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)

JPH2		ENSSSCG00000007369	17:48427877-48432696		CU855736,CH242-249J14,17:48400298-48440601 (Clone quality: bE249J14 on chr=17; Num_of_Contigs=13; )
JPH3		ENSSSCG00000002653	6:574800-662729
JPH4		ENSSSCG00000002014	7:81860348-81866536
JRKL		ENSSSCG00000014973	9:29108207-29108767		CU656004,CH242-323N6,9:29107496-29110594 (Clone quality: bE323N6 on chr=9; Num_of_Contigs=15; )
JUN		ENSSSCG00000003829	6:108925879-108927099		CU695066,CH242-491K2,6:108920156-108949332 (Clone quality: bE491K2 on chr=6; Num_of_Contigs=9; )
JUN		ENSSSCG00000003361	6:43772690-43776772		FP102698,CH242-39I24,6:43772623-43778408 (Clone quality: bE39I24 on chr=6; Num_of_Contigs=5; )
JUN		ENSSSCG00000001429	7:27910968-27995163
JUN		ENSSSCG00000001050	7:9074488-9080825		CT955989,CH242-270H7,7:9062940-9157686 (Clone quality: bE270H7 on chr=7; Num_of_Contigs=2; )
JUN		location ⇒	6:108925879-108926466		CU695066,CH242-491K2,6:108920156-108949332 (Clone quality: bE491K2 on chr=6; Num_of_Contigs=9; )
JUN		location ⇒	6:108926531-108927089		CU695066,CH242-491K2,6:108920156-108949332 (Clone quality: bE491K2 on chr=6; Num_of_Contigs=9; )
JUNB		location ⇒	2:56058224-56059087		CU914382,CH242-275M24,2:56025074-56111468 (Clone quality: bE275M24 on chr=2; Num_of_Contigs=7; )
JUP		ENSSSCG00000017428	12:18670277-18699144		CU928665,CH242-332K23,12:18640749-18703424 (Clone quality: bE332K23 on chr=12; Num_of_Contigs=7; )
JUP		location ⇒	12:18671126-18670583		CU928665,CH242-332K23,12:18640749-18703424 (Clone quality: bE332K23 on chr=12; Num_of_Contigs=7; )
JUP		location ⇒	12:18679817-18679475		CU928665,CH242-332K23,12:18640749-18703424 (Clone quality: bE332K23 on chr=12; Num_of_Contigs=7; )
JUP		location ⇒	12:18685403-18685144		CU928665,CH242-332K23,12:18640749-18703424 (Clone quality: bE332K23 on chr=12; Num_of_Contigs=7; )
JUP		location ⇒	12:18886660-18886117		CU972362,CH242-2B19,12:18872559-18889314 (Clone quality: bE2B19 on chr=12; Num_of_Contigs=14; )

Go to records:
1-49, 50-16

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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).