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)

5S_rRNA		ENSSSCG00000018743	1:240245417-240245528		CU302442,CH242-506H7,1:240042666-240259276 (Clone quality: bE506H7 on chr=1; Num_of_Contigs=5; )
5S_rRNA		ENSSSCG00000019789	5:1997682-1997804		CU694876,CH242-297L18,5:1928860-2011292 (Clone quality: bE297L18 on chr=5; Num_of_Contigs=2; )
5S_rRNA		ENSSSCG00000018736	11:64252973-64253083		CU986273,CH242-12L1,11:64235553-64285794 (Clone quality: bE12L1 on chr=11; Num_of_Contigs=7; )
5S_rRNA		ENSSSCG00000018733	17:10267881-10267987		CU896619,CH242-280F16,17:10265698-10269220 (Clone quality: bE280F16 on chr=17; Num_of_Contigs=13; )
5S_rRNA		ENSSSCG00000020007	4:3118510-3118626		CU550666,CH242-232I20,4:3099747-3243509 (Clone quality: bE232I20 on chr=4; Num_of_Contigs=3; )
5S_rRNA		ENSSSCG00000020022	3:77337010-77337114		CU928032,CH242-392H11,3:77315559-77375613 (Clone quality: bE392H11 on chr=3; Num_of_Contigs=3; )
5S_rRNA		ENSSSCG00000018766	2:37617911-37618029		CU929490,CH242-88D19,2:37606177-37624664 (Clone quality: bE88D19 on chr=2; Num_of_Contigs=15; )
5S_rRNA		ENSSSCG00000018110	7:74313816-74313934		CU467719,CH242-285C4,7:74276201-74335916 (Clone quality: bE285C4 on chr=17; Num_of_Contigs=8; )
5S_rRNA		ENSSSCG00000019640	10:30349301-30349408		CU928770,CH242-471A17,10:30348035-30359133 (Clone quality: bE471A17 on chr=10; Num_of_Contigs=8; )
5_8S_rRNA		ENSSSCG00000019373	13:56634357-56634497		CU914645,CH242-235C15,13:56620538-56642743 (Clone quality: bE235C15 on chr=13; Num_of_Contigs=12; )
5_8S_rRNA		ENSSSCG00000019802	6:254147-254293		FP102614,CH242-198I21,6:249820-254397 (Clone quality: bE198I21 on chr=6; Num_of_Contigs=22; )
5_8S_rRNA		ENSSSCG00000018717	8:41395011-41395144		FP017138,CH242-231O23,8:41352427-41458391 (Clone quality: bE231O23 on chr=8; Num_of_Contigs=2; )

Go to records:
1-49, 50-100, 101-12

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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).