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)

EXOG		ENSSSCG00000011258	13:19209090-19237771
EXOSC1		ENSSSCG00000010518	14:113678993-113685601		CU407093,CH242-523G22,14:113665116-113843304 (Clone quality: bE523G22 on chr=14; Num_of_Contigs=4; )
EXOSC1		location ⇒	14:113679424-113679278		CU407093,CH242-523G22,14:113665116-113843304 (Clone quality: bE523G22 on chr=14; Num_of_Contigs=4; )
EXOSC1		location ⇒	14:113680094-113680015		CU407093,CH242-523G22,14:113665116-113843304 (Clone quality: bE523G22 on chr=14; Num_of_Contigs=4; )
EXOSC1		location ⇒	14:113680287-113680236		CU407093,CH242-523G22,14:113665116-113843304 (Clone quality: bE523G22 on chr=14; Num_of_Contigs=4; )
EXOSC1		location ⇒	14:113684256-113684199		CU407093,CH242-523G22,14:113665116-113843304 (Clone quality: bE523G22 on chr=14; Num_of_Contigs=4; )
EXOSC10		ENSSSCG00000003412	6:48039587-48050382
EXOSC2		ENSSSCG00000005704	1:285930503-285939644		CU914779,CH242-229M12,1:285907442-285977510 (Clone quality: bE229M12 on chr=1; Num_of_Contigs=6; )
EXOSC3		ENSSSCG00000005355	1:249939923-249944720		CU062410,CH242-117J8,1:249873492-249994741 (Clone quality: bE117J8 on chr=1; Num_of_Contigs=2; )
EXOSC4		ENSSSCG00000005925	4:829051-830944		FP085471,CH242-106F14,4:828048-836749 (Clone quality: bE106F14 on chr=4; Num_of_Contigs=12; )
EXOSC5		ENSSSCG00000003015	6:34070051-34072766		FP236582,CH242-238L13,6:34063629-34073800 (Clone quality: bE238L13 on chr=6; Num_of_Contigs=11; )
EXOSC7		ENSSSCG00000011300	13:23566444-23595944
EXOSC8		ENSSSCG00000009358	11:12214101-12412285
EXOSC9		ENSSSCG00000009096	8:87857394-87867317
EXOSC9		location ⇒	8:87861995-87861875		CU861488,CH242-360D22,8:87857361-87862416 (Clone quality: bE360D22 on chr=8; Num_of_Contigs=23; )
EXOSC9		location ⇒	8:87864482-87864343		CU861488,CH242-360D22,8:87862517-87872918 (Clone quality: bE360D22 on chr=8; Num_of_Contigs=23; )
EXOSC9		location ⇒	8:87865468-87865362		CU861488,CH242-360D22,8:87862517-87872918 (Clone quality: bE360D22 on chr=8; Num_of_Contigs=23; )
EXOSC9		location ⇒	8:87867295-87867151		CU861488,CH242-360D22,8:87862517-87872918 (Clone quality: bE360D22 on chr=8; Num_of_Contigs=23; )
EXPH5		ENSSSCG00000015010	9:36146608-36177562
EXT1		ENSSSCG00000006009	4:20453603-20645387
EXT2		ENSSSCG00000013281	2:16664672-16805176
EXTL2		ENSSSCG00000006861	4:122270469-122290829
EXTL3		ENSSSCG00000009680	14:12507675-12556035
EYA1		ENSSSCG00000006189	4:66344104-66344787		CU137699,CH242-75E2,4:66334222-66366831 (Clone quality: bE75E2 on chr=4; Num_of_Contigs=8; )
EYA2		ENSSSCG00000007453	17:51358432-51375109
EYA3		ENSSSCG00000003580	6:58467067-58511135		CU928393,CH242-274K17,6:58465404-58557237 (Clone quality: bE274K17 on chr=6; Num_of_Contigs=5; )
EYA4		ENSSSCG00000004176	1:31742310-31816364
EYS		ENSSSCG00000004266	1:47303611-47335932		CU928313,CH242-267E23,1:47302416-47347966 (Clone quality: bE267E23 on chr=1; Num_of_Contigs=5; )
EZH1		ENSSSCG00000017382	12:17584568-17615820

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).