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)

PAFAH1B2		location ⇒	9:43326937-43326834		CU633260,CH242-267D22,9:43314501-43344182 (Clone quality: bE267D22 on chr=9; Num_of_Contigs=9; )
PAFAH1B2		location ⇒	9:43330192-43330067		CU633260,CH242-267D22,9:43314501-43344182 (Clone quality: bE267D22 on chr=9; Num_of_Contigs=9; )
PAFAH1B2		location ⇒	9:43333127-43333028		CU633260,CH242-267D22,9:43314501-43344182 (Clone quality: bE267D22 on chr=9; Num_of_Contigs=9; )
PAFAH1B2		location ⇒	9:43334559-43334467		CU633260,CH242-267D22,9:43314501-43344182 (Clone quality: bE267D22 on chr=9; Num_of_Contigs=9; )
PAFAH1B3		location ⇒	6:34238035-34238432		FP102452,CH242-68N5,6:34229754-34246960 (Clone quality: bE68N5 on chr=6; Num_of_Contigs=4; )
PAFAH1B3		location ⇒	6:34240245-34240577		FP102452,CH242-68N5,6:34229754-34246960 (Clone quality: bE68N5 on chr=6; Num_of_Contigs=4; )
PAFAH1B3		location ⇒	6:34320133-34319801		FP102858,CH242-504I8,6:34318140-34329428 (Clone quality: bE504I8 on chr=6; Num_of_Contigs=13; )
PAFAH1B3		location ⇒	6:34322343-34321946		FP102858,CH242-504I8,6:34318140-34329428 (Clone quality: bE504I8 on chr=6; Num_of_Contigs=13; )
PAG1		ENSSSCG00000006154	4:57076596-57096490
PAG1		ENSSSCG00000013096	2:8739964-8748044		CU694933,CH242-60C13,2:8702036-8854059 (Clone quality: bE60C13 on chr=2; Num_of_Contigs=4; )
PAG1		location ⇒	4:57104562-57103805		CU467543,CH242-246G10,4:57095918-57117400 (Clone quality: bE246G10 on chr=4; Num_of_Contigs=4; )
PAGE4		ENSSSCG00000012303	X:42997483-43004576		FP085546,CH242-518L20,X:42985511-43108035 (Clone quality: bE518L20 on chr=X; Num_of_Contigs=3; )
PAH		ENSSSCG00000000856	5:76586379-76709960
PAICS		ENSSSCG00000008901	8:47151464-47171190		CU606852,CH242-220F7,8:47084665-47178142 (Clone quality: bE220F7 on chr=8; Num_of_Contigs=9; )
PAIP1		ENSSSCG00000016874	16:25270586-25332899
PAIP2B		ENSSSCG00000008315	3:65727094-65731196		CU929952,CH242-518O20,3:65710717-65732433 (Clone quality: bE518O20 on chr=3; Num_of_Contigs=14; )
PAK1		ENSSSCG00000001041	7:7852285-7864518		CU468900,CH242-267B16,7:7778252-7870334 (Clone quality: bE267B16 on chr=7; Num_of_Contigs=4; )
PAK1		ENSSSCG00000014878	9:11710480-11791400
PAK1		ENSSSCG00000013783	2:57306942-57311220		FP103015,CH242-135B13,2:57305111-57311746 (Clone quality: bE135B13 on chr=2; Num_of_Contigs=14; )
PAK1		location ⇒	9:11512344-11512260		CU469195,CH242-18G22,9:11447610-11601601 (Clone quality: bE18G22 on chr=9; Num_of_Contigs=2; )
PAK1		location ⇒	9:11742890-11741016		CU657950,CH242-17I14,9:11725443-11813100 (Clone quality: bE17I14 on chr=9; Num_of_Contigs=7; )
PAK1		location ⇒	9:11776256-11776042		CU657950,CH242-17I14,9:11725443-11813100 (Clone quality: bE17I14 on chr=9; Num_of_Contigs=7; )
PAK1		location ⇒	9:11791395-11791220		CU657950,CH242-17I14,9:11725443-11813100 (Clone quality: bE17I14 on chr=9; Num_of_Contigs=7; )
PAK1IP1		ENSSSCG00000001041	7:7852285-7864518		CU468900,CH242-267B16,7:7778252-7870334 (Clone quality: bE267B16 on chr=7; Num_of_Contigs=4; )
PAK2		ENSSSCG00000011843	13:100544444-100582707		CU862047,CH242-271N21,13:100539111-100589043 (Clone quality: bE271N21 on chr=13; Num_of_Contigs=5; )
PAK2		location ⇒	13:104934175-104934276		CU633672,CH242-235D16,13:104763788-104940258 (Clone quality: bE235D16 on chr=13; Num_of_Contigs=2; )
PAK2		location ⇒	13:104995019-104995120		CU464151,CH242-19K1,13:104982939-105024362 (Clone quality: bE19K1 on chr=13; Num_of_Contigs=7; )
PAK2		location ⇒	13:62978896-62978993		CU466397,CH242-387F9,13:62957131-62979254 (Clone quality: bE387F9 on chr=13; Num_of_Contigs=9; )
PAK2		location ⇒	13:99358381-99358466		CU582784,CH242-39K20,13:99286999-99359105 (Clone quality: bE39K20 on chr=13; Num_of_Contigs=5; )
PAK6		ENSSSCG00000004781	1:137597492-137601326
PAK6		location ⇒	1:137593764-137593537		CU498975,CH242-47C7,1:137588788-137596449 (Clone quality: bE47C7 on chr=1; Num_of_Contigs=13; )
PAK6		location ⇒	1:137597490-137597816		CU498975,CH242-47C7,1:137596550-137600947 (Clone quality: bE47C7 on chr=1; Num_of_Contigs=13; )
PAK7		ENSSSCG00000007061	17:18397918-18439920
PALB2		ENSSSCG00000010794	10:17317-43988
PALLD		ENSSSCG00000009718	14:20665236-20994694
PALM		ENSSSCG00000013424	2:46275034-46282880		FP015903,CH242-504E7,2:46271419-46293649 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
PALM2		ENSSSCG00000005450	1:263522347-263540201		CU571182,CH242-107K18,1:263501787-263550341 (Clone quality: bE107K18 on chr=1; Num_of_Contigs=4; )
PALMD		ENSSSCG00000006874	4:123209123-123259617
PAM		ENSSSCG00000014184	2:97546841-97702929
PAN2		ENSSSCG00000000393	5:20698852-20712565
PAN3		ENSSSCG00000009319	11:4968475-5092296
PANK1		ENSSSCG00000010456	14:106312317-106341972		CT955956,CH242-196P20,14:106288428-106418350 (Clone quality: bE196P20 on chr=14; Num_of_Contigs=2; )
PANK2		ENSSSCG00000007142	17:33406925-33415283
PANK3		ENSSSCG00000017014	16:52663044-52683632		CU694725,CH242-378M19,16:52635298-52689407 (Clone quality: bE378M19 on chr=16; Num_of_Contigs=12; )
PANX1		ENSSSCG00000014951	9:26755625-26760294		CU896620,CH242-350A15,9:26743571-26761282 (Clone quality: bE350A15 on chr=9; Num_of_Contigs=9; )
PANX2		ENSSSCG00000000975	5:99872666-99880364
PANX3		ENSSSCG00000015194	9:50314347-50320529		CU633633,CH242-140J10,9:50258982-50355264 (Clone quality: bE140J10 on chr=9; Num_of_Contigs=3; )
PAPD4		ENSSSCG00000014114	2:77488969-77542008
PAPLN		ENSSSCG00000002341	7:104592643-104604400		CU914658,CH242-289F14,7:104591764-104620514 (Clone quality: bE289F14 on chr=7; Num_of_Contigs=6; )
PAPLN		location ⇒	7:104574506-104574623		CU914658,CH242-289F14,7:104562553-104580613 (Clone quality: bE289F14 on chr=7; Num_of_Contigs=6; )

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).