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)

CXYorf3		ENSSSCG00000012627	X:96844445-96851850
CYB561		ENSSSCG00000017297	12:13021772-13031579
CYB561D1		ENSSSCG00000006827	4:115149515-115151413		CU633714,CH242-413N19,4:115147581-115211057 (Clone quality: bE413N19 on chr=4; Num_of_Contigs=4; )
CYB561D2		ENSSSCG00000011410	13:27494842-27497381		CU861907,CH242-10C8,13:27490820-27610755 (Clone quality: bE10C8 on chr=13; Num_of_Contigs=3; )
CYB5A		ENSSSCG00000004875	1:157181946-157217542		CU571232,CH242-48P10,1:157151362-157292527 (Clone quality: bE48P10 on chr=1; Num_of_Contigs=3; )
CYB5B		ENSSSCG00000002756	6:12423115-12458561		FP015939,CH242-384D23,6:12371411-12465501 (Clone quality: bE384D23 on chr=6; Num_of_Contigs=2; )
CYB5D2		ENSSSCG00000017876	12:47432754-47441760
CYB5R1		ENSSSCG00000010929	10:24925344-24930635
CYB5R3		ENSSSCG00000000038	5:2835494-2858808
CYB5R3		location ⇒	5:2842685-2842820		CU928642,CH242-477C10,5:2840003-2845438 (Clone quality: bE477C10 on chr=5; Num_of_Contigs=6; )
CYB5R3		location ⇒	5:2849058-2849190		CU928642,CH242-477C10,5:2845539-2874049 (Clone quality: bE477C10 on chr=5; Num_of_Contigs=6; )
CYB5R3		location ⇒	5:2858384-2858558		CU928642,CH242-477C10,5:2845539-2874049 (Clone quality: bE477C10 on chr=5; Num_of_Contigs=6; )
CYB5R3		location ⇒	5:2858625-2858856		CU928642,CH242-477C10,5:2845539-2874049 (Clone quality: bE477C10 on chr=5; Num_of_Contigs=6; )
CYBASC3		ENSSSCG00000013086	2:8448893-8462310
CYBASC3		location ⇒	2:8459292-8459501		CU896534,CH242-169N17,2:8458718-8477319 (Clone quality: bE169N17 on chr=2; Num_of_Contigs=6; )
CYBB		ENSSSCG00000012229	X:33096182-33133043
CYBB		location ⇒	X:33114963-33115152	CU207398,CH242-388N8,X:33096810-33201162 (Clone quality: bE388N8 on chr=X; Num_of_Contigs=2; )
CYBB		location ⇒	X:33118923-33118991	CU207398,CH242-388N8,X:33096810-33201162 (Clone quality: bE388N8 on chr=X; Num_of_Contigs=2; )
CYBB		location ⇒	X:33124961-33125217	CU207398,CH242-388N8,X:33096810-33201162 (Clone quality: bE388N8 on chr=X; Num_of_Contigs=2; )
CYBB		location ⇒	X:33127530-33127679	CU207398,CH242-388N8,X:33096810-33201162 (Clone quality: bE388N8 on chr=X; Num_of_Contigs=2; )
CYBRD1		ENSSSCG00000015946	15:72724087-72738643		CU571010,CH242-167N10,15:72721073-72758631 (Clone quality: bE167N10 on chr=15; Num_of_Contigs=10; )
CYC1		ENSSSCG00000005913	4:584181-586642		FP085492,CH242-176F2,4:573710-645862 (Clone quality: bE176F2 on chr=4; Num_of_Contigs=15; )
CYC_PIG		ENSSSCG00000016714	18:46008082-46010104		FP236676,CH242-236O10,18:45995820-46011919 (Clone quality: bE236O10 on chr=18; Num_of_Contigs=8; )
CYFIP2		ENSSSCG00000017054	16:63538236-63619797
CYGB		ENSSSCG00000017173	12:3213957-3220562		FP009759,CH242-6N4,12:3213783-3222661 (Clone quality: bE6N4 on chr=12; Num_of_Contigs=14; )
CYHR1		ENSSSCG00000005903	4:449645-462836
CYLC1		ENSSSCG00000012455	X:66202173-66207076		CU694935,CH242-69C23,X:66141805-66238682 (Clone quality: bE69C23 on chr=X; Num_of_Contigs=7; )
CYLC2		ENSSSCG00000005401	1:255957346-255961469
CYLD		ENSSSCG00000002837	6:23706695-23882754
CYP		ENSSSCG00000015934	15:71377171-71407147
CYP		ENSSSCG00000003664	6:65624698-65639794	CR956427,CH242-51O7,6:65474974-65651225 (No clone quality info on bE51O7)
CYP		ENSSSCG00000003964	6:120933170-120951473		CU467721,CH242-292B22,6:120927206-120962427 (Clone quality: bE292B22 on chr=6; Num_of_Contigs=5; )
CYP		ENSSSCG00000004557	1:111189586-111195194		CU302261,CH242-182N21,1:111189543-111264608 (Clone quality: bE182N21 on chr=1; Num_of_Contigs=3; )
CYP		ENSSSCG00000008878	8:41236401-41250927		CU896689,CH242-1N13,8:41180262-41282411 (Clone quality: bE1N13 on chr=8; Num_of_Contigs=4; )
CYP		ENSSSCG00000010083	14:51283055-51306558		CU633431,CH242-79C11,14:51180713-51414471 (Clone quality: bE79C11 on chr=14; Num_of_Contigs=4; )
CYP		ENSSSCG00000010330	14:85205810-85212642		CT827949,CH242-259N24,14:85046239-85223409 (Clone quality: bE259N24 on chr=14; Num_of_Contigs=1; )
CYP		location ⇒	15:71379503-71379613		CU467932,CH242-472J8,15:71379184-71393858 (Clone quality: bE472J8 on chr=15; Num_of_Contigs=8; )
CYP		location ⇒	15:71382090-71382179		CU467932,CH242-472J8,15:71379184-71393858 (Clone quality: bE472J8 on chr=15; Num_of_Contigs=8; )
CYP		location ⇒	15:71386544-71386684		CU467932,CH242-472J8,15:71379184-71393858 (Clone quality: bE472J8 on chr=15; Num_of_Contigs=8; )
CYP		location ⇒	15:71405703-71405837		CU466304,CH242-524C22,15:71404584-71414150 (Clone quality: bE524C22 on chr=15; Num_of_Contigs=14; )
CYP17A1		ENSSSCG00000010591	14:118882237-118888672		CU570855,CH242-447M15,14:118871202-118888810 (Clone quality: bE447M15 on chr=14; Num_of_Contigs=8; )
CYP17A1		location ⇒	14:118882678-118882248		CU570855,CH242-447M15,14:118871202-118888810 (Clone quality: bE447M15 on chr=14; Num_of_Contigs=8; )
CYP17A1		location ⇒	14:118884543-118884321		CU570855,CH242-447M15,14:118871202-118888810 (Clone quality: bE447M15 on chr=14; Num_of_Contigs=8; )
CYP17A1		location ⇒	14:118885800-118885571		CU570855,CH242-447M15,14:118871202-118888810 (Clone quality: bE447M15 on chr=14; Num_of_Contigs=8; )
CYP17A1		location ⇒	14:118888509-118888193		CU570855,CH242-447M15,14:118871202-118888810 (Clone quality: bE447M15 on chr=14; Num_of_Contigs=8; )
CYP19A1		location ⇒	X:51730671-51730566		CU693387,CH242-152O22,X:51697853-51839257 (Clone quality: bE152O22 on chr=X; Num_of_Contigs=8; )
CYP19A1		location ⇒	X:54275173-54275068		CU463000,CH242-297H24,X:54266393-54344554 (Clone quality: bE297H24 on chr=X; Num_of_Contigs=5; )
CYP19A1		location ⇒	X:72487851-72487912		CU607039,CH242-282M22,X:72418826-72490973 (Clone quality: bE282M22 on chr=X; Num_of_Contigs=6; )
CYP19A1		location ⇒	X:98272478-98272563	FP015883,CH242-13O19,X:98178848-98296570 (Clone quality: bE13O19 on chr=X; Num_of_Contigs=1; )
CYP1A1		ENSSSCG00000001906	7:64454785-64461043		CU469022,CH242-37P17,7:64436456-64477953 (Clone quality: bE37P17 on chr=7; Num_of_Contigs=3; )

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).