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)

UFAP2_PIG		ENSSSCG00000002480	7:124299009-124309720		CU633316,CH242-69M9,7:124252539-124319088 (Clone quality: bE69M9 on chr=7; Num_of_Contigs=4; )
UFAP2_PIG		ENSSSCG00000002480	7:124299009-124309720		CU633316,CH242-69M9,7:124252539-124319088 (Clone quality: bE69M9 on chr=7; Num_of_Contigs=4; )
UFC1		ENSSSCG00000006363	4:92804743-92819308
UFC1		ENSSSCG00000006363	4:92804743-92819308
UFD1L		ENSSSCG00000010121	14:52225295-52244454
UFM1		ENSSSCG00000009363	11:13439482-13452928
UFSP2		ENSSSCG00000015793	15:43700968-43718337		CU571359,CH242-312E7,15:43699298-43786916 (Clone quality: bE312E7 on chr=15; Num_of_Contigs=3; )
UGCG		ENSSSCG00000005464	1:265494182-265530466		CU638855,CH242-333M22,1:265386028-265560829 (Clone quality: bE333M22 on chr=1; Num_of_Contigs=2; )
UGCGL2		ENSSSCG00000009502	11:66145301-66270474
UGP2		ENSSSCG00000008368	3:71854811-72157362
UGP2		location ⇒	3:71855279-71854821		CU466372,CH242-173O12,3:71834920-71867127 (Clone quality: bE173O12 on chr=3; Num_of_Contigs=11; )
UGP2		location ⇒	3:71860687-71860441		CU466372,CH242-173O12,3:71834920-71867127 (Clone quality: bE173O12 on chr=3; Num_of_Contigs=11; )
UGP2		location ⇒	3:71861420-71861221		CU466372,CH242-173O12,3:71834920-71867127 (Clone quality: bE173O12 on chr=3; Num_of_Contigs=11; )
UGP2		location ⇒	3:71862812-71862512		CU466372,CH242-173O12,3:71834920-71867127 (Clone quality: bE173O12 on chr=3; Num_of_Contigs=11; )
UGT8		ENSSSCG00000009121	8:93037208-93044154
UHMK1		ENSSSCG00000006342	4:91832456-91835172		CU468663,CH242-271J5,4:91830865-91836225 (Clone quality: bE271J5 on chr=4; Num_of_Contigs=24; )
UHRF1		ENSSSCG00000013517	2:48783706-48815063		CU681848,CH242-137M21,2:48779121-48824636 (Clone quality: bE137M21 on chr=2; Num_of_Contigs=18; )
UHRF1BP1		ENSSSCG00000001532	7:35193879-35257569	CT797453,CH242-109D12,7:35137121-35327761 (Clone quality: bE109D12 on chr=7; Num_of_Contigs=2; )
UHRF1BP1L		location ⇒	5:79736768-79736187		FP102446,CH242-4A12,5:79729746-79739493 (Clone quality: bE4A12 on chr=5; Num_of_Contigs=5; )
UHRF1BP1L		location ⇒	5:79740390-79740195		FP102446,CH242-4A12,5:79739594-79746745 (Clone quality: bE4A12 on chr=5; Num_of_Contigs=5; )
UHRF2		ENSSSCG00000005201	1:225536879-225577421
ULBP1		ENSSSCG00000004100	1:17071032-17077234
ULBP1		location ⇒	1:17071584-17071038		CU571230,CH242-42L8,1:17069789-17076467 (Clone quality: bE42L8 on chr=1; Num_of_Contigs=10; )
ULBP1		location ⇒	1:17073748-17073472		CU571230,CH242-42L8,1:17069789-17076467 (Clone quality: bE42L8 on chr=1; Num_of_Contigs=10; )
ULBP1		location ⇒	1:17074233-17073969		CU571230,CH242-42L8,1:17069789-17076467 (Clone quality: bE42L8 on chr=1; Num_of_Contigs=10; )
ULBP1		location ⇒	1:17077234-17077064		CU571230,CH242-42L8,1:17076568-17100459 (Clone quality: bE42L8 on chr=1; Num_of_Contigs=10; )
ULK1		ENSSSCG00000009742	14:23306795-23329622		CU469318,CH242-114E11,14:23178600-23358435 (Clone quality: bE114E11 on chr=14; Num_of_Contigs=2; )
ULK3		ENSSSCG00000001898	7:64200489-64207015		CU468845,CH242-162A4,7:64176153-64332301 (Clone quality: bE162A4 on chr=7; Num_of_Contigs=2; )
ULK4		ENSSSCG00000011275	13:21335838-21567313
UMOD		ENSSSCG00000007859	3:23028653-23037234		CU929688,CH242-143L18,3:23027423-23057527 (Clone quality: bE143L18 on chr=3; Num_of_Contigs=8; )
UMPS		ENSSSCG00000011864	13:102025409-102048107		CU466522,CH242-89F13,13:102025271-102066080 (Clone quality: bE89F13 on chr=13; Num_of_Contigs=11; )
UNC119		ENSSSCG00000017761	12:42472732-42478646
UNC119B		ENSSSCG00000009915	14:40688019-40699379
UNC13A		ENSSSCG00000013880	2:61797108-61943298
UNC13B		ENSSSCG00000005305	1:247073657-247186944
UNC13C		ENSSSCG00000004614	1:121861605-122421065
UNC13D		ENSSSCG00000017200	12:3925666-3940296		CU928029,CH242-304M1,12:3894544-3957078 (Clone quality: bE304M1 on chr=12; Num_of_Contigs=9; )
UNC13D		location ⇒	12:3926205-3926374		CU928029,CH242-304M1,12:3894544-3957078 (Clone quality: bE304M1 on chr=12; Num_of_Contigs=9; )
UNC13D		location ⇒	12:3926786-3926896		CU928029,CH242-304M1,12:3894544-3957078 (Clone quality: bE304M1 on chr=12; Num_of_Contigs=9; )
UNC13D		location ⇒	12:3927135-3927204		CU928029,CH242-304M1,12:3894544-3957078 (Clone quality: bE304M1 on chr=12; Num_of_Contigs=9; )
UNC13D		location ⇒	12:3927459-3927643		CU928029,CH242-304M1,12:3894544-3957078 (Clone quality: bE304M1 on chr=12; Num_of_Contigs=9; )
UNC45A		ENSSSCG00000001821	7:59072075-59086989	CT868688,CH242-510G16,7:59026976-59242142 (Clone quality: bE510G16 on chr=7; Num_of_Contigs=3; )
UNC45B		ENSSSCG00000017717	12:37803026-37826688		CU927946,CH242-204J8,12:37801197-37827766 (Clone quality: bE204J8 on chr=12; Num_of_Contigs=6; )
UNC5A		ENSSSCG00000014049	2:70063070-70078613		CU469199,CH242-222J24,2:70023175-70114180 (Clone quality: bE222J24 on chr=2; Num_of_Contigs=4; )
UNC5A		location ⇒	2:70065875-70065704		CU469199,CH242-222J24,2:70023175-70114180 (Clone quality: bE222J24 on chr=2; Num_of_Contigs=4; )
UNC5A		location ⇒	2:70066209-70066117		CU469199,CH242-222J24,2:70023175-70114180 (Clone quality: bE222J24 on chr=2; Num_of_Contigs=4; )
UNC5A		location ⇒	2:70069145-70068837		CU469199,CH242-222J24,2:70023175-70114180 (Clone quality: bE222J24 on chr=2; Num_of_Contigs=4; )
UNC5B		ENSSSCG00000010276	14:77302358-77387225
UNC5C		ENSSSCG00000001598	7:41421945-41429862		CU469417,CH242-21H17,7:41413531-41439236 (Clone quality: bE21H17 on chr=7; Num_of_Contigs=11; )
UNC5C		ENSSSCG00000010276	14:77302358-77387225

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, 1001-33

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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).