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)

FY		ENSSSCG00000003198	6:38537799-38543333		CU694867,CH242-269H19,6:38488706-38576788 (Clone quality: bE269H19 on chr=6; Num_of_Contigs=4; )
FY		ENSSSCG00000006416	4:94777387-94778855		CU462834,CH242-199I10,4:94761474-94795889 (Clone quality: bE199I10 on chr=4; Num_of_Contigs=5; )
FY		location ⇒	4:94778209-94777439		CU462834,CH242-199I10,4:94761474-94795889 (Clone quality: bE199I10 on chr=4; Num_of_Contigs=5; )
FYB		ENSSSCG00000016855	16:21724011-21824964
FYB		location ⇒	17:46398273-46398129		FP236283,CH242-246C6,17:46397504-46399580 (Clone quality: bE246C6 on chr=17; Num_of_Contigs=15; )
FYB		location ⇒	17:46398935-46398776		FP236283,CH242-246C6,17:46397504-46399580 (Clone quality: bE246C6 on chr=17; Num_of_Contigs=15; )
FYCO1		ENSSSCG00000011317	13:24481363-24557428
FYN		ENSSSCG00000002026	7:82083441-82092042		CU633625,CH242-116C14,7:82041923-82116183 (Clone quality: bE116C14 on chr=7; Num_of_Contigs=8; )
FYN		ENSSSCG00000004421	1:81129201-81174007		CU928753,CH242-47P9,1:81125088-81205344 (Clone quality: bE47P9 on chr=1; Num_of_Contigs=2; )
FYN		ENSSSCG00000004434	1:85584900-85690472
FYN		ENSSSCG00000016855	16:21724011-21824964
FYN		location ⇒	1:81136899-81137070		CU928753,CH242-47P9,1:81125088-81205344 (Clone quality: bE47P9 on chr=1; Num_of_Contigs=2; )
FYN		location ⇒	1:81140676-81140857		CU928753,CH242-47P9,1:81125088-81205344 (Clone quality: bE47P9 on chr=1; Num_of_Contigs=2; )
FYN		location ⇒	1:81142566-81142727		CU928753,CH242-47P9,1:81125088-81205344 (Clone quality: bE47P9 on chr=1; Num_of_Contigs=2; )
FYN		location ⇒	1:81173394-81173605		CU928753,CH242-47P9,1:81125088-81205344 (Clone quality: bE47P9 on chr=1; Num_of_Contigs=2; )
FZD10		ENSSSCG00000009751	14:25010134-25011879		CU019576,CH242-288E21,14:24885177-25019758 (Clone quality: bE288E21 on chr=14; Num_of_Contigs=4; )
FZD3		ENSSSCG00000009679	14:12274326-12364898
FZD4		ENSSSCG00000014920	9:20877821-20879122		FP102391,CH242-358A3,9:20873313-20886557 (Clone quality: bE358A3 on chr=9; Num_of_Contigs=7; )
FZD5		ENSSSCG00000016140	15:103853654-103855414		FP236775,CH242-72J11,15:103845450-103859869 (Clone quality: bE72J11 on chr=15; Num_of_Contigs=5; )
FZD6		ENSSSCG00000006052	4:34189953-34223429		CU138561,CH242-196D23,4:34141527-34263381 (Clone quality: bE196D23 on chr=4; Num_of_Contigs=3; )
FZD7		ENSSSCG00000016111	15:99372790-99374399
FZR1		ENSSSCG00000013481	2:48093587-48099634		CU915719,CH242-157K19,2:48050805-48153822 (Clone quality: bE157K19 on chr=2; Num_of_Contigs=5; )

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, 1001-22

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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).