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)

GSTZ1		ENSSSCG00000002396	7:108338920-108344010		CU468241,CH242-271B5,7:108333979-108345671 (Clone quality: bE271B5 on chr=7; Num_of_Contigs=18; )
GSTZ1		ENSSSCG00000002396	7:108338920-108344010		CU468241,CH242-271B5,7:108333979-108345671 (Clone quality: bE271B5 on chr=7; Num_of_Contigs=18; )
GSX1		ENSSSCG00000009313	11:4659904-4661140		FP236498,CH242-53H4,11:4655015-4661202 (Clone quality: bE53H4 on chr=11; Num_of_Contigs=22; )
GSX2		ENSSSCG00000008840	8:35155365-35157020		FP015892,CH242-190G10,8:35153714-35170140 (Clone quality: bE190G10 on chr=8; Num_of_Contigs=10; )
GTDC1		ENSSSCG00000015670	15:4309981-4502153
GTF2A1		ENSSSCG00000002411	7:111401033-111428101
GTF2A1		location ⇒	7:111401177-111400894		CU407292,CH242-513J1,7:111381878-111414704 (Clone quality: bE513J1 on chr=7; Num_of_Contigs=13; )
GTF2A1		location ⇒	7:111417376-111417145		CU407292,CH242-513J1,7:111414805-111418336 (Clone quality: bE513J1 on chr=7; Num_of_Contigs=13; )
GTF2A1		location ⇒	7:111426050-111425989		CU407292,CH242-513J1,7:111418437-111430499 (Clone quality: bE513J1 on chr=7; Num_of_Contigs=13; )
GTF2A1		location ⇒	7:111428101-111428047		CU407292,CH242-513J1,7:111418437-111430499 (Clone quality: bE513J1 on chr=7; Num_of_Contigs=13; )
GTF2B		ENSSSCG00000006926	4:132178270-132215083
GTF2E2		ENSSSCG00000015845	15:51375357-51458100
GTF2F1		ENSSSCG00000013539	2:49822106-49832755
GTF2H1		ENSSSCG00000013367	2:38101584-38143454
GTF2H3		ENSSSCG00000009769	14:29448417-29466439		CU468658,CH242-245F7,14:29355652-29557150 (Clone quality: bE245F7 on chr=14; Num_of_Contigs=1; )
GTF2H4		ENSSSCG00000001383	7:27355798-27361582	CT971577,CH242-239H1,7:27216113-27394697 (Clone quality: bE239H1 on chr=7; Num_of_Contigs=1; )
GTF2H5		ENSSSCG00000016126	15:102127271-102127480		CU468044,CH242-112E22,15:102088282-102133910 (Clone quality: bE112E22 on chr=15; Num_of_Contigs=9; )
GTF2I		ENSSSCG00000007721	3:9762710-9867848
GTF2IRD1		ENSSSCG00000007720	3:9618826-9658774		CU914415,CH242-263E18,3:9616956-9667073 (Clone quality: bE263E18 on chr=3; Num_of_Contigs=9; )
GTF3A		ENSSSCG00000009305	11:3974744-3981791
GTF3C1		ENSSSCG00000007815	3:17516473-17586874
GTF3C3		ENSSSCG00000016070	15:94337950-94365298
GTF3C4		ENSSSCG00000005731	1:288137121-288156886		CU326339,CH242-262P16,1:288133827-288172670 (Clone quality: bE262P16 on chr=1; Num_of_Contigs=6; )
GTF3C5		ENSSSCG00000005739	1:288397279-288401455		FP102076,CH242-185K22,1:288396717-288402437 (Clone quality: bE185K22 on chr=1; Num_of_Contigs=26; )
GTF3C6		ENSSSCG00000004393	1:79165524-79177699		CU972415,CH242-118C2,1:79152437-79208678 (Clone quality: bE118C2 on chr=1; Num_of_Contigs=10; )
GTPBP1		ENSSSCG00000000095	5:5498821-5521672
GTPBP1		location ⇒	5:5510880-5510533		CU655907,CH242-193M24,5:5459730-5514125 (Clone quality: bE193M24 on chr=5; Num_of_Contigs=6; )
GTPBP1		location ⇒	5:5511635-5511451		CU655907,CH242-193M24,5:5459730-5514125 (Clone quality: bE193M24 on chr=5; Num_of_Contigs=6; )
GTPBP1		location ⇒	5:5521672-5521459		CU655907,CH242-193M24,5:5514226-5558669 (Clone quality: bE193M24 on chr=5; Num_of_Contigs=6; )
GTPBP1		location ⇒	5:5612078-5611731		CU896553,CH242-300P14,5:5606461-5618279 (Clone quality: bE300P14 on chr=5; Num_of_Contigs=16; )
GTPBP10		ENSSSCG00000015305	9:65960717-65979467
GTPBP8		ENSSSCG00000011924	13:109526600-109543811
GTSE1		ENSSSCG00000000002	5:66866-81549
GTSF1		ENSSSCG00000000294	5:18197722-18264111
GUCA1A		ENSSSCG00000001636	7:42924669-42931696
GUCA1B		ENSSSCG00000001637	7:42931098-42937764
GUCA2A		ENSSSCG00000003969	6:121260864-121262804		CU929946,CH242-505M22,6:121250890-121266927 (Clone quality: bE505M22 on chr=6; Num_of_Contigs=10; )
GUCA2B		ENSSSCG00000003970	6:121267055-121269231		CU929946,CH242-505M22,6:121267028-121269270 (Clone quality: bE505M22 on chr=6; Num_of_Contigs=10; )
GUCY1A3		ENSSSCG00000008866	8:38559282-38628048
GUCY1B3		ENSSSCG00000008870	8:38850639-38869167		CU855637,CH242-199L13,8:38842998-38869504 (Clone quality: bE199L13 on chr=8; Num_of_Contigs=2; )
GUCY2C		ENSSSCG00000000613	5:55178393-55188552		CU914634,CH242-15H1,5:55171138-55193193 (Clone quality: bE15H1 on chr=5; Num_of_Contigs=6; )
GUCY2D		ENSSSCG00000017977	12:50457091-50470308
GUCY2F		ENSSSCG00000012580	X:88643002-88748499
GUF1		ENSSSCG00000008807	8:30024610-30047352		FP104561,CH242-178J17,8:30015588-30056007 (Clone quality: bE178J17 on chr=8; Num_of_Contigs=3; )
GULP1		ENSSSCG00000016033	15:87607704-87660703
GVIN1		location ⇒	9:2398614-2397293		FP085603,CH242-271A15,9:2396944-2419148 (Clone quality: bE271A15 on chr=9; Num_of_Contigs=10; )
GVIN1		location ⇒	9:2511129-2509798		FP085603,CH242-271A15,9:2493238-2521528 (Clone quality: bE271A15 on chr=9; Num_of_Contigs=10; )
GYG1		ENSSSCG00000011698	13:72593975-72597627		CU915669,CH242-311K1,13:72584413-72615336 (Clone quality: bE311K1 on chr=13; Num_of_Contigs=12; )
GYG1		location ⇒	13:72593986-72594185		CU915669,CH242-311K1,13:72584413-72615336 (Clone quality: bE311K1 on chr=13; Num_of_Contigs=12; )
GYG1		location ⇒	13:72596728-72596780		CU915669,CH242-311K1,13:72584413-72615336 (Clone quality: bE311K1 on chr=13; Num_of_Contigs=12; )

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

Report problems to zhu

iastate.edu

$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).