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)

PHF6		location ⇒	X:108401230-108401700		CU468475,CH242-274C3,X:108371119-108420183 (Clone quality: bE274C3 on chr=X; Num_of_Contigs=6; )
PHF7		ENSSSCG00000011439	13:29168110-29179835		CU550676,CH242-330J9,13:29135788-29268883 (Clone quality: bE330J9 on chr=13; Num_of_Contigs=4; )
PHF8		ENSSSCG00000012329	X:46109936-46217408
PHGDH		ENSSSCG00000006715	4:105604158-105611683	CR956647,CH242-38B5,4:105599155-105730207 (No clone quality info on bE38B5)
PHGDH		ENSSSCG00000006717	4:105641733-105673902	CR956647,CH242-38B5,4:105599155-105730207 (No clone quality info on bE38B5)
PHGDH		location ⇒	4:105607735-105607608	CR956647,CH242-38B5,4:105599155-105730207 (No clone quality info on bE38B5)
PHGDH		location ⇒	4:105645501-105645374	CR956647,CH242-38B5,4:105599155-105730207 (No clone quality info on bE38B5)
PHGDH		location ⇒	4:105661747-105661694	CR956647,CH242-38B5,4:105599155-105730207 (No clone quality info on bE38B5)
PHGDH		location ⇒	4:105673969-105673904	CR956647,CH242-38B5,4:105599155-105730207 (No clone quality info on bE38B5)
PHGR1		ENSSSCG00000016377	15:132067538-132175516
PHI-1		ENSSSCG00000013035	2:6249844-6252340		CU861533,CH242-1H13,2:6249822-6260732 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PHI-1		location ⇒	2:6249990-6250166		CU861533,CH242-1H13,2:6249822-6260732 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PHI-1		location ⇒	2:6251251-6251339		CU861533,CH242-1H13,2:6249822-6260732 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PHI-1		location ⇒	2:6251994-6252221		CU861533,CH242-1H13,2:6249822-6260732 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PHI-1		location ⇒	2:6252284-6252334		CU861533,CH242-1H13,2:6249822-6260732 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PHIP		ENSSSCG00000004473	1:92087411-92128370
PHKA1		ENSSSCG00000012411	X:57722614-57824659
PHKA2		ENSSSCG00000012157	X:14717147-14797947	CU856551,CH242-127M10,X:14708567-14940302 (Clone quality: bE127M10 on chr=X; Num_of_Contigs=1; )
PHKB		ENSSSCG00000002844	6:24995489-25173289
PHKB		location ⇒	13:1573270-1572803		CU633554,CH242-199A15,13:1536369-1697112 (Clone quality: bE199A15 on chr=13; Num_of_Contigs=1; )
PHKB		location ⇒	13:1573547-1573300		CU633554,CH242-199A15,13:1536369-1697112 (Clone quality: bE199A15 on chr=13; Num_of_Contigs=1; )
PHLDA1		ENSSSCG00000000521	5:39335891-39337054		CU915734,CH242-236O16,5:39334338-39397758 (Clone quality: bE236O16 on chr=5; Num_of_Contigs=8; )
PHLDA1		location ⇒	5:39334891-39335107		CU915734,CH242-236O16,5:39334338-39397758 (Clone quality: bE236O16 on chr=5; Num_of_Contigs=8; )
PHLDA1		location ⇒	5:39335158-39335416		CU915734,CH242-236O16,5:39334338-39397758 (Clone quality: bE236O16 on chr=5; Num_of_Contigs=8; )
PHLDA1		location ⇒	5:39335860-39335950		CU915734,CH242-236O16,5:39334338-39397758 (Clone quality: bE236O16 on chr=5; Num_of_Contigs=8; )
PHLPP1		ENSSSCG00000004896	1:165612119-165726583		CU459053,CH242-153F11,1:165604492-165731324 (Clone quality: bE153F11 on chr=1; Num_of_Contigs=3; )
PHLPP2		ENSSSCG00000002739	6:10407036-10419733		FP016102,CH242-364C5,6:10406224-10422225 (Clone quality: bE364C5 on chr=6; Num_of_Contigs=10; )
PHOSPHO1		location ⇒	8:38611074-38611153		CU928360,CH242-478I21,8:38602816-38613641 (Clone quality: bE478I21 on chr=8; Num_of_Contigs=9; )
PHOSPHO1		location ⇒	8:38839114-38839193		CU855637,CH242-199L13,8:38712595-38842897 (Clone quality: bE199L13 on chr=8; Num_of_Contigs=2; )
PHOSPHO2		ENSSSCG00000015936	15:71442427-71443152		CU466304,CH242-524C22,15:71432007-71447652 (Clone quality: bE524C22 on chr=15; Num_of_Contigs=14; )
PHOX2A		ENSSSCG00000014813	9:6326837-6330594		FP090889,CH242-166B16,9:6323247-6365214 (Clone quality: bE166B16 on chr=9; Num_of_Contigs=3; )
PHP14_PIG		ENSSSCG00000005826	1:294081272-294082732		FP236151,CH242-517G10,1:294077389-294085146 (Clone quality: bE517G10 on chr=1; Num_of_Contigs=14; )
PHP14_PIG		ENSSSCG00000005826	1:294081272-294082732		FP236151,CH242-517G10,1:294077389-294085146 (Clone quality: bE517G10 on chr=1; Num_of_Contigs=14; )
PHTF1		ENSSSCG00000006766	4:111167155-111233521	CU151865,CH242-280G12,4:111145249-111291177 (Clone quality: bE280G12 on chr=4; Num_of_Contigs=2; )
PHTF2		ENSSSCG00000015410	9:95294579-95354155
PHTNS_PIG		ENSSSCG00000001377	7:27168809-27177337	CU480634,CH242-391N4,7:27128408-27216112 (Clone quality: bE391N4 on chr=7; Num_of_Contigs=11; )
PHTNS_PIG		ENSSSCG00000001357	7:26849610-26857315		FP067362,CH242-312H17,7:26849596-26858884 (Clone quality: bE312H17 on chr=7; Num_of_Contigs=15; )
PHYHD1		ENSSSCG00000005665	1:283916974-283928916	CU076102,CH242-68C14,1:283855073-284074390 (Clone quality: bE68C14 on chr=1; Num_of_Contigs=6; )
PHYHIP		ENSSSCG00000010205	14:64946364-65035556
PI15		ENSSSCG00000006172	4:63239911-63263257		CU137733,CH242-64P8,4:63237062-63289866 (Clone quality: bE64P8 on chr=4; Num_of_Contigs=6; )
PI16		ENSSSCG00000001570	7:37233877-37243681	CT841548,CH242-123L1,7:37183904-37318303 (Clone quality: bE123L1 on chr=7; Num_of_Contigs=1; )
PI3		ENSSSCG00000011184	13:1379194-1385231		CU469211,CH242-358D17,13:1378387-1387263 (Clone quality: bE358D17 on chr=13; Num_of_Contigs=18; )
PI3		ENSSSCG00000007387	17:49326622-49328609		CU606931,CH242-44K10,17:49326487-49336362 (Clone quality: bE44K10 on chr=17; Num_of_Contigs=16; )
PI3		ENSSSCG00000003909	6:118327752-118488382
PI3		ENSSSCG00000003749	6:87719282-87897660
PI3		ENSSSCG00000003395	6:47123924-47158575		CU929791,CH242-402I11,6:47086277-47182066 (Clone quality: bE402I11 on chr=6; Num_of_Contigs=3; )
PI3		location ⇒	17:49328450-49328609		CU606931,CH242-44K10,17:49326487-49336362 (Clone quality: bE44K10 on chr=17; Num_of_Contigs=16; )
PI4K2A		ENSSSCG00000010525	14:113851114-113884210		CT867982,CH242-512F14,14:113843305-113912615 (Clone quality: bE512F14 on chr=14; Num_of_Contigs=2; )
PI4KB		ENSSSCG00000006626	4:101884622-101903917	CU179724,CH242-246E20,4:101737894-101911024 (Clone quality: bE246E20 on chr=4; Num_of_Contigs=5; )
PIAS1		ENSSSCG00000004958	1:173268973-173355949

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).