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)

PAPLN		location ⇒	7:104576202-104576306		CU914658,CH242-289F14,7:104562553-104580613 (Clone quality: bE289F14 on chr=7; Num_of_Contigs=6; )
PAPLN		location ⇒	7:104578741-104578874		CU914658,CH242-289F14,7:104562553-104580613 (Clone quality: bE289F14 on chr=7; Num_of_Contigs=6; )
PAPLN		location ⇒	7:104579639-104579764		CU914658,CH242-289F14,7:104562553-104580613 (Clone quality: bE289F14 on chr=7; Num_of_Contigs=6; )
PAPOLA		ENSSSCG00000002505	7:126613974-126676882	CT827800,CH242-193M5,7:126572726-126771267 (Clone quality: bE193M5 on chr=7; Num_of_Contigs=4; )
PAPOLG		ENSSSCG00000008389	3:74704528-74738766		CU467691,CH242-216C17,3:74685792-74740183 (Clone quality: bE216C17 on chr=3; Num_of_Contigs=5; )
PAPPA		ENSSSCG00000005498	1:269749292-270010276
PAPPA2		ENSSSCG00000015512	9:111324093-111443857
PAPSS2		ENSSSCG00000010437	14:104637431-104663609
PAQR3		ENSSSCG00000009259	8:119603671-119623443
PAQR5		ENSSSCG00000004968	1:174793754-174816782
PAQR6		ENSSSCG00000006491	4:97707015-97710720		CU468654,CH242-228K10,4:97649767-97712830 (Clone quality: bE228K10 on chr=4; Num_of_Contigs=7; )
PAQR7		ENSSSCG00000003551	6:57374753-57385654
PAQR9		ENSSSCG00000011685	13:68336312-68337445		CU914238,CH242-182G22,13:68335573-68350440 (Clone quality: bE182G22 on chr=13; Num_of_Contigs=5; )
PARD3		ENSSSCG00000011103	10:53976861-54261515
PARD6B		ENSSSCG00000007471	17:54389463-54405812
PARD6G		ENSSSCG00000005775	1:290940711-290941508		CU466542,CH242-516A21,1:290905754-290948243 (Clone quality: bE516A21 on chr=1; Num_of_Contigs=11; )
PARG		ENSSSCG00000010395	14:94234974-94264689		CU693430,CH242-513G17,14:94178322-94275861 (Clone quality: bE513G17 on chr=14; Num_of_Contigs=11; )
PARK2		ENSSSCG00000004032	1:6518045-7514266
PARK7		ENSSSCG00000003385	6:46257269-46267520
PARL		ENSSSCG00000011779	13:92226463-92281469
PARM1		ENSSSCG00000008966	8:60230012-60270445
PARN		ENSSSCG00000007878	3:26051341-26285676
PARP10		ENSSSCG00000005926	4:845362-852016		FP085471,CH242-106F14,4:844999-852138 (Clone quality: bE106F14 on chr=4; Num_of_Contigs=12; )
PARP11		ENSSSCG00000000728	5:62055954-62094129
PARP12		ENSSSCG00000016502	18:8057793-8097515		CU928390,CH242-238M8,18:8038180-8109791 (Clone quality: bE238M8 on chr=18; Num_of_Contigs=3; )
PARP14		ENSSSCG00000011874	13:103742673-103797150
PARP14		location ⇒	13:103755721-103755520		CU570997,CH242-11L16,13:103742500-103765615 (Clone quality: bE11L16 on chr=13; Num_of_Contigs=7; )
PARP14		location ⇒	13:103758651-103758563		CU570997,CH242-11L16,13:103742500-103765615 (Clone quality: bE11L16 on chr=13; Num_of_Contigs=7; )
PARP14		location ⇒	13:103759095-103759031		CU570997,CH242-11L16,13:103742500-103765615 (Clone quality: bE11L16 on chr=13; Num_of_Contigs=7; )
PARP14		location ⇒	13:103771776-103771552		CU928305,CH242-101M7,13:103765616-103845883 (Clone quality: bE101M7 on chr=13; Num_of_Contigs=4; )
PARP15		ENSSSCG00000011875	13:103820364-103845000		CU928305,CH242-101M7,13:103765616-103845883 (Clone quality: bE101M7 on chr=13; Num_of_Contigs=4; )
PARP6		ENSSSCG00000001929	7:66338234-66366302
PARP8		ENSSSCG00000016882	16:27412673-27588750
PARS2		ENSSSCG00000003843	6:112222581-112223999		CU929610,CH242-266G21,6:112199806-112275212 (Clone quality: bE266G21 on chr=6; Num_of_Contigs=3; )
PARVA		location ⇒	2:5247115-5247225		CU856029,CH242-276E8,2:5229174-5256425 (Clone quality: bE276E8 on chr=2; Num_of_Contigs=9; )
PARVA		location ⇒	2:5376125-5376036	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
PARVA		location ⇒	2:6808882-6808979		FP089542,CH242-41F12,2:6778030-6836536 (Clone quality: bE41F12 on chr=2; Num_of_Contigs=6; )
PARVA		location ⇒	2:7480233-7480314		FP102338,CH242-94E13,2:7473681-7485872 (Clone quality: bE94E13 on chr=2; Num_of_Contigs=10; )
PARVB		ENSSSCG00000000024	5:1678491-1711481
PARVB		location ⇒	5:1686372-1686513		CU694698,CH242-25O16,5:1677812-1697482 (Clone quality: bE25O16 on chr=5; Num_of_Contigs=5; )
PARVB		location ⇒	5:1688289-1688404		CU694698,CH242-25O16,5:1677812-1697482 (Clone quality: bE25O16 on chr=5; Num_of_Contigs=5; )
PARVB		location ⇒	5:1705563-1705667		CU694698,CH242-25O16,5:1697583-1752057 (Clone quality: bE25O16 on chr=5; Num_of_Contigs=5; )
PARVB		location ⇒	5:1711403-1711490		CU694698,CH242-25O16,5:1697583-1752057 (Clone quality: bE25O16 on chr=5; Num_of_Contigs=5; )
PARVG		ENSSSCG00000000025	5:1722676-1746963		CU694698,CH242-25O16,5:1697583-1752057 (Clone quality: bE25O16 on chr=5; Num_of_Contigs=5; )
PARVG		location ⇒	5:1724488-1724587		CU694698,CH242-25O16,5:1697583-1752057 (Clone quality: bE25O16 on chr=5; Num_of_Contigs=5; )
PARVG		location ⇒	5:1727245-1727349		CU694698,CH242-25O16,5:1697583-1752057 (Clone quality: bE25O16 on chr=5; Num_of_Contigs=5; )
PARVG		location ⇒	5:1728002-1728143		CU694698,CH242-25O16,5:1697583-1752057 (Clone quality: bE25O16 on chr=5; Num_of_Contigs=5; )
PARVG		location ⇒	5:1729258-1729373		CU694698,CH242-25O16,5:1697583-1752057 (Clone quality: bE25O16 on chr=5; Num_of_Contigs=5; )
PATE2		ENSSSCG00000015224	9:51661789-51662467		CU928873,CH242-5G4,9:51649520-51666998 (Clone quality: bE5G4 on chr=9; Num_of_Contigs=16; )
PATL1		ENSSSCG00000013124	2:9797003-9872891

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

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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).