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)

PPP1R2		ENSSSCG00000011830	13:99616961-99635515		CU582896,CH242-39I7,13:99614653-99649103 (Clone quality: bE39I7 on chr=13; Num_of_Contigs=5; )
PPP1R2		ENSSSCG00000012256	X:38006993-38007586		FP101956,CH242-132C3,X:38002599-38009631 (Clone quality: bE132C3 on chr=X; Num_of_Contigs=33; )
PPP1R2		location ⇒	X:57793603-57795224		CU466457,CH242-258F7,X:57732299-57807456 (Clone quality: bE258F7 on chr=X; Num_of_Contigs=7; )
PPP1R3B		ENSSSCG00000015852	15:53094713-53095567		CU915454,CH242-177B14,15:53071770-53114679 (Clone quality: bE177B14 on chr=15; Num_of_Contigs=10; )
PPP1R3C		ENSSSCG00000010464	14:108395001-108398066		CU468441,CH242-68K21,14:108305821-108479531 (Clone quality: bE68K21 on chr=14; Num_of_Contigs=1; )
PPP1R3D		ENSSSCG00000007530	17:62582453-62583352		CU915385,CH242-197I13,17:62578020-62643589 (Clone quality: bE197I13 on chr=17; Num_of_Contigs=8; )
PPP1R3E		ENSSSCG00000002021	7:82037079-82038517		CU633625,CH242-116C14,7:81989794-82038828 (Clone quality: bE116C14 on chr=7; Num_of_Contigs=8; )
PPP1R3G		ENSSSCG00000000997	7:1637178-1638060		CU694314,CH242-197B15,7:1595463-1729252 (Clone quality: bE197B15 on chr=7; Num_of_Contigs=3; )
PPP1R7		ENSSSCG00000016376	15:132053136-132063734
PPP1R9A		ENSSSCG00000015329	9:69914784-69916181		CU915625,CH242-136K1,9:69912209-69917925 (Clone quality: bE136K1 on chr=9; Num_of_Contigs=12; )
PPP1R9A		ENSSSCG00000015330	9:70143845-70145786
PPP1R9A		location ⇒	9:105845032-105844974		CU693385,CH242-143F22,9:105742784-105878546 (Clone quality: bE143F22 on chr=9; Num_of_Contigs=2; )
PPP1R9A		location ⇒	9:69916394-69914785		CU915625,CH242-136K1,9:69912209-69917925 (Clone quality: bE136K1 on chr=9; Num_of_Contigs=12; )
PPP1R9A		location ⇒	9:70173532-70173602		CU861966,CH242-276D1,9:70171274-70176390 (Clone quality: bE276D1 on chr=9; Num_of_Contigs=14; )
PPP1R9A		location ⇒	9:70221824-70221766		CU861966,CH242-276D1,9:70220024-70228390 (Clone quality: bE276D1 on chr=9; Num_of_Contigs=14; )
PPP1R9B		ENSSSCG00000017584	12:24727275-24742760
PPP2CA		ENSSSCG00000014298	2:124265735-124274659
PPP2CA		location ⇒	2:124220451-124220501
PPP2CA		location ⇒	2:124268621-124268457		CU694278,CH242-390O19,2:124265868-124282841 (Clone quality: bE390O19 on chr=2; Num_of_Contigs=22; )
PPP2CA		location ⇒	2:124270544-124270369		CU694278,CH242-390O19,2:124265868-124282841 (Clone quality: bE390O19 on chr=2; Num_of_Contigs=22; )
PPP2CA		location ⇒	2:124274657-124274444		CU694278,CH242-390O19,2:124265868-124282841 (Clone quality: bE390O19 on chr=2; Num_of_Contigs=22; )
PPP2CB		ENSSSCG00000015842	15:51239504-51256231		CU855604,CH242-134L11,15:51228220-51331802 (Clone quality: bE134L11 on chr=15; Num_of_Contigs=7; )
PPP2R2A		ENSSSCG00000009657	14:10337015-10424743
PPP2R2A		location ⇒	14:10337087-10337146		CT956083,CH242-326C14,14:10175341-10379801 (Clone quality: bE326C14 on chr=14; Num_of_Contigs=1; )
PPP2R2A		location ⇒	14:10404641-10404800		CT956017,CH242-305F22,14:10379802-10562482 (Clone quality: bE305F22 on chr=14; Num_of_Contigs=1; )
PPP2R2A		location ⇒	14:10413881-10414058		CT956017,CH242-305F22,14:10379802-10562482 (Clone quality: bE305F22 on chr=14; Num_of_Contigs=1; )
PPP2R2A		location ⇒	14:10423738-10424696		CT956017,CH242-305F22,14:10379802-10562482 (Clone quality: bE305F22 on chr=14; Num_of_Contigs=1; )
PPP2R2B		location ⇒	2:134115703-134115010		FP015780,CH242-49F12,2:134092137-134118525 (Clone quality: bE49F12 on chr=2; Num_of_Contigs=2; )
PPP2R2B		location ⇒	2:134129656-134129827		FP015780,CH242-49F12,2:134122522-134137239 (Clone quality: bE49F12 on chr=2; Num_of_Contigs=2; )
PPP2R2C		ENSSSCG00000008712	8:2353771-2498628
PPP2R3A		ENSSSCG00000011649	13:63235906-63245845		CU633269,CH242-284K19,13:63235289-63247380 (Clone quality: bE284K19 on chr=13; Num_of_Contigs=6; )
PPP2R3C		ENSSSCG00000001953	7:70579520-70579705		CU469145,CH242-277H7,7:70578492-70658893 (Clone quality: bE277H7 on chr=7; Num_of_Contigs=4; )
PPP2R4		ENSSSCG00000005672	1:284076470-284104923		CU041302,CH242-13F23,1:284074391-284292479 (Clone quality: bE13F23 on chr=1; Num_of_Contigs=6; )
PPP2R5A		ENSSSCG00000015599	9:123467265-123539036
PPP2R5B		ENSSSCG00000013016	2:5648173-5655110		CU606982,CH242-431G15,2:5575891-5703518 (Clone quality: bE431G15 on chr=2; Num_of_Contigs=4; )
PPP2R5C		ENSSSCG00000002540	7:131904751-132005920
PPP2R5D		ENSSSCG00000001654	7:43902567-43925408	CR956379,CH242-196P11,7:43779717-43958428 (No clone quality info on bE196P11)
PPP2R5E		ENSSSCG00000005113	1:203500553-203556827
PPP3CA		ENSSSCG00000009172	8:102532923-102613200
PPP3CA		location ⇒	8:102458333-102458131		CU855738,CH242-269E10,8:102412811-102479476 (Clone quality: bE269E10 on chr=8; Num_of_Contigs=8; )
PPP3CA		location ⇒	8:102574445-102574522
PPP3CA		location ⇒	8:102679489-102678999		CU627986,CH242-404P11,8:102677434-102681439 (Clone quality: bE404P11 on chr=8; Num_of_Contigs=26; )
PPP3CA		location ⇒	8:102679742-102679530		CU627986,CH242-404P11,8:102677434-102681439 (Clone quality: bE404P11 on chr=8; Num_of_Contigs=26; )
PPP3CB		ENSSSCG00000010301	14:79553070-79606556		CT867945,CH242-262J5,14:79481277-79661085 (Clone quality: bE262J5 on chr=14; Num_of_Contigs=2; )
PPP3CC		ENSSSCG00000009624	14:6695108-6748444
PPP4R1L		ENSSSCG00000007512	17:61040742-61061698	CR956359,CH242-256J18,17:60938475-61076184 (No clone quality info on bE256J18)
PPP5C		ENSSSCG00000003098	6:36181393-36204262
PPP6C		ENSSSCG00000005600	1:280745798-280769960		CU041411,CH242-95A24,1:280727173-280776523 (Clone quality: bE95A24 on chr=1; Num_of_Contigs=8; )
PPPDE1		ENSSSCG00000010876	10:16961130-16981282		CU571186,CH242-132I12,10:16943285-17006969 (Clone quality: bE132I12 on chr=10; Num_of_Contigs=2; )
PPPDE2		ENSSSCG00000000060	5:3474339-3497158

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).