
FAM81A		ENSSSCG00000004586	1:116433416-116486322		CU234144,CH242-252D7,1:116414567-116508602 (Clone quality: bE252D7 on chr=1; Num_of_Contigs=5; )
FAM82A1		ENSSSCG00000008488	3:95203681-95267182
FAM82A2		ENSSSCG00000004765	1:137071439-137088599		CU633257,CH242-257P7,1:137003112-137140964 (Clone quality: bE257P7 on chr=1; Num_of_Contigs=3; )
FAM82B		ENSSSCG00000006136	4:52105222-52143168		CU462951,CH242-345F16,4:51977268-52163454 (Clone quality: bE345F16 on chr=4; Num_of_Contigs=1; )
FAM83B		ENSSSCG00000001483	7:30514791-30595052
FAM83D		ENSSSCG00000007351	17:44167573-44176881
FAM83F		ENSSSCG00000000079	5:4548915-4577008
FAM83G		ENSSSCG00000018047	12:56728453-56742251		FP074851,CH242-203F20,12:56719312-56755196 (Clone quality: bE203F20 on chr=12; Num_of_Contigs=16; )
FAM84A		ENSSSCG00000008664	3:122855456-122856334		CU928804,CH242-136J15,3:122847219-122887870 (Clone quality: bE136J15 on chr=3; Num_of_Contigs=4; )
FAM84B		ENSSSCG00000005967	4:12866199-12867035		CU550687,CH242-51N24,4:12858301-12870247 (Clone quality: bE51N24 on chr=4; Num_of_Contigs=12; )
FAM89A		ENSSSCG00000010178	14:61696429-61713771	CT737333,CH242-133K23,14:61634928-61823678 (Clone quality: bE133K23 on chr=14; Num_of_Contigs=2; )
FAM89B		ENSSSCG00000012989	2:5149389-5149691		CU914305,CH242-95H15,2:5149176-5153998 (Clone quality: bE95H15 on chr=2; Num_of_Contigs=19; )
FAM8A1		ENSSSCG00000001070	7:13919332-13929502		CT990539,CH242-197D23,7:13838982-14049024 (Clone quality: bE197D23 on chr=7; Num_of_Contigs=1; )
FAM92B		ENSSSCG00000002668	6:2409614-2587761
FAM96A		ENSSSCG00000004559	1:111321908-111337637
FAM98A		ENSSSCG00000008508	3:99586176-99602635
FAM98B		ENSSSCG00000004792	1:139519982-139540264		CU861587,CH242-171J17,1:139482903-139563221 (Clone quality: bE171J17 on chr=1; Num_of_Contigs=1; )
FAM98C		ENSSSCG00000002959	6:32523878-32527926		FP236590,CH242-507G2,6:32461085-32547641 (Clone quality: bE507G2 on chr=6; Num_of_Contigs=4; )
FANCB		ENSSSCG00000012130	X:10633809-10650515
FANCC		ENSSSCG00000010942	10:26089458-26123602		CU929857,CH242-94A4,10:26072068-26162227 (Clone quality: bE94A4 on chr=10; Num_of_Contigs=10; )
FANCC		ENSSSCG00000002908	6:30335794-30337089		FP243365,CH242-219O7,6:30335763-30338040 (Clone quality: bE219O7 on chr=6; Num_of_Contigs=6; )
FANCD2		ENSSSCG00000011563	13:55418189-55492273
FANCF		ENSSSCG00000013342	2:34271227-34272306		CU695040,CH242-255L3,2:34221299-34371289 (Clone quality: bE255L3 on chr=2; Num_of_Contigs=3; )
FANCG		ENSSSCG00000005304	1:247020808-247027706		CU856695,CH242-238C15,1:246903923-247036412 (Clone quality: bE238C15 on chr=1; Num_of_Contigs=2; )
FANCI		ENSSSCG00000001837	7:60215005-60290465
FANCL		ENSSSCG00000008394	3:77328986-77335598		CU928032,CH242-392H11,3:77315559-77375613 (Clone quality: bE392H11 on chr=3; Num_of_Contigs=3; )
FANCM		ENSSSCG00000005000	1:183822135-183888685		CU570961,CH242-89I4,1:183793786-183899389 (Clone quality: bE89I4 on chr=1; Num_of_Contigs=2; )
FANK1		ENSSSCG00000010745	14:142192568-142293599
FAP		ENSSSCG00000015896	15:64095733-64166537
FAP		ENSSSCG00000006904	4:128954136-129039420
FAP		location ⇒	15:64122421-64122293		CU928330,CH242-283H10,15:64095602-64136328 (Clone quality: bE283H10 on chr=15; Num_of_Contigs=3; )
FAP		location ⇒	15:64127641-64127536		CU928330,CH242-283H10,15:64095602-64136328 (Clone quality: bE283H10 on chr=15; Num_of_Contigs=3; )
FAP		location ⇒	15:64139393-64139288		CU928330,CH242-283H10,15:64136429-64143299 (Clone quality: bE283H10 on chr=15; Num_of_Contigs=3; )
FAP		location ⇒	15:64141518-64141379		CU928330,CH242-283H10,15:64136429-64143299 (Clone quality: bE283H10 on chr=15; Num_of_Contigs=3; )
FAR2		ENSSSCG00000000541	5:42987179-43026163
FARP1		ENSSSCG00000009512	11:68473116-68481672
FARP2		ENSSSCG00000016371	15:131912300-131938084
FARS2		ENSSSCG00000001016	7:3592457-3695579
FARSA		ENSSSCG00000013745	2:56273410-56282314		CU463133,CH242-121E19,2:56264935-56304744 (Clone quality: bE121E19 on chr=2; Num_of_Contigs=6; )
FARSB		ENSSSCG00000016226	15:115181046-115248303
FAS		ENSSSCG00000000206	5:14411877-14437905
FAS		ENSSSCG00000003877	6:115045559-115426189
FAS		ENSSSCG00000010448	14:105826565-105852532		CT737322,CH242-203A14,14:105756080-105909175 (Clone quality: bE203A14 on chr=14; Num_of_Contigs=1; )
FAS		ENSSSCG00000001509	7:34084220-34087457	CU607018,CH242-138E20,7:33930957-34116846 (Clone quality: bE138E20 on chr=7; Num_of_Contigs=1; )

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, 1001-22

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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).