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)

OTOG		location ⇒	2:38784140-38784074		CU928425,CH242-515C3,2:38778695-38802660 (Clone quality: bE515C3 on chr=2; Num_of_Contigs=6; )
OTOG		location ⇒	2:38784333-38784251		CU928425,CH242-515C3,2:38778695-38802660 (Clone quality: bE515C3 on chr=2; Num_of_Contigs=6; )
OTOG		location ⇒	2:38788555-38788433		CU928425,CH242-515C3,2:38778695-38802660 (Clone quality: bE515C3 on chr=2; Num_of_Contigs=6; )
OTOG		location ⇒	2:38788767-38788700		CU928425,CH242-515C3,2:38778695-38802660 (Clone quality: bE515C3 on chr=2; Num_of_Contigs=6; )
OTOP1		ENSSSCG00000008731	8:4572122-4594275
OTOP2		ENSSSCG00000017222	12:4524075-4532433		CU640421,CH242-384L19,12:4520955-4534685 (Clone quality: bE384L19 on chr=12; Num_of_Contigs=8; )
OTOP3		ENSSSCG00000017220	12:4467615-4474402		CU640421,CH242-384L19,12:4443050-4475806 (Clone quality: bE384L19 on chr=12; Num_of_Contigs=8; )
OTOR		ENSSSCG00000007082	17:25888189-25891233		CU607041,CH242-365I22,17:25887099-25897367 (Clone quality: bE365I22 on chr=17; Num_of_Contigs=14; )
OTOS		ENSSSCG00000016355	15:131350358-131351357
OTP		ENSSSCG00000014099	2:75467243-75475222		CU856635,CH242-150I3,2:75355000-75519413 (Clone quality: bE150I3 on chr=2; Num_of_Contigs=1; )
OTUB1		ENSSSCG00000013045	2:6461871-6469136		CU914709,CH242-316G24,2:6453896-6478840 (Clone quality: bE316G24 on chr=2; Num_of_Contigs=6; )
OTUB1		location ⇒	2:6462454-6462193		CU914709,CH242-316G24,2:6453896-6478840 (Clone quality: bE316G24 on chr=2; Num_of_Contigs=6; )
OTUB1		location ⇒	2:6462777-6462581		CU914709,CH242-316G24,2:6453896-6478840 (Clone quality: bE316G24 on chr=2; Num_of_Contigs=6; )
OTUB1		location ⇒	2:6463267-6463145		CU914709,CH242-316G24,2:6453896-6478840 (Clone quality: bE316G24 on chr=2; Num_of_Contigs=6; )
OTUB1		location ⇒	2:6466906-6466805		CU914709,CH242-316G24,2:6453896-6478840 (Clone quality: bE316G24 on chr=2; Num_of_Contigs=6; )
OTUB2		ENSSSCG00000002469	7:123639810-123658207		CT990641,CH242-259C22,7:123630146-123710826 (Clone quality: bE259C22 on chr=7; Num_of_Contigs=4; )
OTUD1		ENSSSCG00000011076	10:49284989-49429694
OTUD1		location ⇒	10:49283819-49283722		CU986280,CH242-53P3,10:49276828-49285962 (Clone quality: bE53P3 on chr=10; Num_of_Contigs=7; )
OTUD1		location ⇒	10:49285946-49284355		CU986280,CH242-53P3,10:49276828-49285962 (Clone quality: bE53P3 on chr=10; Num_of_Contigs=7; )
OTUD5		ENSSSCG00000000969	5:99733499-100088859
OTUD6A		ENSSSCG00000012383	X:55088841-55089710		CU487220,CH242-264C4,X:55082571-55100202 (Clone quality: bE264C4 on chr=X; Num_of_Contigs=10; )
OTUD6B		ENSSSCG00000006120	4:46313514-46327697	CU179670,CH242-299E13,4:46296919-46490242 (Clone quality: bE299E13 on chr=4; Num_of_Contigs=2; )
OTUD7A		ENSSSCG00000004840	1:150977423-151015033
OTUD7B		ENSSSCG00000006663	4:103065448-103119195
OTX1		ENSSSCG00000008371	3:72633333-72636523		FP236233,CH242-133O13,3:72609768-72688083 (Clone quality: bE133O13 on chr=3; Num_of_Contigs=4; )
OTX2		ENSSSCG00000005063	1:194652747-194656414		CU463093,CH242-186A15,1:194621655-194661065 (Clone quality: bE186A15 on chr=1; Num_of_Contigs=2; )
OVCH1		ENSSSCG00000000540	5:42960294-42984846
OVGP1		ENSSSCG00000006791	4:113289690-113301717		CU311186,CH242-230C12,4:113251594-113376287 (Clone quality: bE230C12 on chr=4; Num_of_Contigs=3; )
OVOL1		ENSSSCG00000012976	2:4929034-4939351
OVOL2		ENSSSCG00000007091	17:27070662-27097686
OX2R_PIG		ENSSSCG00000001482	7:30352218-30361122		CU468942,CH242-164A10,7:30342615-30421326 (Clone quality: bE164A10 on chr=7; Num_of_Contigs=3; )
OXA1L		ENSSSCG00000002042	7:82469850-82500420		CT737318,CH242-17H24,7:82408265-82613937 (Clone quality: bE17H24 on chr=7; Num_of_Contigs=1; )
OXCT		ENSSSCG00000016863	16:23873614-24022635
OXCT		location ⇒	16:23874086-23873857		FP017290,CH242-237P13,16:23871061-23879789 (Clone quality: bE237P13 on chr=16; Num_of_Contigs=1; )
OXCT		location ⇒	16:23991509-23991460		CU993811,CH242-60F1,16:23991456-24002073 (Clone quality: bE60F1 on chr=16; Num_of_Contigs=4; )
OXCT		location ⇒	16:23997166-23997012		CU993811,CH242-60F1,16:23991456-24002073 (Clone quality: bE60F1 on chr=16; Num_of_Contigs=4; )
OXCT		location ⇒	16:24022702-24022557		CU993811,CH242-60F1,16:24022476-24040926 (Clone quality: bE60F1 on chr=16; Num_of_Contigs=4; )
OXCT1		ENSSSCG00000016863	16:23873614-24022635
OXCT2		ENSSSCG00000003659	6:65370590-65372758	CR956622,PigE-219N9,6:65300804-65474973 (No clone quality info on bT219N9)
OXDD_PIG		ENSSSCG00000004401	1:79616452-79641334
OXNAD1		ENSSSCG00000011197	13:2820029-2860926		CU466353,CH242-456O2,13:2815927-2874609 (Clone quality: bE456O2 on chr=13; Num_of_Contigs=4; )
OXR1		ENSSSCG00000006037	4:30812317-30907841
OXSM		ENSSSCG00000011215	13:10518533-10523009		CU633283,CH242-369O19,13:10518523-10523557 (Clone quality: bE369O19 on chr=13; Num_of_Contigs=5; )
OXSR1_PIG		ENSSSCG00000011252	13:18952317-19025261
OXT		ENSSSCG00000007164	17:34178421-34179296		CU302217,CH242-196N9,17:34159575-34193292 (Clone quality: bE196N9 on chr=17; Num_of_Contigs=10; )

Go to records:
1-49, 50-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-45

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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).