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)

CPNE6		ENSSSCG00000002011	7:81553835-81558788		CT961055,CH242-32K2,7:81553653-81626917 (Clone quality: bE32K2 on chr=7; Num_of_Contigs=2; )
CPNE8		ENSSSCG00000000778	5:66203055-66269619
CPNE9		ENSSSCG00000011544	13:55089124-55104526
CPO		ENSSSCG00000016135	15:102985837-103014779		CU468982,CH242-208J15,15:102904822-103089642 (Clone quality: bE208J15 on chr=15; Num_of_Contigs=1; )
CPOX		ENSSSCG00000011978	13:118552383-118564776		CU695046,CH242-269K10,13:118508361-118570024 (Clone quality: bE269K10 on chr=13; Num_of_Contigs=6; )
CPPED1		ENSSSCG00000007876	3:25844413-25941935
CPS1		ENSSSCG00000016159	15:106465468-106551048
CPSF1		ENSSSCG00000005906	4:499626-508181
CPSF2		ENSSSCG00000002448	7:121698468-121703842		CU468363,CH242-488L12,7:121692012-121705168 (Clone quality: bE488L12 on chr=7; Num_of_Contigs=13; )
CPSF3L		ENSSSCG00000003339	6:42908729-42919813		FP102596,CH242-173K23,6:42905835-42937819 (Clone quality: bE173K23 on chr=6; Num_of_Contigs=10; )
CPSF4		ENSSSCG00000007615	3:5624909-5832347
CPSF6		ENSSSCG00000000490	5:32451235-32458128
CPSF7		ENSSSCG00000013083	2:8394734-8412259		CU896534,CH242-169N17,2:8375072-8412883 (Clone quality: bE169N17 on chr=2; Num_of_Contigs=6; )
CPT1A		ENSSSCG00000012881	2:2491906-2501270		CU694814,CH242-124N20,2:2488335-2518805 (Clone quality: bE124N20 on chr=2; Num_of_Contigs=8; )
CPT1B		location ⇒	2:2500361-2500294		CU694814,CH242-124N20,2:2488335-2518805 (Clone quality: bE124N20 on chr=2; Num_of_Contigs=8; )
CPT2		ENSSSCG00000003851	6:112930177-112952350
CPVL		ENSSSCG00000016688	18:41992393-42112037
CPXM1		ENSSSCG00000007170	17:34418343-34425013		CU915714,CH242-485K7,17:34418153-34455757 (Clone quality: bE485K7 on chr=17; Num_of_Contigs=3; )
CPXM1		location ⇒	17:34420464-34420608		CU915714,CH242-485K7,17:34418153-34455757 (Clone quality: bE485K7 on chr=17; Num_of_Contigs=3; )
CPXM1		location ⇒	17:34420710-34420804		CU915714,CH242-485K7,17:34418153-34455757 (Clone quality: bE485K7 on chr=17; Num_of_Contigs=3; )
CPXM1		location ⇒	17:34421413-34421564		CU915714,CH242-485K7,17:34418153-34455757 (Clone quality: bE485K7 on chr=17; Num_of_Contigs=3; )
CPXM1		location ⇒	17:34421646-34421737		CU915714,CH242-485K7,17:34418153-34455757 (Clone quality: bE485K7 on chr=17; Num_of_Contigs=3; )
CPXM2		ENSSSCG00000010728	14:139754314-139851804		CT737316,CH242-164D4,14:139753804-139871447 (Clone quality: bE164D4 on chr=14; Num_of_Contigs=2; )
CPXM2		location ⇒	14:139769770-139769554		CT737316,CH242-164D4,14:139753804-139871447 (Clone quality: bE164D4 on chr=14; Num_of_Contigs=2; )
CPXM2		location ⇒	14:139774926-139774743		CT737316,CH242-164D4,14:139753804-139871447 (Clone quality: bE164D4 on chr=14; Num_of_Contigs=2; )
CPXM2		location ⇒	14:139776147-139775949		CT737316,CH242-164D4,14:139753804-139871447 (Clone quality: bE164D4 on chr=14; Num_of_Contigs=2; )
CPXM2		location ⇒	14:139777480-139777352		CT737316,CH242-164D4,14:139753804-139871447 (Clone quality: bE164D4 on chr=14; Num_of_Contigs=2; )
CR		ENSSSCG00000015749	15:31993420-32018200
CR		ENSSSCG00000002013	7:81581893-81595363		CT961055,CH242-32K2,7:81553653-81626917 (Clone quality: bE32K2 on chr=7; Num_of_Contigs=2; )
CR		ENSSSCG00000002730	6:10120471-10149583
CR1		location ⇒	9:63475235-63475321		CU928329,CH242-216P17,9:63462184-63501413 (Clone quality: bE216P17 on chr=9; Num_of_Contigs=5; )
CR1		location ⇒	9:63490116-63490194		CU928329,CH242-216P17,9:63462184-63501413 (Clone quality: bE216P17 on chr=9; Num_of_Contigs=5; )
CR1		location ⇒	9:63512545-63512624		CU928329,CH242-216P17,9:63501514-63525591 (Clone quality: bE216P17 on chr=9; Num_of_Contigs=5; )
CR1		location ⇒	9:63512546-63512624		CU928329,CH242-216P17,9:63501514-63525591 (Clone quality: bE216P17 on chr=9; Num_of_Contigs=5; )
CR1L		location ⇒	9:63488293-63488398		CU928329,CH242-216P17,9:63462184-63501413 (Clone quality: bE216P17 on chr=9; Num_of_Contigs=5; )
CR1L		location ⇒	9:63504208-63504324		CU928329,CH242-216P17,9:63501514-63525591 (Clone quality: bE216P17 on chr=9; Num_of_Contigs=5; )
CR1L		location ⇒	9:63510803-63510890		CU928329,CH242-216P17,9:63501514-63525591 (Clone quality: bE216P17 on chr=9; Num_of_Contigs=5; )
CR1L		location ⇒	9:63512545-63512626		CU928329,CH242-216P17,9:63501514-63525591 (Clone quality: bE216P17 on chr=9; Num_of_Contigs=5; )
CR2		location ⇒	X:11179142-11179057		CU302208,CH242-168N3,X:11177177-11179277 (Clone quality: bE168N3 on chr=X; Num_of_Contigs=5; )
CR2		location ⇒	X:11216696-11216761		CU302208,CH242-168N3,X:11183295-11238328 (Clone quality: bE168N3 on chr=X; Num_of_Contigs=5; )
CR2		location ⇒	X:11287162-11287061	CU633586,CH242-423M21,X:11281835-11399819 (Clone quality: bE423M21 on chr=X; Num_of_Contigs=2; )
CR2		location ⇒	X:9692135-9692062		CU633296,CH242-43B19,X:9678250-9692718 (Clone quality: bE43B19 on chr=X; Num_of_Contigs=6; )
CR956640.1		ENSSSCG00000007492	17:59476535-59488099	CR956640,CH242-155M9,17:59463698-59643740 (No clone quality info on bE155M9)
CRABP2		ENSSSCG00000006472	4:97081032-97087113		CU582900,CH242-5K23,4:97070908-97120572 (Clone quality: bE5K23 on chr=4; Num_of_Contigs=3; )
CRABP2		location ⇒	4:97086626-97086684		CU582900,CH242-5K23,4:97070908-97120572 (Clone quality: bE5K23 on chr=4; Num_of_Contigs=3; )
CRABP2		location ⇒	4:97086863-97086921		CU582900,CH242-5K23,4:97070908-97120572 (Clone quality: bE5K23 on chr=4; Num_of_Contigs=3; )
CRABP2		location ⇒	4:97152247-97152305		FP102690,CH242-379E5,4:97150231-97152658 (Clone quality: bE379E5 on chr=4; Num_of_Contigs=15; )
CRABP2		location ⇒	4:97152484-97152542		FP102690,CH242-379E5,4:97150231-97152658 (Clone quality: bE379E5 on chr=4; Num_of_Contigs=15; )
CRADD		ENSSSCG00000000911	5:84220514-84220882		CU914474,CH242-208I20,5:84214277-84228332 (Clone quality: bE208I20 on chr=5; Num_of_Contigs=13; )
CRADD		location ⇒	5:84219196-84219284		CU914474,CH242-208I20,5:84214277-84228332 (Clone quality: bE208I20 on chr=5; Num_of_Contigs=13; )

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).