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)

RXRG		location ⇒	4:88932177-88932425		CU469086,CH242-497N7,4:88757283-88960914 (Clone quality: bE497N7 on chr=4; Num_of_Contigs=1; )
RXRG		location ⇒	4:88944869-88945051		CU469086,CH242-497N7,4:88757283-88960914 (Clone quality: bE497N7 on chr=4; Num_of_Contigs=1; )
RXRG		location ⇒	4:88963311-88963779	CU462963,CH242-397E14,4:88960915-89107378 (Clone quality: bE397E14 on chr=4; Num_of_Contigs=4; )
RYBP		ENSSSCG00000011517	13:45455083-45456428		CU633640,CH242-164P16,13:45386486-45505220 (Clone quality: bE164P16 on chr=13; Num_of_Contigs=4; )
RYK		ENSSSCG00000011642	13:61704268-61778619
RYR1		ENSSSCG00000002961	6:32548456-32666600
RYR1		ENSSSCG00000002964	6:32706687-32735141
RYR1		location ⇒	6:32581240-32581638		FP102670,CH242-297E4,6:32558505-32592202 (Clone quality: bE297E4 on chr=6; Num_of_Contigs=4; )
RYR1		location ⇒	6:32589105-32589725		FP102670,CH242-297E4,6:32558505-32592202 (Clone quality: bE297E4 on chr=6; Num_of_Contigs=4; )
RYR1		location ⇒	6:32650883-32651229		FP102670,CH242-297E4,6:32648546-32654495 (Clone quality: bE297E4 on chr=6; Num_of_Contigs=4; )
RYR1		location ⇒	6:32846589-32846935		FP245504,CH242-1N8,6:32834786-32851510 (Clone quality: bE1N8 on chr=6; Num_of_Contigs=9; )
RYR2		ENSSSCG00000010142	14:54786053-55331185
RYR2		location ⇒	14:54799130-54799064		CT737377,CH242-194D19,14:54686568-54870699 (Clone quality: bE194D19 on chr=14; Num_of_Contigs=1; )
RYR2		location ⇒	14:54826319-54826235		CT737377,CH242-194D19,14:54686568-54870699 (Clone quality: bE194D19 on chr=14; Num_of_Contigs=1; )
RYR2		location ⇒	14:54885619-54885567		CU407083,CH242-459F22,14:54870700-54909598 (Clone quality: bE459F22 on chr=14; Num_of_Contigs=4; )
RYR2		location ⇒	14:54913393-54913304		CU407083,CH242-459F22,14:54909699-54985999 (Clone quality: bE459F22 on chr=14; 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, 851-900, 901-950, 951-1000, 1001-16

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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).