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)

CD138		ENSSSCG00000008601	3:109603804-109608153		CU856117,CH242-479B3,3:109586437-109610385 (Clone quality: bE479B3 on chr=3; Num_of_Contigs=16; )
CD14		ENSSSCG00000014369	2:129356198-129357848		CU459055,CH242-430O11,2:129351567-129383244 (Clone quality: bE430O11 on chr=2; Num_of_Contigs=5; )
CD14		location ⇒	2:129357385-129356198		CU459055,CH242-430O11,2:129351567-129383244 (Clone quality: bE430O11 on chr=2; Num_of_Contigs=5; )
CD14		location ⇒	2:129357736-129357508		CU459055,CH242-430O11,2:129351567-129383244 (Clone quality: bE430O11 on chr=2; Num_of_Contigs=5; )
CD140a		ENSSSCG00000008841	8:35262065-35303473
CD15		ENSSSCG00000014958	9:27018823-27020121		FP236710,CH242-260H20,9:26999281-27022484 (Clone quality: bE260H20 on chr=9; Num_of_Contigs=2; )
CD150		ENSSSCG00000006380	4:93320018-93356552		CU915315,CH242-208F9,4:93261946-93408226 (Clone quality: bE208F9 on chr=4; Num_of_Contigs=2; )
CD151		ENSSSCG00000012840	2:137153-261661
CD151		location ⇒	2:137857-137151		CU928976,CH242-144M19,2:43742-170991 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
CD151		location ⇒	2:138308-138147		CU928976,CH242-144M19,2:43742-170991 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
CD151		location ⇒	2:139621-139429		CU928976,CH242-144M19,2:43742-170991 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
CD151		location ⇒	2:139828-139712		CU928976,CH242-144M19,2:43742-170991 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
CD152		ENSSSCG00000016122	15:100704141-100709270
CD155		ENSSSCG00000003079	6:35616165-35627447		CU929755,CH242-284D18,6:35587258-35702275 (Clone quality: bE284D18 on chr=6; Num_of_Contigs=4; )
CD156a		ENSSSCG00000010772	14:147966527-147977088
CD156c		ENSSSCG00000004595	1:117373024-117514373
CD157		ENSSSCG00000008743	8:8432710-8445584
CD160		location ⇒	4:103660767-103661289		CU467072,CH242-100P4,4:103582921-103758989 (Clone quality: bE100P4 on chr=4; Num_of_Contigs=2; )
CD161		ENSSSCG00000000658	5:58934596-58947949
CD163		location ⇒	14:148351048-148350944		CU570634,CH242-125P2,14:148320735-148373783 (Clone quality: bE125P2 on chr=14; Num_of_Contigs=15; )
CD163L1		location ⇒	14:138811886-138811926		CU633935,CH242-129O9,14:138804633-138892331 (Clone quality: bE129O9 on chr=14; Num_of_Contigs=4; )
CD163L1		location ⇒	14:148351039-148350944		CU570634,CH242-125P2,14:148320735-148373783 (Clone quality: bE125P2 on chr=14; Num_of_Contigs=15; )
CD163L1		location ⇒	14:148352813-148352759		CU570634,CH242-125P2,14:148320735-148373783 (Clone quality: bE125P2 on chr=14; Num_of_Contigs=15; )
CD163L1		location ⇒	14:148352999-148352929		CU570634,CH242-125P2,14:148320735-148373783 (Clone quality: bE125P2 on chr=14; Num_of_Contigs=15; )
CD164		ENSSSCG00000003575	6:58268804-58272265		CU466983,CH242-5M3,6:58217448-58296419 (Clone quality: bE5M3 on chr=6; Num_of_Contigs=5; )
CD164		ENSSSCG00000004414	1:80531982-80546382		CU075452,CH242-39D23,1:80450203-80633251 (Clone quality: bE39D23 on chr=1; Num_of_Contigs=2; )
CD164		location ⇒	1:80547307-80547785		CU075452,CH242-39D23,1:80450203-80633251 (Clone quality: bE39D23 on chr=1; Num_of_Contigs=2; )
CD164		location ⇒	1:80547307-80547785		CU075452,CH242-39D23,1:80450203-80633251 (Clone quality: bE39D23 on chr=1; Num_of_Contigs=2; )
CD164		location ⇒	1:80548089-80548301		CU075452,CH242-39D23,1:80450203-80633251 (Clone quality: bE39D23 on chr=1; Num_of_Contigs=2; )
CD164		location ⇒	1:80548089-80548301		CU075452,CH242-39D23,1:80450203-80633251 (Clone quality: bE39D23 on chr=1; Num_of_Contigs=2; )
CD164L2		ENSSSCG00000003575	6:58268804-58272265		CU466983,CH242-5M3,6:58217448-58296419 (Clone quality: bE5M3 on chr=6; Num_of_Contigs=5; )
CD168		ENSSSCG00000017022	16:57785304-57826403
CD17		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CD170		ENSSSCG00000003236	6:39481730-39501436		CU019573,CH242-21M5,6:39444132-39502362 (Clone quality: bE21M5 on chr=6; Num_of_Contigs=9; )
CD171		ENSSSCG00000012787	X:122708635-122721188
CD177		ENSSSCG00000003051	6:34833102-34861440
CD18		location ⇒	8:59307168-59307260		CU633185,CH242-328O16,8:59296534-59311008 (Clone quality: bE328O16 on chr=8; Num_of_Contigs=4; )
CD18		location ⇒	8:59307581-59307651		CU633185,CH242-328O16,8:59296534-59311008 (Clone quality: bE328O16 on chr=8; Num_of_Contigs=4; )
CD180		ENSSSCG00000016957	16:43042267-43059049		CU928455,CH242-465J21,16:42987832-43074430 (Clone quality: bE465J21 on chr=16; Num_of_Contigs=3; )
CD184		ENSSSCG00000015688	15:14081271-14084327
CD185		ENSSSCG00000015098	9:44724736-44735301		FP089499,CH242-36G7,9:44609302-44750256 (Clone quality: bE36G7 on chr=9; Num_of_Contigs=3; )
CD19		ENSSSCG00000007807	3:16705752-16714070		CU928476,CH242-24P1,3:16696480-16718074 (Clone quality: bE24P1 on chr=3; Num_of_Contigs=5; )
CD19		location ⇒	3:16706092-16706382		CU928476,CH242-24P1,3:16696480-16718074 (Clone quality: bE24P1 on chr=3; Num_of_Contigs=5; )
CD19		location ⇒	3:16706691-16706895		CU928476,CH242-24P1,3:16696480-16718074 (Clone quality: bE24P1 on chr=3; Num_of_Contigs=5; )
CD19		location ⇒	3:16707017-16707308		CU928476,CH242-24P1,3:16696480-16718074 (Clone quality: bE24P1 on chr=3; Num_of_Contigs=5; )
CD19		location ⇒	3:16713479-16713632		CU928476,CH242-24P1,3:16696480-16718074 (Clone quality: bE24P1 on chr=3; Num_of_Contigs=5; )
CD1A		location ⇒	4:95670877-95670604		CU570749,CH242-3I5,4:95650992-95680714 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1A		location ⇒	4:95700546-95700462		CU570749,CH242-3I5,4:95680815-95725403 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1A		location ⇒	4:95702920-95702862		CU570749,CH242-3I5,4:95680815-95725403 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1A		location ⇒	4:95730123-95729850		CU570749,CH242-3I5,4:95725504-95735613 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )

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).