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)

PTX3		location ⇒	13:77151636-77152042		CU633549,CH242-178L15,13:77122444-77202872 (Clone quality: bE178L15 on chr=13; Num_of_Contigs=4; )
PTX3		location ⇒	13:77155654-77156817		CU633549,CH242-178L15,13:77122444-77202872 (Clone quality: bE178L15 on chr=13; Num_of_Contigs=4; )
PUM1		ENSSSCG00000003591	6:59768386-59817202
PUM2		ENSSSCG00000008600	3:109490435-109567035
PUNC		ENSSSCG00000004931	1:170390013-170403202		CU633232,CH242-191H9,1:170387390-170434800 (Clone quality: bE191H9 on chr=1; Num_of_Contigs=6; )
PUNC		ENSSSCG00000004932	1:170410018-170452342
PUNC		location ⇒	1:170412949-170413247		CU633232,CH242-191H9,1:170387390-170434800 (Clone quality: bE191H9 on chr=1; Num_of_Contigs=6; )
PUNC		location ⇒	1:170452673-170452729		CU633232,CH242-191H9,1:170434901-170493452 (Clone quality: bE191H9 on chr=1; Num_of_Contigs=6; )
PUNC		location ⇒	1:170453360-170453545		CU633232,CH242-191H9,1:170434901-170493452 (Clone quality: bE191H9 on chr=1; Num_of_Contigs=6; )
PUNC		location ⇒	1:170453758-170453820		CU633232,CH242-191H9,1:170434901-170493452 (Clone quality: bE191H9 on chr=1; Num_of_Contigs=6; )
PURB		ENSSSCG00000016739	18:49099009-49099707
PUS1		ENSSSCG00000009741	14:23282353-23300172		CU469318,CH242-114E11,14:23178600-23358435 (Clone quality: bE114E11 on chr=14; Num_of_Contigs=2; )
PUS10		ENSSSCG00000008385	3:74320412-74573966
PUS3		location ⇒	9:51579705-51579398		CU928873,CH242-5G4,9:51579056-51585313 (Clone quality: bE5G4 on chr=9; Num_of_Contigs=16; )
PUS3		location ⇒	9:51580037-51579849		CU928873,CH242-5G4,9:51579056-51585313 (Clone quality: bE5G4 on chr=9; Num_of_Contigs=16; )
PUS3		location ⇒	9:51581087-51580522		CU928873,CH242-5G4,9:51579056-51585313 (Clone quality: bE5G4 on chr=9; Num_of_Contigs=16; )
PUS3		location ⇒	9:51581593-51581193		CU928873,CH242-5G4,9:51579056-51585313 (Clone quality: bE5G4 on chr=9; Num_of_Contigs=16; )
PUS7		ENSSSCG00000015428	9:98413133-98584731
PUSL1		ENSSSCG00000003338	6:42905835-42908845
PVALB		ENSSSCG00000000138	5:7325480-7342788		CU407327,CH242-127L5,5:7317383-7358806 (Clone quality: bE127L5 on chr=5; Num_of_Contigs=4; )
PVR		ENSSSCG00000003079	6:35616165-35627447		CU929755,CH242-284D18,6:35587258-35702275 (Clone quality: bE284D18 on chr=6; Num_of_Contigs=4; )
PVRIG		ENSSSCG00000007656	3:6594341-6596393		CU464007,CH242-351O3,3:6593493-6614733 (Clone quality: bE351O3 on chr=3; Num_of_Contigs=5; )
PVRL1		ENSSSCG00000015124	9:45499515-45554433
PVRL2		ENSSSCG00000003090	6:35908889-35947716
Pvrl2		location ⇒	6:35621621-35621564		CU929755,CH242-284D18,6:35587258-35702275 (Clone quality: bE284D18 on chr=6; Num_of_Contigs=4; )
Pvrl2		location ⇒	6:35917027-35916622		CU459172,CH242-480J10,6:35908168-35933908 (Clone quality: bE480J10 on chr=6; Num_of_Contigs=12; )
Pvrl2		location ⇒	6:35934772-35934474		CU459172,CH242-480J10,6:35934009-35953888 (Clone quality: bE480J10 on chr=6; Num_of_Contigs=12; )
Pvrl2		location ⇒	6:35937211-35936816		CU459172,CH242-480J10,6:35934009-35953888 (Clone quality: bE480J10 on chr=6; Num_of_Contigs=12; )
PVRL3		ENSSSCG00000011933	13:111141197-111166125		CU914400,CH242-126E9,13:111116261-111220774 (Clone quality: bE126E9 on chr=13; Num_of_Contigs=5; )
PVRL3		location ⇒	13:111153520-111153639		CU914400,CH242-126E9,13:111116261-111220774 (Clone quality: bE126E9 on chr=13; Num_of_Contigs=5; )
PVRL3		location ⇒	13:111158758-111158911		CU914400,CH242-126E9,13:111116261-111220774 (Clone quality: bE126E9 on chr=13; Num_of_Contigs=5; )
PVRL3		location ⇒	13:111165543-111165848		CU914400,CH242-126E9,13:111116261-111220774 (Clone quality: bE126E9 on chr=13; Num_of_Contigs=5; )
PVRL4		ENSSSCG00000006368	4:92863024-92879047		CU463216,CH242-293N2,4:92861165-92884929 (Clone quality: bE293N2 on chr=4; Num_of_Contigs=6; )
PVRL4		location ⇒	4:92872591-92872763		CU463216,CH242-293N2,4:92861165-92884929 (Clone quality: bE293N2 on chr=4; Num_of_Contigs=6; )
PVRL4		location ⇒	4:92874319-92874610		CU463216,CH242-293N2,4:92861165-92884929 (Clone quality: bE293N2 on chr=4; Num_of_Contigs=6; )
PVRL4		location ⇒	4:92876741-92876890		CU463216,CH242-293N2,4:92861165-92884929 (Clone quality: bE293N2 on chr=4; Num_of_Contigs=6; )
PVRL4		location ⇒	4:92877139-92877192		CU463216,CH242-293N2,4:92861165-92884929 (Clone quality: bE293N2 on chr=4; Num_of_Contigs=6; )
PWP1		ENSSSCG00000000161	5:10888863-10917072
PWWP2A		ENSSSCG00000017038	16:61047681-61048286		FP085377,CH242-270A12,16:61022156-61080268 (Clone quality: bE270A12 on chr=16; Num_of_Contigs=2; )
PX19		ENSSSCG00000014042	2:69747970-69752516	CU915382,CH242-167E23,2:69697156-69852996 (Clone quality: bE167E23 on chr=2; Num_of_Contigs=8; )
PX19		location ⇒	5:26097586-26098298		CU570929,CH242-211J6,5:26080544-26105794 (Clone quality: bE211J6 on chr=5; Num_of_Contigs=7; )
PX19		location ⇒	5:26338178-26338890		CU576526,CH242-119D7,5:26311374-26353494 (Clone quality: bE119D7 on chr=5; Num_of_Contigs=13; )
PXDN		ENSSSCG00000008655	3:121265240-121274481		FP102317,CH242-206A23,3:121263634-121296355 (Clone quality: bE206A23 on chr=3; Num_of_Contigs=8; )
PXDN		location ⇒	3:121265915-121266746		FP102317,CH242-206A23,3:121263634-121296355 (Clone quality: bE206A23 on chr=3; Num_of_Contigs=8; )
PXMP3		ENSSSCG00000006168	4:61490446-61491363		CU179688,CH242-247C7,4:61462207-61516774 (Clone quality: bE247C7 on chr=4; Num_of_Contigs=6; )
PXMP4		ENSSSCG00000007269	17:39122979-39135792		CU407167,CH242-230G19,17:39116497-39141577 (Clone quality: bE230G19 on chr=17; Num_of_Contigs=9; )
PXN		ENSSSCG00000008655	3:121265240-121274481		FP102317,CH242-206A23,3:121263634-121296355 (Clone quality: bE206A23 on chr=3; Num_of_Contigs=8; )
PXN		location ⇒	14:40367300-40367522		CU407045,CH242-216A8,14:40363299-40369237 (No clone quality info on )
PXN		location ⇒	14:40367804-40367923		CU407045,CH242-216A8,14:40363299-40369237 (No clone quality info on )
PXN		location ⇒	14:40368350-40368488		CU407045,CH242-216A8,14:40363299-40369237 (No clone quality info on )

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).