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)

CYP1A1		location ⇒	7:64305721-64306589		CU468845,CH242-162A4,7:64176153-64332301 (Clone quality: bE162A4 on chr=7; Num_of_Contigs=2; )
CYP1A1		location ⇒	7:64308051-64309530		CU468845,CH242-162A4,7:64176153-64332301 (Clone quality: bE162A4 on chr=7; Num_of_Contigs=2; )
CYP1A1		location ⇒	7:64456266-64454787		CU469022,CH242-37P17,7:64436456-64477953 (Clone quality: bE37P17 on chr=7; Num_of_Contigs=3; )
CYP1A1		location ⇒	7:64458587-64457719		CU469022,CH242-37P17,7:64436456-64477953 (Clone quality: bE37P17 on chr=7; Num_of_Contigs=3; )
CYP1A2		ENSSSCG00000001901	7:64280270-64285232		CU468845,CH242-162A4,7:64176153-64332301 (Clone quality: bE162A4 on chr=7; Num_of_Contigs=2; )
CYP1B1		ENSSSCG00000008489	3:95306777-95307367		CU896570,CH242-142J2,3:95288561-95309682 (Clone quality: bE142J2 on chr=3; Num_of_Contigs=8; )
CYP1B1		location ⇒	3:95305959-95305909		CU896570,CH242-142J2,3:95288561-95309682 (Clone quality: bE142J2 on chr=3; Num_of_Contigs=8; )
CYP1B1		location ⇒	3:95307365-95306712		CU896570,CH242-142J2,3:95288561-95309682 (Clone quality: bE142J2 on chr=3; Num_of_Contigs=8; )
CYP21A2		ENSSSCG00000001428	7:27908299-27911241	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
CYP21A21589		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CYP24A1		ENSSSCG00000007486	17:57339613-57360530	CR956635,CH242-184L20,17:57161867-57371607 (No clone quality info on bE184L20)
CYP26A1		ENSSSCG00000010475	14:109670849-109674324		CT827851,CH242-289B12,14:109662353-109720416 (Clone quality: bE289B12 on chr=14; Num_of_Contigs=7; )
CYP26B1		ENSSSCG00000008311	3:64757607-64774508
CYP26B1		location ⇒	3:64768923-64769017		FP067358,CH242-257N17,3:64755419-64769954 (Clone quality: bE257N17 on chr=3; Num_of_Contigs=4; )
CYP26B1		location ⇒	3:64769313-64769818		FP067358,CH242-257N17,3:64755419-64769954 (Clone quality: bE257N17 on chr=3; Num_of_Contigs=4; )
CYP26B1		location ⇒	3:64770232-64770709		FP067358,CH242-257N17,3:64770055-64775311 (Clone quality: bE257N17 on chr=3; Num_of_Contigs=4; )
CYP26B1		location ⇒	3:64771726-64772225		FP067358,CH242-257N17,3:64770055-64775311 (Clone quality: bE257N17 on chr=3; Num_of_Contigs=4; )
CYP26C1		ENSSSCG00000010474	14:109659829-109666189
CYP27A1		ENSSSCG00000016199	15:113821914-113824354
CYP27B1		location ⇒	3:12474814-12474899		CU694713,CH242-31L6,3:12473581-12487344 (Clone quality: bE31L6 on chr=3; Num_of_Contigs=3; )
CYP27B1		location ⇒	3:13334753-13334668		FP102233,CH242-11F6,3:13257115-13340412 (Clone quality: bE11F6 on chr=3; Num_of_Contigs=2; )
CYP27B1		location ⇒	3:5805700-5805631		FP102617,CH242-199P18,3:5759765-5834782 (Clone quality: bE199P18 on chr=3; Num_of_Contigs=6; )
CYP27B1		location ⇒	3:6971965-6971860		FP102710,CH242-46P3,3:6961441-6977385 (Clone quality: bE46P3 on chr=3; Num_of_Contigs=3; )
CYP2B6		ENSSSCG00000003006	6:33882573-33906774
CYP2B7P1		ENSSSCG00000003006	6:33882573-33906774
CYP2C34		location ⇒	14:111423506-111423614		CU468555,CH242-152J23,14:111414955-111429963 (Clone quality: bE152J23 on chr=14; Num_of_Contigs=10; )
CYP2C34		location ⇒	14:111484145-111484694		CU468555,CH242-152J23,14:111432294-111533070 (Clone quality: bE152J23 on chr=14; Num_of_Contigs=10; )
CYP2C34		location ⇒	14:111596187-111596260		CU481650,CH242-83I16,14:111591508-111616490 (Clone quality: bE83I16 on chr=14; Num_of_Contigs=10; )
CYP2C34		location ⇒	14:111666868-111667418		CU392852,CH242-517O10,14:111617888-111696161 (Clone quality: bE517O10 on chr=14; Num_of_Contigs=2; )
CYP2E1		ENSSSCG00000010780	14:148132846-148145308		CU582843,CH242-221E3,14:148105591-148151995 (Clone quality: bE221E3 on chr=14; Num_of_Contigs=12; )
CYP2F1		ENSSSCG00000002994	6:33650186-33662178
CYP2G1P		ENSSSCG00000002992	6:33596132-33608954		CU928654,CH242-130A3,6:33589010-33635086 (Clone quality: bE130A3 on chr=6; Num_of_Contigs=6; )
CYP2J2		ENSSSCG00000003825	6:107693667-107723360
CYP2R1		ENSSSCG00000013389	2:41501759-41519677		CU606994,CH242-513N24,2:41487352-41529702 (Clone quality: bE513N24 on chr=2; Num_of_Contigs=5; )
CYP2U1		ENSSSCG00000009151	8:97852755-97869047		CU463204,CH242-487A14,8:97767700-97882787 (Clone quality: bE487A14 on chr=8; Num_of_Contigs=2; )
CYP2W1		ENSSSCG00000007549	3:426367-431382		CU928365,CH242-185G1,3:426338-433376 (Clone quality: bE185G1 on chr=3; Num_of_Contigs=21; )
CYP46A1		ENSSSCG00000002510	7:129916145-129979541
CYP4A24		location ⇒	6:117673508-117674529		FP102856,CH242-411M18,6:117663074-117675500 (Clone quality: bE411M18 on chr=6; Num_of_Contigs=16; )
CYP4A24		location ⇒	6:88753709-88753788		CU467007,CH242-257B4,6:88671282-88779821 (Clone quality: bE257B4 on chr=6; Num_of_Contigs=2; )
CYP4A24		location ⇒	6:88755753-88755821		CU467007,CH242-257B4,6:88671282-88779821 (Clone quality: bE257B4 on chr=6; Num_of_Contigs=2; )
CYP4A24		location ⇒	6:88755972-88756047		CU467007,CH242-257B4,6:88671282-88779821 (Clone quality: bE257B4 on chr=6; Num_of_Contigs=2; )
CYP4B1		ENSSSCG00000003894	6:117760201-117779328		FP102856,CH242-411M18,6:117731449-117792877 (Clone quality: bE411M18 on chr=6; Num_of_Contigs=16; )
CYP4F3		location ⇒	2:60438785-60438870		CU942397,CH242-289F11,2:60411276-60446933 (Clone quality: bE289F11 on chr=2; Num_of_Contigs=10; )
CYP4F3		location ⇒	2:60989957-60990011		CU694762,CH242-123E16,2:60899482-61017915 (Clone quality: bE123E16 on chr=2; Num_of_Contigs=2; )
CYP4F3		location ⇒	2:61065933-61065856		CU694762,CH242-123E16,2:61018016-61070712 (Clone quality: bE123E16 on chr=2; Num_of_Contigs=2; )
CYP4F3		location ⇒	2:68983522-68983453	FP085445,CH242-191I1,2:68882349-69082246 (Clone quality: bE191I1 on chr=2; Num_of_Contigs=1; )
CYP4V2		ENSSSCG00000015800	15:44229729-44232929		CU466336,CH242-451P14,15:44219570-44237229 (Clone quality: bE451P14 on chr=15; Num_of_Contigs=7; )
CYP51A1		ENSSSCG00000015311	9:67541228-67562863		CU856027,CH242-272P11,9:67469412-67568808 (Clone quality: bE272P11 on chr=9; Num_of_Contigs=6; )
CYP7A1		ENSSSCG00000006238	4:77173363-77202771
CYP7B1		ENSSSCG00000006221	4:72197760-72353680

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).