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)

CNTROB		ENSSSCG00000017968	12:50169413-50422040
COASY		ENSSSCG00000017398	12:17815100-17819507		FP016109,CH242-242A5,12:17788506-17858714 (Clone quality: bE242A5 on chr=12; Num_of_Contigs=4; )
COBLL1		ENSSSCG00000015902	15:66438764-66637142
COBRA1		ENSSSCG00000005846	1:294329079-294336799		CU928955,CH242-34I15,1:294322778-294354935 (Clone quality: bE34I15 on chr=1; Num_of_Contigs=4; )
COCH		location ⇒	9:118368738-118368646		CU929515,CH242-277D8,9:118353536-118369861 (Clone quality: bE277D8 on chr=9; Num_of_Contigs=5; )
COG1		ENSSSCG00000017248	12:5857481-5872333		CU466404,CH242-455N10,12:5857365-5908364 (Clone quality: bE455N10 on chr=12; Num_of_Contigs=7; )
COG2		ENSSSCG00000010183	14:62006500-62040103		CU468914,CH242-84B3,14:62004957-62047223 (Clone quality: bE84B3 on chr=14; Num_of_Contigs=14; )
COG5		ENSSSCG00000015441	9:100183270-100365315
COG7		ENSSSCG00000010799	10:171630-185823		CU929008,CH242-207N16,10:137774-191372 (Clone quality: bE207N16 on chr=10; Num_of_Contigs=6; )
COG8		ENSSSCG00000002759	6:12473081-12479917		FP015939,CH242-384D23,6:12465602-12559923 (Clone quality: bE384D23 on chr=6; Num_of_Contigs=2; )
COIL		ENSSSCG00000017613	12:30970298-30981372		FP245413,CH242-143I10,12:30969549-30983123 (Clone quality: bE143I10 on chr=12; Num_of_Contigs=14; )
COL10A1		ENSSSCG00000004436	1:85743574-85750572		CU062641,CH242-133O6,1:85642635-85794341 (Clone quality: bE133O6 on chr=1; Num_of_Contigs=1; )
COL10A1		location ⇒	1:85745446-85743574		CU062641,CH242-133O6,1:85642635-85794341 (Clone quality: bE133O6 on chr=1; Num_of_Contigs=1; )
COL10A1		location ⇒	1:85749876-85749699		CU062641,CH242-133O6,1:85642635-85794341 (Clone quality: bE133O6 on chr=1; Num_of_Contigs=1; )
COL10A1		location ⇒	1:85750572-85750491		CU062641,CH242-133O6,1:85642635-85794341 (Clone quality: bE133O6 on chr=1; Num_of_Contigs=1; )
COL11A1		ENSSSCG00000006857	4:120628176-120831557
COL11A2		ENSSSCG00000001473	7:29580939-29610542	CT737383,CH242-215D15,7:29573904-29764538 (Clone quality: bE215D15 on chr=7; Num_of_Contigs=3; )
COL12A1		ENSSSCG00000004484	1:95859639-95990154
COL12A1		location ⇒	1:95979775-95979848		CU302424,CH242-266B2,1:95948626-96021907 (Clone quality: bE266B2 on chr=1; Num_of_Contigs=2; )
COL12A1		location ⇒	1:95984654-95984845		CU302424,CH242-266B2,1:95948626-96021907 (Clone quality: bE266B2 on chr=1; Num_of_Contigs=2; )
COL12A1		location ⇒	1:95987227-95987399		CU302424,CH242-266B2,1:95948626-96021907 (Clone quality: bE266B2 on chr=1; Num_of_Contigs=2; )
COL12A1		location ⇒	1:95989595-95989668		CU302424,CH242-266B2,1:95948626-96021907 (Clone quality: bE266B2 on chr=1; Num_of_Contigs=2; )
COL13A1		ENSSSCG00000010256	14:75801525-75890517		CT990472,CH242-325O12,14:75752136-75928284 (Clone quality: bE325O12 on chr=14; Num_of_Contigs=1; )
COL14A1		ENSSSCG00000005997	4:18341932-18616105
COL14A1		location ⇒	4:18431658-18431498		CU302271,CH242-266K8,4:18327232-18456403 (Clone quality: bE266K8 on chr=4; Num_of_Contigs=2; )
COL14A1		location ⇒	4:18436320-18436211		CU302271,CH242-266K8,4:18327232-18456403 (Clone quality: bE266K8 on chr=4; Num_of_Contigs=2; )
COL14A1		location ⇒	4:18439234-18439092		CU302271,CH242-266K8,4:18327232-18456403 (Clone quality: bE266K8 on chr=4; Num_of_Contigs=2; )
COL14A1		location ⇒	4:18443987-18443847		CU302271,CH242-266K8,4:18327232-18456403 (Clone quality: bE266K8 on chr=4; Num_of_Contigs=2; )
COL15A1		ENSSSCG00000005380	1:252356422-252431941
COL15A1		ENSSSCG00000005381	1:252417491-252425102		CU571046,CH242-46J18,1:252392469-252425614 (Clone quality: bE46J18 on chr=1; Num_of_Contigs=4; )
COL15A1		location ⇒	1:252417952-252418196		CU571046,CH242-46J18,1:252392469-252425614 (Clone quality: bE46J18 on chr=1; Num_of_Contigs=4; )
COL15A1		location ⇒	1:252419521-252419639		CU571046,CH242-46J18,1:252392469-252425614 (Clone quality: bE46J18 on chr=1; Num_of_Contigs=4; )
COL15A1		location ⇒	1:252420862-252421048		CU571046,CH242-46J18,1:252392469-252425614 (Clone quality: bE46J18 on chr=1; Num_of_Contigs=4; )
COL15A1		location ⇒	1:252425041-252425095		CU571046,CH242-46J18,1:252392469-252425614 (Clone quality: bE46J18 on chr=1; Num_of_Contigs=4; )
COL16A1		ENSSSCG00000003603	6:60474036-60526973
COL16A1		location ⇒	6:60474415-60474123		CU856262,CH242-97A12,6:60434458-60488383 (Clone quality: bE97A12 on chr=6; Num_of_Contigs=8; )
COL16A1		location ⇒	6:60475535-60475454		CU856262,CH242-97A12,6:60434458-60488383 (Clone quality: bE97A12 on chr=6; Num_of_Contigs=8; )
COL16A1		location ⇒	6:60475871-60475693		CU856262,CH242-97A12,6:60434458-60488383 (Clone quality: bE97A12 on chr=6; Num_of_Contigs=8; )
COL16A1		location ⇒	6:60477135-60477018		CU856262,CH242-97A12,6:60434458-60488383 (Clone quality: bE97A12 on chr=6; Num_of_Contigs=8; )
COL17A1		ENSSSCG00000010607	14:120066639-120108932
COL17A1		location ⇒	14:120086507-120086441		CT737413,CH242-152J3,14:120085580-120213865 (Clone quality: bE152J3 on chr=14; Num_of_Contigs=2; )
COL17A1		location ⇒	14:120087390-120087284		CT737413,CH242-152J3,14:120085580-120213865 (Clone quality: bE152J3 on chr=14; Num_of_Contigs=2; )
COL17A1		location ⇒	14:120088075-120088011		CT737413,CH242-152J3,14:120085580-120213865 (Clone quality: bE152J3 on chr=14; Num_of_Contigs=2; )
COL17A1		location ⇒	14:120090622-120090405		CT737413,CH242-152J3,14:120085580-120213865 (Clone quality: bE152J3 on chr=14; Num_of_Contigs=2; )
COL19A1		ENSSSCG00000004273	1:52527875-52866036
COL19A1		location ⇒	1:52580551-52580679		CU074296,CH242-137L19,1:52548617-52730097 (Clone quality: bE137L19 on chr=1; Num_of_Contigs=1; )
COL19A1		location ⇒	1:52581760-52581825		CU074296,CH242-137L19,1:52548617-52730097 (Clone quality: bE137L19 on chr=1; Num_of_Contigs=1; )
COL19A1		location ⇒	1:52590119-52590176		CU074296,CH242-137L19,1:52548617-52730097 (Clone quality: bE137L19 on chr=1; Num_of_Contigs=1; )
COL1A1		location ⇒	12:24685448-24685382		CU694879,CH242-301O20,12:24681689-24690254 (Clone quality: bE301O20 on chr=12; Num_of_Contigs=13; )
COL1A1		location ⇒	12:24686520-24686469		CU694879,CH242-301O20,12:24681689-24690254 (Clone quality: bE301O20 on chr=12; 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).