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)

AGT		ENSSSCG00000010184	14:62045553-62049221
AGT		ENSSSCG00000016402	15:134535557-134540514		FP236135,CH242-170N3,15:134508778-134541103 (Clone quality: bE170N3 on chr=15; Num_of_Contigs=5; )
AGT		ENSSSCG00000016829	16:18114319-18154625
AGTPBP1		ENSSSCG00000010957	10:28377205-28489262
AGTPBP1		location ⇒	10:28338965-28339017		CU915641,CH242-181A3,10:28312276-28372822 (Clone quality: bE181A3 on chr=10; Num_of_Contigs=4; )
AGTPBP1		location ⇒	10:28365905-28365970		CU915641,CH242-181A3,10:28312276-28372822 (Clone quality: bE181A3 on chr=10; Num_of_Contigs=4; )
AGTPBP1		location ⇒	10:28427297-28428015		CU915641,CH242-181A3,10:28372923-28434888 (Clone quality: bE181A3 on chr=10; Num_of_Contigs=4; )
AGTPBP1		location ⇒	10:28488871-28489293		CU640444,CH242-184P22,10:28482269-28501754 (Clone quality: bE184P22 on chr=10; Num_of_Contigs=5; )
AGTR1		ENSSSCG00000011695	13:72514649-72515728		CU915416,CH242-389L23,13:72468376-72518914 (Clone quality: bE389L23 on chr=13; Num_of_Contigs=4; )
AGTR1		location ⇒	13:72515624-72516331		CU915416,CH242-389L23,13:72468376-72518914 (Clone quality: bE389L23 on chr=13; Num_of_Contigs=4; )
AGTR2		ENSSSCG00000012600	X:93114188-93115276	FP085380,CH242-287G14,X:93011417-93184761 (Clone quality: bE287G14 on chr=X; Num_of_Contigs=1; )
AGXT		ENSSSCG00000016402	15:134535557-134540514		FP236135,CH242-170N3,15:134508778-134541103 (Clone quality: bE170N3 on chr=15; Num_of_Contigs=5; )
AGXT2		ENSSSCG00000016829	16:18114319-18154625
AGXT2L1		ENSSSCG00000009144	8:97368295-97387605
AGXT2L2		ENSSSCG00000014030	2:69320573-69329150		CU468334,CH242-242B23,2:69313971-69357520 (Clone quality: bE242B23 on chr=2; Num_of_Contigs=5; )
AHCTF1		ENSSSCG00000010863	10:14888936-14924297
AHCY		ENSSSCG00000000593	5:52541556-52542757		CU457493,CH242-37H2,5:52522501-52544070 (Clone quality: bE37H2 on chr=5; Num_of_Contigs=1; )
AHCYL2		ENSSSCG00000016568	18:17421740-17599356
AHDC1		ENSSSCG00000003579	6:58451122-58455933		CU469239,CH242-509G5,6:58448416-58460403 (Clone quality: bE509G5 on chr=6; Num_of_Contigs=22; )
AHI1		ENSSSCG00000004166	1:29985859-30146915
AHNAK		ENSSSCG00000013059	2:7454006-7454908		FP102338,CH242-94E13,2:7443569-7455251 (Clone quality: bE94E13 on chr=2; Num_of_Contigs=10; )
AHNAK2		ENSSSCG00000002549	7:132968312-133137600
AHR		ENSSSCG00000015364	9:81024216-81081616
AHR		location ⇒	9:81058298-81058443		FP102833,CH242-2P23,9:81053070-81083399 (Clone quality: bE2P23 on chr=9; Num_of_Contigs=6; )
AHR		location ⇒	9:81072848-81072953		FP102833,CH242-2P23,9:81053070-81083399 (Clone quality: bE2P23 on chr=9; Num_of_Contigs=6; )
AHR		location ⇒	9:81077060-81077186		FP102833,CH242-2P23,9:81053070-81083399 (Clone quality: bE2P23 on chr=9; Num_of_Contigs=6; )
AHR		location ⇒	9:81077855-81077984		FP102833,CH242-2P23,9:81053070-81083399 (Clone quality: bE2P23 on chr=9; Num_of_Contigs=6; )
AHSA1		ENSSSCG00000002406	7:108752247-108760414
AHSA2		ENSSSCG00000008383	3:74205292-74211578
AHSG		location ⇒	13:57157681-57157846		CU656036,CH242-92G17,13:57156255-57159743 (Clone quality: bE92G17 on chr=13; Num_of_Contigs=31; )
AHSG		location ⇒	13:94029206-94029409		CU466376,CH242-17J7,13:94023487-94030485 (Clone quality: bE17J7 on chr=13; Num_of_Contigs=6; )
AHSG		location ⇒	13:94032616-94032781		CU633961,CH242-82L2,13:94030486-94043444 (Clone quality: bE82L2 on chr=13; Num_of_Contigs=4; )
AHSG		location ⇒	13:94035484-94036191		CU633961,CH242-82L2,13:94030486-94043444 (Clone quality: bE82L2 on chr=13; Num_of_Contigs=4; )
AIBP_PIG		ENSSSCG00000006480	4:97329396-97332301		CU633176,CH242-238D11,4:97318135-97342444 (Clone quality: bE238D11 on chr=4; Num_of_Contigs=11; )
AICDA		ENSSSCG00000000667	5:59527012-59535739		CU929253,CH242-247J12,5:59524343-59540519 (Clone quality: bE247J12 on chr=5; Num_of_Contigs=6; )
AICDA		location ⇒	5:59532901-59533052		CU929253,CH242-247J12,5:59524343-59540519 (Clone quality: bE247J12 on chr=5; Num_of_Contigs=6; )
AICDA		location ⇒	5:59534235-59534507		CU929253,CH242-247J12,5:59524343-59540519 (Clone quality: bE247J12 on chr=5; Num_of_Contigs=6; )
AICDA		location ⇒	5:59535082-59535200		CU929253,CH242-247J12,5:59524343-59540519 (Clone quality: bE247J12 on chr=5; Num_of_Contigs=6; )
AICDA		location ⇒	5:59535572-59535728		CU929253,CH242-247J12,5:59524343-59540519 (Clone quality: bE247J12 on chr=5; Num_of_Contigs=6; )
AIDA		ENSSSCG00000010835	10:11560935-11595952
AIF1		ENSSSCG00000001408	7:27687983-27690564	CU467793,CH242-60C3,7:27581747-27762222 (Clone quality: bE60C3 on chr=7; Num_of_Contigs=1; )
AIF1		location ⇒	7:21591-21676		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
AIF1		location ⇒	7:24940-24820		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
AIF1		location ⇒	7:30847-30912		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
AIF1		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
AIF1L		ENSSSCG00000005709	1:286207595-286229412
AIFM1		ENSSSCG00000012657	X:104844971-104876692		CU929735,CH242-243F6,X:104772754-104881607 (Clone quality: bE243F6 on chr=X; Num_of_Contigs=3; )
AIFM2		location ⇒	14:75998296-75998134		CU468481,CH242-304F15,14:75947571-76010684 (Clone quality: bE304F15 on chr=14; Num_of_Contigs=5; )
AIFM2		location ⇒	14:76000077-75999923		CU468481,CH242-304F15,14:75947571-76010684 (Clone quality: bE304F15 on chr=14; Num_of_Contigs=5; )
AIFM2		location ⇒	14:76184670-76184824		CU633580,CH242-307B6,14:76183309-76195363 (Clone quality: bE307B6 on chr=14; Num_of_Contigs=16; )

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, 1751-32

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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).