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)

GM2A		location ⇒	7:35726128-35726330		CU571051,CH242-525J6,7:35686365-35735821 (Clone quality: bE525J6 on chr=7; Num_of_Contigs=14; )
GMCL1		ENSSSCG00000008335	3:66585291-66642915
GMDS		ENSSSCG00000000994	7:935558-1297300
GMFB		ENSSSCG00000005048	1:192431690-192437314
GMFG		ENSSSCG00000010705	14:138603427-138609784		FP236263,CH242-159G20,14:138601735-138609805 (Clone quality: bE159G20 on chr=14; Num_of_Contigs=8; )
GMIP		ENSSSCG00000013931	2:63377883-63386824		FP017144,CH242-263C22,2:63368725-63394740 (Clone quality: bE263C22 on chr=2; Num_of_Contigs=8; )
GMNN		ENSSSCG00000001095	7:20622259-20631596		CT737315,CH242-160B2,7:20607639-20790901 (Clone quality: bE160B2 on chr=7; Num_of_Contigs=1; )
GMPPB		ENSSSCG00000011389	13:27010151-27012594		CU914539,CH242-222N14,13:26945819-27078203 (Clone quality: bE222N14 on chr=13; Num_of_Contigs=2; )
GMPR		ENSSSCG00000001064	7:12682613-12725233
GMPR2		ENSSSCG00000001995	7:81401607-81410790		CU019590,CH242-406B17,7:81281809-81421007 (Clone quality: bE406B17 on chr=7; Num_of_Contigs=4; )
GMPS		ENSSSCG00000011725	13:76590230-76606368
GNA12		ENSSSCG00000007562	3:1285962-1339521
GNA13		ENSSSCG00000017263	12:10201158-10240160
GNA15		ENSSSCG00000013473	2:47715655-47736050
GNAI1		ENSSSCG00000015407	9:93680571-93712052		CU914252,CH242-232G21,9:93642980-93730828 (Clone quality: bE232G21 on chr=9; Num_of_Contigs=4; )
GNAI1		location ⇒	9:93680714-93680848		CU914252,CH242-232G21,9:93642980-93730828 (Clone quality: bE232G21 on chr=9; Num_of_Contigs=4; )
GNAI1		location ⇒	9:93690244-93690402		CU914252,CH242-232G21,9:93642980-93730828 (Clone quality: bE232G21 on chr=9; Num_of_Contigs=4; )
GNAI1		location ⇒	9:93711490-93712358		CU914252,CH242-232G21,9:93642980-93730828 (Clone quality: bE232G21 on chr=9; Num_of_Contigs=4; )
GNAI1		location ⇒	9:93713278-93713594		CU914252,CH242-232G21,9:93642980-93730828 (Clone quality: bE232G21 on chr=9; Num_of_Contigs=4; )
GNAI2		ENSSSCG00000011399	13:27373708-27394273
GNAI3		ENSSSCG00000006824	4:115048532-115095151
GNAO1		ENSSSCG00000002823	6:20353786-20382729
GNAQ		ENSSSCG00000005285	1:241341403-241643773
GNAQ		location ⇒	1:241341654-241341463		CU633598,CH242-512I14,1:241262468-241354608 (Clone quality: bE512I14 on chr=1; Num_of_Contigs=3; )
GNAQ		location ⇒	1:241347457-241347301		CU633598,CH242-512I14,1:241262468-241354608 (Clone quality: bE512I14 on chr=1; Num_of_Contigs=3; )
GNAQ		location ⇒	1:241428798-241428642		CU062637,CH242-116F17,1:241408060-241468730 (Clone quality: bE116F17 on chr=1; Num_of_Contigs=7; )
GNAQ		location ⇒	1:241530642-241530456		CU062637,CH242-116F17,1:241471152-241559027 (Clone quality: bE116F17 on chr=1; Num_of_Contigs=7; )
GNAS		ENSSSCG00000007520	17:61615817-61669884
GNAT2		ENSSSCG00000006823	4:115037780-115038933		CU633714,CH242-413N19,4:115036944-115062663 (Clone quality: bE413N19 on chr=4; Num_of_Contigs=4; )
GNAT3		ENSSSCG00000015406	9:93392138-93439209
GNAZ		ENSSSCG00000010046	14:50049081-50071848
GNB2		ENSSSCG00000007669	3:6850484-6855705		FP102710,CH242-46P3,3:6842494-6864616 (Clone quality: bE46P3 on chr=3; Num_of_Contigs=3; )
GNB2L1		location ⇒	5:82723383-82723503		CU442719,CH242-91J22,5:82711655-82750752 (Clone quality: bE91J22 on chr=5; Num_of_Contigs=5; )
GNB3		ENSSSCG00000000682	5:59881227-59887326		CU457492,CH242-370K21,5:59880009-59901315 (Clone quality: bE370K21 on chr=5; Num_of_Contigs=10; )
GNB5		ENSSSCG00000004622	1:124405686-124451142
GNE		ENSSSCG00000005342	1:248180249-248286918
GNE		location ⇒	1:29420796-29420700		CU302220,CH242-254N21,1:29415483-29526418 (Clone quality: bE254N21 on chr=1; Num_of_Contigs=7; )
GNE		location ⇒	1:90904277-90904382		FP102401,CH242-384I12,1:90900750-90909730 (Clone quality: bE384I12 on chr=1; Num_of_Contigs=14; )
GNE		location ⇒	1:94699651-94699598		CU928687,CH242-200O2,1:94697553-94702044 (Clone quality: bE200O2 on chr=1; Num_of_Contigs=12; )
GNE		location ⇒	1:94758790-94758843		FP236620,CH242-128M22,1:94757686-94798633 (Clone quality: bE128M22 on chr=1; Num_of_Contigs=5; )
GNG10		location ⇒	1:265294148-265294275		CU928768,CH242-206J15,1:265292870-265295859 (Clone quality: bE206J15 on chr=1; Num_of_Contigs=17; )
GNG10		location ⇒	1:265342989-265343116		FP016086,CH242-109H23,1:265339899-265346666 (Clone quality: bE109H23 on chr=1; Num_of_Contigs=3; )
GNG10		location ⇒	1:265344618-265344760		FP016086,CH242-109H23,1:265339899-265346666 (Clone quality: bE109H23 on chr=1; Num_of_Contigs=3; )
GNG11		ENSSSCG00000015324	9:69011692-69016488
GNG13		ENSSSCG00000008011	3:35822578-35822926		FP016225,CH242-86N4,3:35815598-35830527 (Clone quality: bE86N4 on chr=3; Num_of_Contigs=9; )
GNG2		ENSSSCG00000005028	1:189783161-189911249
GNG4		ENSSSCG00000010152	14:56921124-56921606		CT978605,CH242-112N20,14:56914986-56949604 (Clone quality: bE112N20 on chr=14; Num_of_Contigs=7; )
GNGT1		ENSSSCG00000015323	9:68990426-69000452		CU656013,CH242-365B18,9:68897446-69005342 (Clone quality: bE365B18 on chr=9; Num_of_Contigs=2; )
GNL3		ENSSSCG00000011449	13:29446555-29454495		CU469164,CH242-456I18,13:29421147-29460847 (Clone quality: bE456I18 on chr=13; Num_of_Contigs=15; )
GNL3L		ENSSSCG00000012336	X:46871234-46899221		CU694774,CH242-193E13,X:46832107-46989622 (Clone quality: bE193E13 on chr=X; Num_of_Contigs=2; )

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, 851-25

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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).