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)

PTPLAD1		ENSSSCG00000004935	1:170629212-170669040		CU463002,CH242-312G12,1:170566222-170696309 (Clone quality: bE312G12 on chr=1; Num_of_Contigs=4; )
PTPLAD2		ENSSSCG00000005164	1:210650171-210672959		CU407268,CH242-471I15,1:210647629-210684078 (Clone quality: bE471I15 on chr=1; Num_of_Contigs=19; )
PTPMT1		ENSSSCG00000013226	2:13068848-13074399		CU856103,CH242-271O6,2:12985573-13119992 (Clone quality: bE271O6 on chr=2; Num_of_Contigs=3; )
PTPN1		ENSSSCG00000007469	17:54211406-54281046
PTPN1		location ⇒	17:54274629-54274835	CR956376,CH242-7P5,17:54246817-54397383 (No clone quality info on bE7P5)
PTPN1		location ⇒	17:54277685-54277751	CR956376,CH242-7P5,17:54246817-54397383 (No clone quality info on bE7P5)
PTPN1		location ⇒	17:54279374-54279629	CR956376,CH242-7P5,17:54246817-54397383 (No clone quality info on bE7P5)
PTPN1		location ⇒	17:54280335-54280830	CR956376,CH242-7P5,17:54246817-54397383 (No clone quality info on bE7P5)
PTPN12		ENSSSCG00000015411	9:95427072-95467282		CU862033,CH242-157L15,9:95425990-95572442 (Clone quality: bE157L15 on chr=9; Num_of_Contigs=2; )
PTPN13		location ⇒	8:8002502-8002580		CU928759,CH242-80M6,8:7998708-8014353 (Clone quality: bE80M6 on chr=8; Num_of_Contigs=5; )
PTPN13		location ⇒	8:8061647-8061725		FP089472,CH242-122C5,8:8040243-8118614 (Clone quality: bE122C5 on chr=8; Num_of_Contigs=3; )
PTPN13		location ⇒	8:87111140-87111046		CU861495,CH242-8E23,8:87041129-87162511 (Clone quality: bE8E23 on chr=8; Num_of_Contigs=3; )
PTPN13		location ⇒	8:8845132-8845047		CU928550,CH242-138F6,8:8837754-8853627 (Clone quality: bE138F6 on chr=8; Num_of_Contigs=3; )
PTPN14		ENSSSCG00000015582	9:121678361-121730182
PTPN18		ENSSSCG00000015735	15:29037050-29056732
PTPN2		location ⇒	2:65488439-65489184		CU928593,CH242-110L5,2:65422424-65498963 (Clone quality: bE110L5 on chr=2; Num_of_Contigs=5; )
PTPN2		location ⇒	2:65489455-65489722		CU928593,CH242-110L5,2:65422424-65498963 (Clone quality: bE110L5 on chr=2; Num_of_Contigs=5; )
PTPN21		ENSSSCG00000002425	7:118245871-118318622
PTPN21		location ⇒	7:118246721-118246574		CT757500,CH242-29G23,7:118096292-118255857 (Clone quality: bE29G23 on chr=7; Num_of_Contigs=2; )
PTPN21		location ⇒	7:118247636-118247400		CT757500,CH242-29G23,7:118096292-118255857 (Clone quality: bE29G23 on chr=7; Num_of_Contigs=2; )
PTPN21		location ⇒	7:118247962-118247831		CT757500,CH242-29G23,7:118096292-118255857 (Clone quality: bE29G23 on chr=7; Num_of_Contigs=2; )
PTPN21		location ⇒	7:118253625-118253462		CT757500,CH242-29G23,7:118096292-118255857 (Clone quality: bE29G23 on chr=7; Num_of_Contigs=2; )
PTPN22		ENSSSCG00000006764	4:111066816-111117519
PTPN22		location ⇒	4:111048396-111049058		CU651648,CH242-226J22,4:110972280-111079200 (Clone quality: bE226J22 on chr=4; Num_of_Contigs=4; )
PTPN23		ENSSSCG00000011338	13:25331710-25340317		CU633348,CH242-158N8,13:25277659-25344664 (Clone quality: bE158N8 on chr=13; Num_of_Contigs=9; )
PTPN3		ENSSSCG00000005449	1:263189632-263223249		CU627995,CH242-236N5,1:263188502-263225702 (Clone quality: bE236N5 on chr=1; Num_of_Contigs=7; )
PTPN4		ENSSSCG00000015743	15:29500425-29714051
PTPN4		location ⇒	15:29605466-29605346		CU693397,CH242-211B19,15:29562489-29707052 (Clone quality: bE211B19 on chr=15; Num_of_Contigs=2; )
PTPN4		location ⇒	15:29608887-29608799		CU693397,CH242-211B19,15:29562489-29707052 (Clone quality: bE211B19 on chr=15; Num_of_Contigs=2; )
PTPN4		location ⇒	15:29624452-29624361		CU693397,CH242-211B19,15:29562489-29707052 (Clone quality: bE211B19 on chr=15; Num_of_Contigs=2; )
PTPN4		location ⇒	15:29643178-29643003		CU693397,CH242-211B19,15:29562489-29707052 (Clone quality: bE211B19 on chr=15; Num_of_Contigs=2; )
PTPN5		ENSSSCG00000013358	2:37675894-37692393		CU915335,CH242-299H5,2:37673371-37742014 (Clone quality: bE299H5 on chr=2; Num_of_Contigs=5; )
PTPN9		ENSSSCG00000001878	7:63302924-63419418
PTPN9		location ⇒	7:63364997-63365151
PTPN9		location ⇒	7:63398173-63398350
PTPN9		location ⇒	7:63404242-63404335		CU467588,CH242-455O20,7:63398173-63451857 (Clone quality: bE455O20 on chr=7; Num_of_Contigs=6; )
PTPN9		location ⇒	7:63416820-63416972		CU467588,CH242-455O20,7:63398173-63451857 (Clone quality: bE455O20 on chr=7; Num_of_Contigs=6; )
PTPNS1		ENSSSCG00000007181	17:35100996-35142659		CU076083,CH242-165N9,17:35094633-35142680 (Clone quality: bE165N9 on chr=17; Num_of_Contigs=11; )
PTPNS1		location ⇒	17:35101249-35100496		CU076083,CH242-165N9,17:35094633-35142680 (Clone quality: bE165N9 on chr=17; Num_of_Contigs=11; )
PTPNS1		location ⇒	17:35123743-35123375		CU076083,CH242-165N9,17:35094633-35142680 (Clone quality: bE165N9 on chr=17; Num_of_Contigs=11; )
PTPNS1		location ⇒	17:35229201-35228833		CU407174,CH242-240D14,17:35216522-35282296 (Clone quality: bE240D14 on chr=17; Num_of_Contigs=11; )
PTPNS1		location ⇒	17:35486113-35485745		CU855972,CH242-152H19,17:35476390-35490184 (Clone quality: bE152H19 on chr=17; Num_of_Contigs=30; )
PTPRA		ENSSSCG00000007166	17:34211675-34370646
PTPRA		location ⇒	17:34212315-34212010		CU302217,CH242-196N9,17:34201308-34233423 (Clone quality: bE196N9 on chr=17; Num_of_Contigs=10; )
PTPRA		location ⇒	17:34215470-34215318		CU302217,CH242-196N9,17:34201308-34233423 (Clone quality: bE196N9 on chr=17; Num_of_Contigs=10; )
PTPRA		location ⇒	17:34223538-34223389		CU302217,CH242-196N9,17:34201308-34233423 (Clone quality: bE196N9 on chr=17; Num_of_Contigs=10; )
PTPRA		location ⇒	17:34224996-34224826		CU302217,CH242-196N9,17:34201308-34233423 (Clone quality: bE196N9 on chr=17; Num_of_Contigs=10; )
PTPRB		ENSSSCG00000000504	5:33526871-33623177
PTPRB		location ⇒	5:33526943-33527174		CU463092,CH242-445F23,5:33506486-33585419 (Clone quality: bE445F23 on chr=5; Num_of_Contigs=4; )
PTPRB		location ⇒	5:33529818-33529940		CU463092,CH242-445F23,5:33506486-33585419 (Clone quality: bE445F23 on chr=5; Num_of_Contigs=4; )

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).