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)

C19orf15		ENSSSCG00000002955	6:32461675-32491246		FP236590,CH242-507G2,6:32461085-32547641 (Clone quality: bE507G2 on chr=6; Num_of_Contigs=4; )
C19orf18		ENSSSCG00000003994	6:122889925-122899179		CU928745,CH242-204A5,6:122888090-122899550 (Clone quality: bE204A5 on chr=6; Num_of_Contigs=6; )
C19orf21		ENSSSCG00000013425	2:46327923-46329392		FP015903,CH242-504E7,2:46319798-46329665 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
C19orf21		location ⇒	2:46328116-46328198		FP015903,CH242-504E7,2:46319798-46329665 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
C19orf22		ENSSSCG00000013419	2:46168896-46178500		FP015903,CH242-504E7,2:46128360-46188530 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
C19orf26		ENSSSCG00000013430	2:46457555-46462053		CU929580,CH242-161G11,2:46439429-46462140 (Clone quality: bE161G11 on chr=2; Num_of_Contigs=11; )
C19orf29		ENSSSCG00000013489	2:48159892-48174731
C19orf29OS		ENSSSCG00000013488	2:48159889-48379376
C19orf33		ENSSSCG00000002953	6:32416163-32417327		FP236590,CH242-507G2,6:32409521-32460984 (Clone quality: bE507G2 on chr=6; Num_of_Contigs=4; )
C19orf35		ENSSSCG00000013461	2:47219608-47223787		FP089467,CH242-185G23,2:47173729-47314390 (Clone quality: bE185G23 on chr=2; Num_of_Contigs=3; )
C19orf36		ENSSSCG00000013455	2:47057078-47060080		CU929035,CH242-88G19,2:47055332-47060548 (Clone quality: bE88G19 on chr=2; Num_of_Contigs=27; )
C19orf38		ENSSSCG00000013632	2:52713277-52727559
C19orf39		ENSSSCG00000013619	2:52285863-52287644		CU855518,CH242-272A5,2:52278123-52289160 (Clone quality: bE272A5 on chr=2; Num_of_Contigs=10; )
C19orf42		ENSSSCG00000013863	2:61188597-61196663
C19orf43		ENSSSCG00000013727	2:55975158-55978161		CU856041,CH242-32I13,2:55919380-55991729 (Clone quality: bE32I13 on chr=2; Num_of_Contigs=2; )
C19orf44		ENSSSCG00000013859	2:61063855-61079289
C19orf45		ENSSSCG00000013571	2:50930030-50934501
C19orf50		ENSSSCG00000013906	2:62538363-62546391		FP102402,CH242-83K20,2:62531972-62552811 (Clone quality: bE83K20 on chr=2; Num_of_Contigs=3; )
C19orf52		ENSSSCG00000013635	2:52775312-52776187		CU928849,CH242-1G23,2:52764937-52777072 (Clone quality: bE1G23 on chr=2; Num_of_Contigs=8; )
C19orf53		ENSSSCG00000013757	2:56822887-56826748
C19orf54		ENSSSCG00000002999	6:33709433-33716248		CU928654,CH242-130A3,6:33678287-33731769 (Clone quality: bE130A3 on chr=6; Num_of_Contigs=6; )
C19orf55		ENSSSCG00000002900	6:30180792-30355856
C19orf56		ENSSSCG00000013721	2:55915448-55929080
C19orf57		ENSSSCG00000013760	2:56896547-56915878		FP016000,CH242-10C10,2:56824783-56952713 (Clone quality: bE10C10 on chr=2; Num_of_Contigs=2; )
C19orf58		location ⇒	11:17466794-17466935		CU463930,CH242-429K24,11:17465671-17491943 (Clone quality: bE429K24 on chr=11; Num_of_Contigs=5; )
C19orf59		ENSSSCG00000013574	2:51019089-51021306		CU929919,CH242-334A8,2:51013584-51060863 (Clone quality: bE334A8 on chr=2; Num_of_Contigs=7; )
C19orf60		ENSSSCG00000013908	2:62552109-62554947
C19orf61		ENSSSCG00000003068	6:35153848-35165440
C19orf63		ENSSSCG00000003220	6:39078070-39083495		FP102476,CH242-133P5,6:39060907-39089695 (Clone quality: bE133P5 on chr=6; Num_of_Contigs=12; )
C19orf64		ENSSSCG00000013486	2:48140485-48142887		CU915719,CH242-157K19,2:48050805-48153822 (Clone quality: bE157K19 on chr=2; Num_of_Contigs=5; )
C19orf66		ENSSSCG00000013664	2:53413416-53418268		CU462940,CH242-319N14,2:53390856-53454909 (Clone quality: bE319N14 on chr=2; Num_of_Contigs=3; )
C19orf67		ENSSSCG00000013769	2:57064940-57067713		FP086609,CH242-184K22,2:57017365-57071189 (Clone quality: bE184K22 on chr=2; Num_of_Contigs=6; )
C19orf68		ENSSSCG00000003129	6:37342236-37357436		FP102640,CH242-235B10,6:37275907-37358125 (Clone quality: bE235B10 on chr=6; Num_of_Contigs=12; )
C19orf69		ENSSSCG00000003010	6:33958690-33960738		FP236582,CH242-238L13,6:33956610-33964983 (Clone quality: bE238L13 on chr=6; Num_of_Contigs=11; )
C19orf70		ENSSSCG00000013524	2:49381105-49383144		FP089464,CH242-231P22,2:49368415-49462890 (Clone quality: bE231P22 on chr=2; Num_of_Contigs=4; )
C19orf71		ENSSSCG00000013482	2:48105573-48106327		CU915719,CH242-157K19,2:48050805-48153822 (Clone quality: bE157K19 on chr=2; Num_of_Contigs=5; )
C19orf76		ENSSSCG00000003190	6:38406225-38407157		CU694867,CH242-269H19,6:38400485-38449566 (Clone quality: bE269H19 on chr=6; Num_of_Contigs=4; )
C19orf77		ENSSSCG00000013480	2:48043523-48046550
C1D		ENSSSCG00000008354	3:68165515-68181331		CU915705,CH242-440I14,3:68131955-68208627 (Clone quality: bE440I14 on chr=3; Num_of_Contigs=1; )
C1GALT1		ENSSSCG00000015341	9:72920013-72954561		CU656006,CH242-325A14,9:72914790-72962448 (Clone quality: bE325A14 on chr=9; Num_of_Contigs=6; )
C1GALT1C1		ENSSSCG00000012602	X:95696449-95697405	CU693400,CH242-226A14,X:95672406-95723202 (Clone quality: bE226A14 on chr=X; Num_of_Contigs=6; )
C1GALT1C1		location ⇒	X:95694084-95694236	CU693400,CH242-226A14,X:95672406-95723202 (Clone quality: bE226A14 on chr=X; Num_of_Contigs=6; )
C1GALT1C1		location ⇒	X:95696211-95696326	CU693400,CH242-226A14,X:95672406-95723202 (Clone quality: bE226A14 on chr=X; Num_of_Contigs=6; )
C1GALT1C1		location ⇒	X:95696450-95697403	CU693400,CH242-226A14,X:95672406-95723202 (Clone quality: bE226A14 on chr=X; Num_of_Contigs=6; )
C1orf100		ENSSSCG00000010873	10:16692545-16704532		CU655951,CH242-505J11,10:16691427-16714722 (Clone quality: bE505J11 on chr=10; Num_of_Contigs=21; )
C1orf101		ENSSSCG00000010875	10:16841241-16927727		CU571186,CH242-132I12,10:16826399-16943184 (Clone quality: bE132I12 on chr=10; Num_of_Contigs=2; )
C1orf103		ENSSSCG00000006799	4:113705267-113710293		CU467047,CH242-12L18,4:113684895-113719839 (Clone quality: bE12L18 on chr=4; Num_of_Contigs=6; )
C1orf110		ENSSSCG00000006336	4:91314860-91322221		CT990609,CH242-14I4,4:91314215-91483053 (Clone quality: bE14I4 on chr=4; Num_of_Contigs=3; )
C1orf111		ENSSSCG00000006343	4:91880454-91882860
C1orf112		ENSSSCG00000006284	4:84266378-84306640

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).