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)

PDZRN3		ENSSSCG00000011521	13:46253260-46271541		CU861920,CH242-148F5,13:46248984-46315362 (Clone quality: bE148F5 on chr=13; Num_of_Contigs=2; )
PDZRN4		ENSSSCG00000000791	5:69164686-69235000
PEA15		ENSSSCG00000006389	4:93712042-93720847	CU138477,CH242-105O19,4:93708821-93889364 (Clone quality: bE105O19 on chr=4; Num_of_Contigs=5; )
PEAR1		ENSSSCG00000006463	4:96872398-96886298		CU151867,CH242-283E3,4:96858244-96970867 (Clone quality: bE283E3 on chr=4; Num_of_Contigs=3; )
PEBP1		ENSSSCG00000009851	14:34756187-34762104		CU468330,CH242-221D19,14:34740150-34832482 (Clone quality: bE221D19 on chr=14; Num_of_Contigs=2; )
PEBP4		ENSSSCG00000009631	14:6959726-7056452		CT737218,CH242-19C13,14:6949751-7085055 (Clone quality: bE19C13 on chr=14; Num_of_Contigs=2; )
PEC-60		ENSSSCG00000010997	10:31771645-31849736
PEC-60		location ⇒	10:31771787-31771661		CU694297,CH242-168B13,10:31763640-31823504 (Clone quality: bE168B13 on chr=10; Num_of_Contigs=6; )
PEC-60		location ⇒	10:31773615-31773502		CU694297,CH242-168B13,10:31763640-31823504 (Clone quality: bE168B13 on chr=10; Num_of_Contigs=6; )
PEC-60		location ⇒	10:31781038-31780960		CU694297,CH242-168B13,10:31763640-31823504 (Clone quality: bE168B13 on chr=10; Num_of_Contigs=6; )
PECAM1		location ⇒	12:12245606-12245900		CU915676,CH242-81E24,12:12245137-12303002 (Clone quality: bE81E24 on chr=12; Num_of_Contigs=5; )
PECAM1		location ⇒	12:12249864-12250172		CU915676,CH242-81E24,12:12245137-12303002 (Clone quality: bE81E24 on chr=12; Num_of_Contigs=5; )
PECAM1		location ⇒	12:12258934-12259210		CU915676,CH242-81E24,12:12245137-12303002 (Clone quality: bE81E24 on chr=12; Num_of_Contigs=5; )
PECAM1		location ⇒	12:12262865-12263154		CU915676,CH242-81E24,12:12245137-12303002 (Clone quality: bE81E24 on chr=12; Num_of_Contigs=5; )
PECI		ENSSSCG00000001000	7:2295124-2311768
PECI		location ⇒	7:2302770-2302876		CU607065,CH242-35C2,7:2302076-2306993 (Clone quality: bE35C2 on chr=7; Num_of_Contigs=17; )
PECI		location ⇒	7:2303465-2303588		CU607065,CH242-35C2,7:2302076-2306993 (Clone quality: bE35C2 on chr=7; Num_of_Contigs=17; )
PECI		location ⇒	7:2310430-2310576		CU607065,CH242-35C2,7:2307094-2318446 (Clone quality: bE35C2 on chr=7; Num_of_Contigs=17; )
PECI		location ⇒	7:2311081-2311288		CU607065,CH242-35C2,7:2307094-2318446 (Clone quality: bE35C2 on chr=7; Num_of_Contigs=17; )
PEF1		ENSSSCG00000003602	6:60448720-60466519		CU856262,CH242-97A12,6:60434458-60488383 (Clone quality: bE97A12 on chr=6; Num_of_Contigs=8; )
PEG3		ENSSSCG00000003326	6:42739741-42747604
PEG3		location ⇒	6:42738489-42738425		FP236248,CH242-286C2,6:42732170-42747458 (Clone quality: bE286C2 on chr=6; Num_of_Contigs=4; )
PEG3		location ⇒	6:42739269-42739199		FP236248,CH242-286C2,6:42732170-42747458 (Clone quality: bE286C2 on chr=6; Num_of_Contigs=4; )
PEG3		location ⇒	6:42743835-42743746		FP236248,CH242-286C2,6:42732170-42747458 (Clone quality: bE286C2 on chr=6; Num_of_Contigs=4; )
PEG3		location ⇒	6:42748077-42748017		FP236248,CH242-286C2,6:42747559-42750237 (Clone quality: bE286C2 on chr=6; Num_of_Contigs=4; )
PELI1		ENSSSCG00000008366	3:71824109-71828400		CU928831,CH242-4C2,3:71810936-71829919 (Clone quality: bE4C2 on chr=3; Num_of_Contigs=4; )
PELI2		ENSSSCG00000005061	1:193971065-194179354
PELI3		ENSSSCG00000012944	2:4318313-4327076		CU928034,CH242-426E24,2:4300015-4401092 (Clone quality: bE426E24 on chr=2; Num_of_Contigs=5; )
PELI3		location ⇒	2:4318292-4318439		CU928034,CH242-426E24,2:4300015-4401092 (Clone quality: bE426E24 on chr=2; Num_of_Contigs=5; )
PELI3		location ⇒	2:4319541-4319697		CU928034,CH242-426E24,2:4300015-4401092 (Clone quality: bE426E24 on chr=2; Num_of_Contigs=5; )
PELI3		location ⇒	2:4322364-4322497		CU928034,CH242-426E24,2:4300015-4401092 (Clone quality: bE426E24 on chr=2; Num_of_Contigs=5; )
PELI3		location ⇒	2:4323062-4323165		CU928034,CH242-426E24,2:4300015-4401092 (Clone quality: bE426E24 on chr=2; Num_of_Contigs=5; )
PELO		ENSSSCG00000016884	16:29156701-29158147		CU463114,CH242-218M18,16:29125333-29233947 (Clone quality: bE218M18 on chr=16; Num_of_Contigs=3; )
PEMT		ENSSSCG00000018055	12:57002205-57008689		CU927962,CH242-273I13,12:57001622-57013525 (Clone quality: bE273I13 on chr=12; Num_of_Contigs=8; )
PENK		ENSSSCG00000006243	4:78422054-78426548		CU462960,CH242-392H23,4:78385334-78466679 (Clone quality: bE392H23 on chr=4; Num_of_Contigs=4; )
PENK		location ⇒	4:78422009-78422071		CU462960,CH242-392H23,4:78385334-78466679 (Clone quality: bE392H23 on chr=4; Num_of_Contigs=4; )
PENK		location ⇒	4:78422709-78422842		CU462960,CH242-392H23,4:78385334-78466679 (Clone quality: bE392H23 on chr=4; Num_of_Contigs=4; )
PEPA_PIG		ENSSSCG00000013092	2:8592036-8600552		CU462918,CH242-143A4,2:8550914-8626150 (Clone quality: bE143A4 on chr=2; Num_of_Contigs=7; )
PEPB_PIG		ENSSSCG00000006792	4:113312454-113322817		CU311186,CH242-230C12,4:113251594-113376287 (Clone quality: bE230C12 on chr=4; Num_of_Contigs=3; )
PEPD		ENSSSCG00000002868	6:28901848-28925843		CU929902,CH242-260F18,6:28809182-28963405 (Clone quality: bE260F18 on chr=6; Num_of_Contigs=2; )
PER1		ENSSSCG00000017502	12:20622594-20637983		CU640399,CH242-251F23,12:20578579-20644206 (Clone quality: bE251F23 on chr=12; Num_of_Contigs=5; )
PER1		ENSSSCG00000017983	12:50588370-50599114		CU914306,CH242-98O15,12:50562814-50608727 (Clone quality: bE98O15 on chr=12; Num_of_Contigs=9; )
PER2		ENSSSCG00000016338	15:130270122-130390174
PERP		ENSSSCG00000004153	1:27726703-27782898
PERP		location ⇒	1:27464089-27464230		CU407278,CH242-501B23,1:27453921-27464600 (Clone quality: bE501B23 on chr=1; Num_of_Contigs=25; )
PERP		location ⇒	1:27726793-27727095		CU633601,CH242-56B12,1:27724361-27727635 (Clone quality: bE56B12 on chr=1; Num_of_Contigs=11; )
PERP		location ⇒	1:27782215-27782588		CU633601,CH242-56B12,1:27773032-27789332 (Clone quality: bE56B12 on chr=1; Num_of_Contigs=11; )
PERP		location ⇒	1:27913383-27913753		CU914302,CH242-92E17,1:27911941-27923116 (Clone quality: bE92E17 on chr=1; Num_of_Contigs=10; )
PES1		ENSSSCG00000010010	14:48285072-48302722		CT827803,CH242-235K4,14:48269978-48304323 (Clone quality: bE235K4 on chr=14; Num_of_Contigs=6; )
PET112L		ENSSSCG00000009015	8:66350577-66405180

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, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-21

Report problems to zhu

iastate.edu

$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).