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)

C16orf78		ENSSSCG00000002839	6:24255606-24259466		CU463014,CH242-509I5,6:24105953-24265490 (Clone quality: bE509I5 on chr=6; Num_of_Contigs=1; )
C16orf79		ENSSSCG00000008045	3:36568338-36579840
C16orf80		ENSSSCG00000002805	6:19603585-19618268		FP102099,CH242-149H9,6:19582030-19624690 (Clone quality: bE149H9 on chr=6; Num_of_Contigs=10; )
C16orf90		ENSSSCG00000007957	3:34763688-34765096		CU469160,CH242-310A1,3:34761089-34765112 (Clone quality: bE310A1 on chr=3; Num_of_Contigs=18; )
C17orf102		ENSSSCG00000017719	12:38129084-38131612
C17orf104		ENSSSCG00000017351	12:16567218-16661365
C17orf105		ENSSSCG00000017373	12:17242210-17246676		CU928405,CH242-149G4,12:17230645-17278372 (Clone quality: bE149G4 on chr=12; Num_of_Contigs=4; )
C17orf106		ENSSSCG00000017194	12:3789743-3803159		CU928029,CH242-304M1,12:3750666-3894443 (Clone quality: bE304M1 on chr=12; Num_of_Contigs=9; )
C17orf107		ENSSSCG00000017910	12:49209881-49210670		FP015831,CH242-271O18,12:49169208-49243291 (Clone quality: bE271O18 on chr=12; Num_of_Contigs=4; )
C17orf28		ENSSSCG00000017219	12:4446958-4465855		CU640421,CH242-384L19,12:4443050-4475806 (Clone quality: bE384L19 on chr=12; Num_of_Contigs=8; )
C17orf37		ENSSSCG00000017496	12:20553936-20555633		CU640399,CH242-251F23,12:20530232-20578478 (Clone quality: bE251F23 on chr=12; Num_of_Contigs=5; )
C17orf37		location ⇒	12:20553984-20554072		CU640399,CH242-251F23,12:20530232-20578478 (Clone quality: bE251F23 on chr=12; Num_of_Contigs=5; )
C17orf37		location ⇒	12:20554175-20554276		CU640399,CH242-251F23,12:20530232-20578478 (Clone quality: bE251F23 on chr=12; Num_of_Contigs=5; )
C17orf37		location ⇒	12:20555017-20555096		CU640399,CH242-251F23,12:20530232-20578478 (Clone quality: bE251F23 on chr=12; Num_of_Contigs=5; )
C17orf42		ENSSSCG00000017741	12:40689842-40700908		CU915522,CH242-75P19,12:40680480-40719109 (Clone quality: bE75P19 on chr=12; Num_of_Contigs=8; )
C17orf46		ENSSSCG00000017331	12:16056443-16059333		FP067380,CH242-32K16,12:15988019-16156790 (Clone quality: bE32K16 on chr=12; Num_of_Contigs=1; )
C17orf47		ENSSSCG00000017644	12:32818267-32820640		CU681830,CH242-364G8,12:32816335-32845074 (Clone quality: bE364G8 on chr=12; Num_of_Contigs=5; )
C17orf48		ENSSSCG00000018009	12:52499820-52501391		CU856557,CH242-14N5,12:52466634-52504582 (Clone quality: bE14N5 on chr=12; Num_of_Contigs=6; )
C17orf49		ENSSSCG00000017928	12:49576064-49579007		CU914703,CH242-254H21,12:49564591-49589172 (Clone quality: bE254H21 on chr=12; Num_of_Contigs=9; )
C17orf50		ENSSSCG00000017709	12:37571028-37572870		CU914398,CH242-121H9,12:37483147-37597733 (Clone quality: bE121H9 on chr=12; Num_of_Contigs=11; )
C17orf53		ENSSSCG00000017364	12:17021849-17028417
C17orf57		ENSSSCG00000017305	12:14289474-14425338
C17orf61		ENSSSCG00000011757	13:85539044-85539367		CU861914,CH242-131L1,13:85523241-85566244 (Clone quality: bE131L1 on chr=13; Num_of_Contigs=4; )
C17orf63		ENSSSCG00000017774	12:42736575-42738263		FP016171,CH242-62B5,12:42734240-42743407 (Clone quality: bE62B5 on chr=12; Num_of_Contigs=5; )
C17orf64		ENSSSCG00000017679	12:35695057-35702761		CU928876,CH242-112G14,12:35636225-35717646 (Clone quality: bE112G14 on chr=12; Num_of_Contigs=4; )
C17orf65		ENSSSCG00000017353	12:16633391-16951700
C17orf66		ENSSSCG00000017706	12:37427527-37444125		CU896616,CH242-206O9,12:37393181-37445015 (Clone quality: bE206O9 on chr=12; Num_of_Contigs=7; )
C17orf67		ENSSSCG00000017612	12:30937361-30953924		CU655876,CH242-162A9,12:30890861-30966026 (Clone quality: bE162A9 on chr=12; Num_of_Contigs=9; )
C17orf72		ENSSSCG00000017281	12:12542070-12543972		CU694679,CH242-184I12,12:12462076-12561338 (Clone quality: bE184I12 on chr=12; Num_of_Contigs=5; )
C17orf75		ENSSSCG00000017733	12:40301423-40312721
C17orf78		ENSSSCG00000017696	12:37114900-37117700		CU466977,CH242-506H19,12:37097631-37118806 (Clone quality: bE506H19 on chr=12; Num_of_Contigs=13; )
C17orf79		ENSSSCG00000017746	12:40879384-40886183		FP089481,CH242-212P22,12:40732922-40899579 (Clone quality: bE212P22 on chr=12; Num_of_Contigs=1; )
C17orf80		ENSSSCG00000017246	12:5822129-5832401	CU929672,CH242-62J22,12:5703604-5857364 (Clone quality: bE62J22 on chr=12; Num_of_Contigs=4; )
C17orf85		ENSSSCG00000017870	12:47162456-47194019
C17orf87		ENSSSCG00000017896	12:48896971-48945264
C17orf97		ENSSSCG00000017814	12:45240306-45243211		CU929257,CH242-474H6,12:45237324-45248153 (Clone quality: bE474H6 on chr=12; Num_of_Contigs=7; )
C18orf12		ENSSSCG00000015076	9:43344338-43344592		CU633260,CH242-267D22,9:43344283-43365992 (Clone quality: bE267D22 on chr=9; Num_of_Contigs=9; )
C18orf22		ENSSSCG00000005773	1:290810029-290825625
C18orf24		ENSSSCG00000004518	1:103005528-103072722
C18orf24		location ⇒	13:136335791-136335721		CU927949,CH242-237L3,13:136311182-136433862 (Clone quality: bE237L3 on chr=13; Num_of_Contigs=3; )
C18orf24		location ⇒	13:65121233-65121359		CU469155,CH242-385D18,13:65098963-65184725 (Clone quality: bE385D18 on chr=13; Num_of_Contigs=8; )
C18orf24		location ⇒	13:69135269-69135208		FP085534,CH242-399F17,13:69085421-69144435 (Clone quality: bE399F17 on chr=13; Num_of_Contigs=12; )
C18orf25		ENSSSCG00000004500	1:99827399-99872158
C18orf34		ENSSSCG00000003735	6:81241546-81275322
C18orf51		ENSSSCG00000004871	1:157088902-157095025		CU862032,CH242-156K20,1:157088901-157095237 (Clone quality: bE156K20 on chr=1; Num_of_Contigs=4; )
C18orf54		ENSSSCG00000004531	1:106719232-106740820		CU694517,CH242-313D11,1:106640135-106799320 (Clone quality: bE313D11 on chr=1; Num_of_Contigs=2; )
C18orf55		ENSSSCG00000004872	1:157105544-157105849		CU571232,CH242-48P10,1:157100238-157122969 (Clone quality: bE48P10 on chr=1; Num_of_Contigs=3; )
C18orf58		ENSSSCG00000003677	6:66842185-66890558		CU856282,CH242-55M10,6:66829980-66896155 (Clone quality: bE55M10 on chr=6; Num_of_Contigs=3; )
C18orf8		ENSSSCG00000003706	6:73760861-73762371		CU657945,CH242-224H7,6:73760605-73773583 (Clone quality: bE224H7 on chr=6; Num_of_Contigs=4; )
C19orf12		ENSSSCG00000002853	6:26928394-26928561		FP102582,CH242-162B21,6:26923178-26929728 (Clone quality: bE162B21 on chr=6; Num_of_Contigs=12; )

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).