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)

Grb2		location ⇒	12:4190088-4190349	CU928991,CH242-32C19,12:4079494-4242296 (Clone quality: bE32C19 on chr=12; Num_of_Contigs=2; )
GRB7		ENSSSCG00000017495	12:20540396-20548980		CU640399,CH242-251F23,12:20530232-20578478 (Clone quality: bE251F23 on chr=12; Num_of_Contigs=5; )
GREB1L		ENSSSCG00000003699	6:72454526-72708612
GREM1		ENSSSCG00000004808	1:144236968-144237522		CU467670,CH242-141P19,1:144228616-144242116 (Clone quality: bE141P19 on chr=1; Num_of_Contigs=16; )
GREM1		location ⇒	1:144239137-144239953		CU467670,CH242-141P19,1:144228616-144242116 (Clone quality: bE141P19 on chr=1; Num_of_Contigs=16; )
GRHL2		ENSSSCG00000006060	4:35710395-35858443
GRHL3		ENSSSCG00000003539	6:56366772-56390456
GRHPR		ENSSSCG00000005349	1:249563815-249574652
GRIA3		ENSSSCG00000012638	X:98677656-98877329
GRID1		ENSSSCG00000010352	14:89989247-90223283
GRID2		ENSSSCG00000009197	8:107925517-107928843		CU464003,CH242-220H23,8:107843572-107959060 (Clone quality: bE220H23 on chr=8; Num_of_Contigs=3; )
GRIK2		ENSSSCG00000003038	6:34491612-34517905
GRIK2		ENSSSCG00000004361	1:71654466-72084710
GRIK3		ENSSSCG00000003640	6:62951269-63077626
GRIK4		ENSSSCG00000015131	9:46599491-46746737
GRIK5		ENSSSCG00000003038	6:34491612-34517905
GRIN2B		ENSSSCG00000000614	5:55953038-56011319
GRIN2C		ENSSSCG00000017229	12:4619001-4623731		CU640434,CH242-126A11,12:4617992-4631049 (Clone quality: bE126A11 on chr=12; Num_of_Contigs=11; )
GRIN2D		ENSSSCG00000003133	6:37438100-37478314
GRIN3A		ENSSSCG00000005400	1:254877299-255092934
GRINL1A		ENSSSCG00000004598	1:118360812-118454964
GRIP1		ENSSSCG00000000478	5:30644817-30965514
GRIP2		ENSSSCG00000011599	13:58123049-58204955
GRK1		ENSSSCG00000009562	11:79022191-79067334
GRK4		ENSSSCG00000008694	8:1040237-1115691
GRK5		ENSSSCG00000010683	14:135097278-135330360
GRK7		ENSSSCG00000011675	13:67365647-67416131		CU914638,CH242-182J3,13:67262584-67431184 (Clone quality: bE182J3 on chr=13; Num_of_Contigs=1; )
GRLF1		ENSSSCG00000003107	6:36494878-36577230
GRLF1		location ⇒	6:36496298-36495568		FP102520,CH242-105K10,6:36483037-36498830 (Clone quality: bE105K10 on chr=6; Num_of_Contigs=11; )
GRM1		ENSSSCG00000004119	1:20324753-20475688
GRM2		ENSSSCG00000011423	13:28695708-28699491		CU928637,CH242-39L16,13:28695022-28704722 (Clone quality: bE39L16 on chr=13; Num_of_Contigs=10; )
GRM3		ENSSSCG00000015395	9:87410355-87515290
GRM3		location ⇒	9:87437156-87436771		CU570934,CH242-240C4,9:87343073-87456806 (Clone quality: bE240C4 on chr=9; Num_of_Contigs=4; )
GRM4		ENSSSCG00000001523	7:34587089-34675558
GRM5		ENSSSCG00000014925	9:22006564-22040694
GRM5		location ⇒	9:21993777-21993318		FP236398,CH242-323O14,9:21987420-21997942 (Clone quality: bE323O14 on chr=9; Num_of_Contigs=11; )
GRM5		location ⇒	9:21996935-21995385		FP236398,CH242-323O14,9:21987420-21997942 (Clone quality: bE323O14 on chr=9; Num_of_Contigs=11; )
GRM5		location ⇒	9:22646907-22646980		FP090912,CH242-516I19,9:22644997-22695116 (Clone quality: bE516I19 on chr=9; Num_of_Contigs=4; )
GRM5		location ⇒	9:22662045-22662754		FP090912,CH242-516I19,9:22644997-22695116 (Clone quality: bE516I19 on chr=9; Num_of_Contigs=4; )
GRM6		ENSSSCG00000014027	2:68873329-68876165		CU928965,CH242-128O9,2:68872291-68877348 (Clone quality: bE128O9 on chr=2; Num_of_Contigs=28; )
GRN		ENSSSCG00000017355	12:16808514-16812389		CU468984,CH242-216D12,12:16806181-16813556 (Clone quality: bE216D12 on chr=12; Num_of_Contigs=22; )
GRN		location ⇒	12:16810759-16811007		CU468984,CH242-216D12,12:16806181-16813556 (Clone quality: bE216D12 on chr=12; Num_of_Contigs=22; )
GRN		location ⇒	12:16810759-16811007		CU468984,CH242-216D12,12:16806181-16813556 (Clone quality: bE216D12 on chr=12; Num_of_Contigs=22; )
GRN		location ⇒	12:16811917-16812324		CU468984,CH242-216D12,12:16806181-16813556 (Clone quality: bE216D12 on chr=12; Num_of_Contigs=22; )
GRN		location ⇒	12:16811917-16812324		CU468984,CH242-216D12,12:16806181-16813556 (Clone quality: bE216D12 on chr=12; Num_of_Contigs=22; )
GRPEL2		ENSSSCG00000014432	2:135962637-135969108		CU694929,CH242-55J13,2:135930184-135975329 (Clone quality: bE55J13 on chr=2; Num_of_Contigs=3; )
GRPR		ENSSSCG00000012144	X:12243450-12279446		CU656021,CH242-386L22,X:12178827-12285351 (Clone quality: bE386L22 on chr=X; Num_of_Contigs=4; )
GRSF1		ENSSSCG00000008940	8:57412878-57428051		CU638721,CH242-211A6,8:57396895-57483105 (Clone quality: bE211A6 on chr=8; Num_of_Contigs=2; )
GRTP1		ENSSSCG00000009554	11:78805019-78809462
GRWD1		ENSSSCG00000003134	6:37477615-37483555		FP102301,CH242-20J11,6:37475901-37499164 (Clone quality: bE20J11 on chr=6; Note=In Finishing;)

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).