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)

DGAT2L6		ENSSSCG00000012381	X:54989002-54995168		CU487220,CH242-264C4,X:54986607-54998118 (Clone quality: bE264C4 on chr=X; Num_of_Contigs=10; )
DGCR14		ENSSSCG00000010114	14:52056050-52067011
DGCR2		ENSSSCG00000010111	14:51994311-52046513
DGCR2		location ⇒	14:51994961-51992574		CU468322,CH242-201I2,14:51981060-52028952 (Clone quality: bE201I2 on chr=14; Num_of_Contigs=7; )
DGCR2		location ⇒	14:51996469-51996233		CU468322,CH242-201I2,14:51981060-52028952 (Clone quality: bE201I2 on chr=14; Num_of_Contigs=7; )
DGCR2		location ⇒	14:52001423-52001220		CU468322,CH242-201I2,14:51981060-52028952 (Clone quality: bE201I2 on chr=14; Num_of_Contigs=7; )
DGCR2		location ⇒	14:52010075-52009854		CU468322,CH242-201I2,14:51981060-52028952 (Clone quality: bE201I2 on chr=14; Num_of_Contigs=7; )
DGCR8		ENSSSCG00000010135	14:52728045-52742722		CT737345,CH242-178J1,14:52723116-52857619 (Clone quality: bE178J1 on chr=14; Num_of_Contigs=3; )
DGKA		ENSSSCG00000000370	5:20284080-20308013	CU606916,CH242-141C7,5:20252909-20311092 (Clone quality: bE141C7 on chr=5; Num_of_Contigs=1; )
DGKB		ENSSSCG00000015355	9:78609213-78671763
DGKD		ENSSSCG00000016302	15:126410023-126415046		CU914742,CH242-379G11,15:126407721-126418411 (Clone quality: bE379G11 on chr=15; Num_of_Contigs=12; )
DGKE		ENSSSCG00000017615	12:31010743-31036581
DGKH		ENSSSCG00000009432	11:23825047-23942094
DGKI		ENSSSCG00000016521	18:10254873-10586592
DGKZ		ENSSSCG00000013259	2:14223249-14232715		CU467768,CH242-445K9,2:14222547-14372056 (Clone quality: bE445K9 on chr=2; Num_of_Contigs=4; )
DGUOK		ENSSSCG00000008293	3:63564723-63600971
DHDDS		ENSSSCG00000003556	6:57503407-57519584
DHDH		ENSSSCG00000003158	6:37871266-37873006		FP102974,CH242-517N5,6:37865887-37873197 (Clone quality: bE517N5 on chr=6; Num_of_Contigs=15; )
DHFR		location ⇒	1:3256481-3256377		CU234145,CH242-273F9,1:3088134-3261979 (Clone quality: bE273F9 on chr=1; Num_of_Contigs=3; )
DHFR		location ⇒	1:3540269-3540152		CU041408,CH242-65D13,1:3477011-3565892 (Clone quality: bE65D13 on chr=1; Num_of_Contigs=3; )
DHFR		location ⇒	1:649637-649725		CU633311,CH242-59H8,1:648679-651418 (Clone quality: bE59H8 on chr=1; Num_of_Contigs=14; )
DHFR		location ⇒	1:700883-700971		CU914405,CH242-180N18,1:690613-757674 (Clone quality: bE180N18 on chr=1; Num_of_Contigs=5; )
DHH		ENSSSCG00000000188	5:13737776-13742470		CU633656,CH242-19B12,5:13726338-13743074 (Clone quality: bE19B12 on chr=5; Num_of_Contigs=10; )
DHODH		ENSSSCG00000002746	6:10709721-10715772
DHPS		ENSSSCG00000013723	2:55934221-55938570		CU856041,CH242-32I13,2:55919380-55991729 (Clone quality: bE32I13 on chr=2; Num_of_Contigs=2; )
DHRS1		ENSSSCG00000001991	7:81333076-81343098		CU019590,CH242-406B17,7:81281809-81421007 (Clone quality: bE406B17 on chr=7; Num_of_Contigs=4; )
DHRS11		ENSSSCG00000017690	12:36249444-36258776		CU694881,CH242-311G5,12:36223352-36296162 (Clone quality: bE311G5 on chr=12; Num_of_Contigs=3; )
DHRS13		ENSSSCG00000017778	12:42855064-42857459		FP236132,CH242-148L9,12:42852131-42858868 (Clone quality: bE148L9 on chr=12; Num_of_Contigs=4; )
DHRS3		ENSSSCG00000003439	6:49555242-49715697
DHRS7		ENSSSCG00000005083	1:197874387-197891379		CU407153,CH242-197C17,1:197870120-197957670 (Clone quality: bE197C17 on chr=1; Num_of_Contigs=5; )
DHRS7C		ENSSSCG00000017996	12:51694391-51708234
DHRS9		ENSSSCG00000015930	15:71172002-71194266		CU915387,CH242-209P21,15:71151549-71206449 (Clone quality: bE209P21 on chr=15; Num_of_Contigs=5; )
DHSD_PIG		ENSSSCG00000015034	9:38652878-38665903		CU655934,CH242-367F19,9:38605255-38672831 (Clone quality: bE367F19 on chr=9; Num_of_Contigs=8; )
DHTKD1		ENSSSCG00000011115	10:56797685-56840907
DHX15		ENSSSCG00000008756	8:15186349-15244726
DHX16		ENSSSCG00000001365	7:26985174-27002559	CU326403,CH242-198M20,7:26882096-27123407 (Clone quality: bE198M20 on chr=7; Num_of_Contigs=9; )
DHX29		ENSSSCG00000016907	16:31854587-31904523
DHX30		ENSSSCG00000011342	13:25625184-25655612		CU633694,CH242-277F5,13:25598668-25748928 (Clone quality: bE277F5 on chr=13; Num_of_Contigs=2; )
DHX32		ENSSSCG00000010744	14:142138057-142176655
DHX34		ENSSSCG00000003114	6:36884128-36908481
DHX35		ENSSSCG00000007352	17:44186386-44263903
DHX37		ENSSSCG00000009758	14:28218450-28224391
DHX38		ENSSSCG00000002748	6:10759125-10769555		CU914723,CH242-491H10,6:10738269-10769930 (Clone quality: bE491H10 on chr=6; Num_of_Contigs=16; )
DHX40		ENSSSCG00000017665	12:33917589-33963642		CU694896,CH242-358P9,12:33849013-33994738 (Clone quality: bE358P9 on chr=12; Num_of_Contigs=3; )
DHX57		ENSSSCG00000008479	3:94436576-94740264
DHX58		ENSSSCG00000017416	12:18380106-18388791		CU856598,CH242-362F6,12:18319906-18418389 (Clone quality: bE362F6 on chr=12; Num_of_Contigs=5; )
DHX8		ENSSSCG00000017378	12:17447100-17477589
DHX9		ENSSSCG00000015552	9:116468328-116472304		CU914751,CH242-417L17,9:116467833-116472497 (Clone quality: bE417L17 on chr=9; Num_of_Contigs=22; )
DHX9		location ⇒	9:116469449-116469319		CU914751,CH242-417L17,9:116467833-116472497 (Clone quality: bE417L17 on chr=9; Num_of_Contigs=22; )
DHX9		location ⇒	9:116471247-116471016		CU914751,CH242-417L17,9:116467833-116472497 (Clone quality: bE417L17 on chr=9; Num_of_Contigs=22; )

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, 751-16

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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).