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)

GYLTL1B		ENSSSCG00000013266	2:14845158-14850179		FP101987,CH242-521A18,2:14831953-14928280 (Clone quality: bE521A18 on chr=2; Num_of_Contigs=9; )
GYPA		location ⇒	8:72537305-72537391		CU856644,CH242-197H16,8:72428832-72562979 (Clone quality: bE197H16 on chr=8; Num_of_Contigs=2; )
GYPB		location ⇒	8:72508182-72508284		CU856644,CH242-197H16,8:72428832-72562979 (Clone quality: bE197H16 on chr=8; Num_of_Contigs=2; )
GYPB		location ⇒	8:72511967-72512052		CU856644,CH242-197H16,8:72428832-72562979 (Clone quality: bE197H16 on chr=8; Num_of_Contigs=2; )
GYPB		location ⇒	8:72526101-72526458		CU856644,CH242-197H16,8:72428832-72562979 (Clone quality: bE197H16 on chr=8; Num_of_Contigs=2; )
GYPC		ENSSSCG00000015724	15:24313500-24313697		CU928614,CH242-504F3,15:24289485-24314494 (Clone quality: bE504F3 on chr=15; Num_of_Contigs=13; )
GYPC		location ⇒	15:24315052-24315229		CU928614,CH242-504F3,15:24314595-24325079 (Clone quality: bE504F3 on chr=15; Num_of_Contigs=13; )
GYS1		ENSSSCG00000003154	6:37768073-37822241
GYS2		ENSSSCG00000000577	5:49866777-49914407
GZMA		ENSSSCG00000016903	16:31705031-31711729
GZMA		location ⇒	16:31706615-31706559		CU570832,CH242-249C24,16:31668453-31708697 (Clone quality: bE249C24 on chr=16; Num_of_Contigs=4; )
GZMA		location ⇒	16:31708557-31708416		CU570832,CH242-249C24,16:31668453-31708697 (Clone quality: bE249C24 on chr=16; Num_of_Contigs=4; )
GZMA		location ⇒	16:31709287-31709015		CU856640,CH242-178B1,16:31708698-31727373 (Clone quality: bE178B1 on chr=16; Num_of_Contigs=10; )
GZMA		location ⇒	16:31711729-31711570		CU856640,CH242-178B1,16:31708698-31727373 (Clone quality: bE178B1 on chr=16; Num_of_Contigs=10; )
GZMB		ENSSSCG00000001978	7:81022391-81025806
GZMB		location ⇒	7:81023466-81023616		CU457450,CH242-202K1,7:81023102-81026427 (Clone quality: bE202K1 on chr=7; Num_of_Contigs=16; )
GZMB		location ⇒	7:81024419-81024676		CU457450,CH242-202K1,7:81023102-81026427 (Clone quality: bE202K1 on chr=7; Num_of_Contigs=16; )
GZMB		location ⇒	7:81142627-81142569		CT997804,CH242-280B15,7:81125347-81169003 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
GZMB		location ⇒	7:81165956-81165901		CT997804,CH242-280B15,7:81125347-81169003 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
GZMH		ENSSSCG00000001981	7:81163872-81167691		CT997804,CH242-280B15,7:81125347-81169003 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
GZMH		location ⇒	7:81023457-81023520		CU457450,CH242-202K1,7:81023102-81026427 (Clone quality: bE202K1 on chr=7; Num_of_Contigs=16; )
GZMH		location ⇒	7:81074225-81074127		CT997804,CH242-280B15,7:81065282-81125246 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
GZMH		location ⇒	7:81164144-81163882		CT997804,CH242-280B15,7:81125347-81169003 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
GZMH		location ⇒	7:81164947-81164683		CT997804,CH242-280B15,7:81125347-81169003 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
GZMK		ENSSSCG00000016901	16:31638470-31647268		CU570832,CH242-249C24,16:31513287-31668352 (Clone quality: bE249C24 on chr=16; Num_of_Contigs=4; )

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).