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)

CYR61		ENSSSCG00000006940	4:135349745-135352503		CU302351,CH242-235J1,4:135274335-135442929 (Clone quality: bE235J1 on chr=4; Num_of_Contigs=3; )
CYR61		location ⇒	4:135351446-135351142		CU302351,CH242-235J1,4:135274335-135442929 (Clone quality: bE235J1 on chr=4; Num_of_Contigs=3; )
CYR61		location ⇒	4:135352019-135351805		CU302351,CH242-235J1,4:135274335-135442929 (Clone quality: bE235J1 on chr=4; Num_of_Contigs=3; )
CYR61		location ⇒	4:135352504-135352288		CU302351,CH242-235J1,4:135274335-135442929 (Clone quality: bE235J1 on chr=4; Num_of_Contigs=3; )
CYSLTR1		ENSSSCG00000012443	X:61853427-61854449		FP236267,CH242-520A13,X:61848885-61869807 (Clone quality: bE520A13 on chr=X; Num_of_Contigs=18; )
CYSLTR2		ENSSSCG00000009399	11:18443351-18444289
CYSLTR2		location ⇒	11:18444152-18443264		CU466398,CH242-38N16,11:18441110-18444154 (Clone quality: bE38N16 on chr=11; Num_of_Contigs=6; )
CYTH1		ENSSSCG00000017167	12:1975893-2044159	CU942393,CH242-200M2,12:1864056-2044534 (Clone quality: bE200M2 on chr=14; Num_of_Contigs=6; )
CYTH2		ENSSSCG00000003136	6:37497074-37506716
CYTH4		ENSSSCG00000000130	5:6883939-6914392		CU915640,CH242-153F17,5:6859806-6948922 (Clone quality: bE153F17 on chr=5; Num_of_Contigs=5; )
CYTSA		ENSSSCG00000010053	14:50407704-50505710
CYYR1		ENSSSCG00000012024	13:135830477-135843348		CU550653,CH242-147K14,13:135766436-135852706 (Clone quality: bE147K14 on chr=13; Num_of_Contigs=7; )

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, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-2250, 2251-2300, 2301-2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-2650, 2651-2700, 2701-2750, 2751-2800, 2801-2850, 2851-2900, 2901-2950, 2951-3000, 3001-3050, 3051-3100, 3101-3150, 3151-3200, 3201-3250, 3251-3300, 3301-3350, 3351-3400, 3401-3450, 3451-3500, 3501-3550, 3551-3600, 3601-3650, 3651-3700, 3701-3750, 3751-3800, 3801-3850, 3851-3900, 3901-12

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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).