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)

GAD2		location ⇒	10:46549819-46550055		CU929835,CH242-56F1,10:46528213-46585609 (Clone quality: bE56F1 on chr=10; Num_of_Contigs=4; )
GAD2		location ⇒	10:46621493-46621702		CU929835,CH242-56F1,10:46585710-46674330 (Clone quality: bE56F1 on chr=10; Num_of_Contigs=4; )
GADD45		ENSSSCG00000009585	14:1365346-1366898		CU407316,CH242-264A7,14:1362971-1403074 (Clone quality: bE264A7 on chr=14; Num_of_Contigs=11; )
GADD45		location ⇒	14:1366065-1366121		CU407316,CH242-264A7,14:1362971-1403074 (Clone quality: bE264A7 on chr=14; Num_of_Contigs=11; )
GADD45A1647		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
GADD45G		ENSSSCG00000009585	14:1365346-1366898		CU407316,CH242-264A7,14:1362971-1403074 (Clone quality: bE264A7 on chr=14; Num_of_Contigs=11; )
GADD45GIP1		ENSSSCG00000013748	2:56298013-56300277		CU463133,CH242-121E19,2:56264935-56304744 (Clone quality: bE121E19 on chr=2; Num_of_Contigs=6; )
GADL1		ENSSSCG00000011224	13:14745236-14979947
GAK		location ⇒	8:45679-45543		FP102972,CH242-47L5,8:43508-48739 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
GAK		location ⇒	8:46493-46369		FP102972,CH242-47L5,8:43508-48739 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
GAK		location ⇒	8:47087-46934		FP102972,CH242-47L5,8:43508-48739 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
GAK		location ⇒	8:47708-47656		FP102972,CH242-47L5,8:43508-48739 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
GAL		ENSSSCG00000012883	2:2594110-2658445
GAL3ST1		ENSSSCG00000010009	14:48264673-48271317
GAL3ST4		ENSSSCG00000007648	3:6412903-6418246		CU694680,CH242-187A15,3:6349164-6471889 (Clone quality: bE187A15 on chr=3; Num_of_Contigs=2; )
GALK1		ENSSSCG00000017203	12:3992686-4001867	CU928968,CH242-19M24,12:3978819-4017836 (Clone quality: bE19M24 on chr=12; Num_of_Contigs=4; )
GALK2		ENSSSCG00000004651	1:127724684-127875709
GALM		ENSSSCG00000008486	3:94763251-94780512		FP102731,CH242-53K21,3:94740369-94785648 (Clone quality: bE53K21 on chr=3; Num_of_Contigs=3; )
GALNS		ENSSSCG00000002645	6:370750-380888
GALNT1		ENSSSCG00000003743	6:83007355-83137932
GALNT10		ENSSSCG00000017072	16:66104431-66230894
GALNT11		ENSSSCG00000016430	18:4498913-4533561		CU928751,CH242-406P15,18:4484632-4554699 (Clone quality: bE406P15 on chr=18; Num_of_Contigs=7; )
GALNT12		ENSSSCG00000005379	1:252170751-252212039
GALNT14		ENSSSCG00000008524	3:101481447-101696762
GALNT2		ENSSSCG00000010185	14:62252286-62335747
GALNT3		ENSSSCG00000015907	15:67554847-67577728		CU914203,CH242-290B3,15:67551702-67595790 (Clone quality: bE290B3 on chr=15; Num_of_Contigs=11; )
GALNT7		ENSSSCG00000009705	14:16313768-16338675		CT827844,CH242-252N8,14:16304166-16433033 (Clone quality: bE252N8 on chr=14; Num_of_Contigs=4; )
GALNT8		ENSSSCG00000000718	5:61410150-61447664
GALNT9		ENSSSCG00000009738	14:22961418-23030382
GALNTL1		ENSSSCG00000002306	7:101403296-101434739
GALNTL2		ENSSSCG00000011195	13:2754445-2792993		CU466353,CH242-456O2,13:2697357-2800021 (Clone quality: bE456O2 on chr=13; Num_of_Contigs=4; )
GALNTL4		ENSSSCG00000013403	2:44464545-44659742
GALNTL5		ENSSSCG00000016431	18:4562299-4624098
GALNTL6		ENSSSCG00000009706	14:16530390-16642724
GALP		ENSSSCG00000003318	6:42093958-42160033
GALR3		ENSSSCG00000000121	5:6568703-6570456		CU633527,CH242-104A9,5:6548130-6585057 (Clone quality: bE104A9 on chr=5; Num_of_Contigs=3; )
GALT		ENSSSCG00000010969	10:30595359-30598970		CU928717,CH242-142N10,10:30573702-30613538 (Clone quality: bE142N10 on chr=10; Num_of_Contigs=7; )
GAN		ENSSSCG00000002690	6:5068344-5122238
GANC		ENSSSCG00000004729	1:135277615-135352151
GANC		location ⇒	1:135211555-135211479		CU694786,CH242-266K24,1:135203872-135227748 (Clone quality: bE266K24 on chr=1; Num_of_Contigs=5; )
GANC		location ⇒	1:135213583-135213514		CU694786,CH242-266K24,1:135203872-135227748 (Clone quality: bE266K24 on chr=1; Num_of_Contigs=5; )
GANC		location ⇒	1:135288204-135288128		CU463161,CH242-286I1,1:135227749-135313166 (Clone quality: bE286I1 on chr=1; Num_of_Contigs=2; )
GANC		location ⇒	1:135290232-135290163		CU463161,CH242-286I1,1:135227749-135313166 (Clone quality: bE286I1 on chr=1; Num_of_Contigs=2; )
GAP-B3		ENSSSCG00000017578	12:24655910-24790905
GAPDH		ENSSSCG00000000694	5:60050521-60051338		CU914489,CH242-100M5,5:60050517-60080104 (Clone quality: bE100M5 on chr=5; Num_of_Contigs=13; )
GAPDHS		ENSSSCG00000002888	6:30056787-30066132
GAPT		ENSSSCG00000016926	16:35422379-35422834		CU914321,CH242-270D14,16:35409456-35535651 (Clone quality: bE270D14 on chr=16; Num_of_Contigs=4; )
GAPVD1		ENSSSCG00000005602	1:280841222-280846745		CU929944,CH242-502D22,1:280839019-280851978 (Clone quality: bE502D22 on chr=1; Num_of_Contigs=7; )
GAR1		ENSSSCG00000009137	8:96564650-96575872		CU463265,CH242-237G17,8:96455649-96640359 (Clone quality: bE237G17 on chr=8; Num_of_Contigs=1; )
GARNL3		ENSSSCG00000005609	1:282141125-282272600

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, 851-25

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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).