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)

EIF2C1		ENSSSCG00000003630	6:62366408-62394026
EIF2C2		ENSSSCG00000005935	4:1717726-1759572
EIF2C3		ENSSSCG00000003631	6:62425783-62451997
EIF2C4		ENSSSCG00000003629	6:62304808-62332390
EIF2S1		ENSSSCG00000002289	7:99493545-99516098		CT967298,CH242-176H11,7:99387011-99569801 (Clone quality: bE176H11 on chr=7; Num_of_Contigs=1; )
EIF2S3		location ⇒	5:80230797-80231905		CU655919,CH242-25G16,5:80142611-80241144 (Clone quality: bE25G16 on chr=5; Num_of_Contigs=2; )
EIF2S3		location ⇒	5:80231904-80232193		CU655919,CH242-25G16,5:80142611-80241144 (Clone quality: bE25G16 on chr=5; Num_of_Contigs=2; )
EIF3A		ENSSSCG00000010679	14:134958001-134996823		CU407047,CH242-224G2,14:134885099-135000492 (Clone quality: bE224G2 on chr=14; Num_of_Contigs=3; )
EIF3B		ENSSSCG00000007571	3:1855464-1869309		FP102725,CH242-525I24,3:1850706-1874345 (Clone quality: bE525I24 on chr=3; Note=un_improved;)
EIF3D		ENSSSCG00000000141	5:7628707-7645055		CU861543,CH242-228E12,5:7494498-7671966 (Clone quality: bE228E12 on chr=5; Num_of_Contigs=1; )
EIF3E		ENSSSCG00000006033	4:29305063-29347624
EIF3G		ENSSSCG00000013660	2:53390198-53394297
EIF3H		ENSSSCG00000006016	4:21766965-21865352
EIF3I		ENSSSCG00000003612	6:60841813-60848666
EIF3J		ENSSSCG00000004685	1:132789334-132794272		CU640392,CH242-218F20,1:132787084-132823427 (Clone quality: bE218F20 on chr=1; Num_of_Contigs=3; )
EIF3K		ENSSSCG00000002963	6:32691464-32698624
EIF3L		ENSSSCG00000000119	5:6521161-6541601		CU633527,CH242-104A9,5:6517032-6548029 (Clone quality: bE104A9 on chr=5; Num_of_Contigs=3; )
EIF3M		ENSSSCG00000009103	8:89561774-89563431		CU638686,CH242-511I21,8:89441314-89612797 (Clone quality: bE511I21 on chr=8; Num_of_Contigs=2; )
EIF3M		ENSSSCG00000009103	8:89561774-89563431		CU638686,CH242-511I21,8:89441314-89612797 (Clone quality: bE511I21 on chr=8; Num_of_Contigs=2; )
EIF3M		location ⇒	8:89561797-89562718		CU638686,CH242-511I21,8:89441314-89612797 (Clone quality: bE511I21 on chr=8; Num_of_Contigs=2; )
EIF3M		location ⇒	8:89562989-89563183		CU638686,CH242-511I21,8:89441314-89612797 (Clone quality: bE511I21 on chr=8; Num_of_Contigs=2; )
EIF4A1		ENSSSCG00000017957	12:50063792-50069544	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
EIF4A2		ENSSSCG00000011803	13:94180998-94187232		CU633961,CH242-82L2,13:94145951-94228460 (Clone quality: bE82L2 on chr=13; Num_of_Contigs=4; )
EIF4A3		ENSSSCG00000017155	12:1285295-1311016
EIF4E		ENSSSCG00000009187	8:104074224-104126823
EIF4E1B		ENSSSCG00000014052	2:70296838-70299905		CU915506,CH242-450C12,2:70276939-70304316 (Clone quality: bE450C12 on chr=2; Num_of_Contigs=12; )
EIF4E2		ENSSSCG00000016289	15:125427259-125513024
EIF4E3		ENSSSCG00000011516	13:45060311-45081827
EIF4EBP2		ENSSSCG00000010268	14:76447309-76494374
EIF4ENIF1		ENSSSCG00000010030	14:49041754-49088471
EIF4G2		ENSSSCG00000013405	2:45157794-45169303		CU606995,CH242-524E9,2:45156442-45179549 (Clone quality: bE524E9 on chr=2; Num_of_Contigs=8; )
EIF4G2		location ⇒	2:16488020-16488457		CU856190,CH242-18D3,2:16470772-16494322 (Clone quality: bE18D3 on chr=2; Num_of_Contigs=5; )
EIF4G2		location ⇒	2:16590637-16590200		CU914469,CH242-397I1,2:16574561-16607879 (Clone quality: bE397I1 on chr=2; Num_of_Contigs=11; )
EIF4G2		location ⇒	2:28276587-28275652	CU855928,CH242-91B8,2:28235789-28280025 (Clone quality: bE91B8 on chr=2; Num_of_Contigs=11; )
EIF4G2		location ⇒	2:45168645-45169477		CU606995,CH242-524E9,2:45156442-45179549 (Clone quality: bE524E9 on chr=2; Num_of_Contigs=8; )
EIF4G3		ENSSSCG00000003512	6:54352166-54751418
EIF5A		ENSSSCG00000017939	12:49790559-49795422
EIF5A		location ⇒	X:67792305-67792132	CU462992,CH242-250A21,X:67717463-67844690 (Clone quality: bE250A21 on chr=X; Num_of_Contigs=2; )
EIF5B		ENSSSCG00000008180	3:50519455-50701400
EIF5B		location ⇒	3:50519915-50519224		CU972417,CH242-139I23,3:50474227-50604116 (Clone quality: bE139I23 on chr=3; Num_of_Contigs=3; )
EIF5B		location ⇒	3:50558124-50558074		CU972417,CH242-139I23,3:50474227-50604116 (Clone quality: bE139I23 on chr=3; Num_of_Contigs=3; )
EIF5B		location ⇒	3:50560383-50559939		CU972417,CH242-139I23,3:50474227-50604116 (Clone quality: bE139I23 on chr=3; Num_of_Contigs=3; )
EIF5B		location ⇒	3:50672571-50672521		FP102935,CH242-65E14,3:50671980-50704035 (Clone quality: bE65E14 on chr=3; Num_of_Contigs=4; )
ELA1_PIG		ENSSSCG00000000222	5:15234969-15294617
ELA2		location ⇒	6:51234117-51234249		CU972459,CH242-507K2,6:51221604-51240678 (Clone quality: bE507K2 on chr=6; Num_of_Contigs=12; )
ELA2		location ⇒	6:51237620-51237757		CU972459,CH242-507K2,6:51221604-51240678 (Clone quality: bE507K2 on chr=6; Num_of_Contigs=12; )
ELA2		location ⇒	6:51240159-51240305		CU972459,CH242-507K2,6:51221604-51240678 (Clone quality: bE507K2 on chr=6; Num_of_Contigs=12; )
ELA2		location ⇒	6:51242171-51242325		CU972459,CH242-507K2,6:51240779-51258595 (Clone quality: bE507K2 on chr=6; Num_of_Contigs=12; )
ELA2A_PIG		ENSSSCG00000003459	6:51213481-51266606
ELA2A_PIG		ENSSSCG00000003459	6:51213481-51266606

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, 651-29

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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).