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)

COL4A6		location ⇒	11:77459009-77459180		CU041289,CH242-99E18,11:77457463-77465791 (Clone quality: bE99E18 on chr=11; Num_of_Contigs=10; )
COL4A6		location ⇒	11:77460210-77460497		CU041289,CH242-99E18,11:77457463-77465791 (Clone quality: bE99E18 on chr=11; Num_of_Contigs=10; )
COL4A6		location ⇒	11:77461641-77461953		CU041289,CH242-99E18,11:77457463-77465791 (Clone quality: bE99E18 on chr=11; Num_of_Contigs=10; )
COL5A1		ENSSSCG00000005750	1:289321453-289449374
COL5A1		location ⇒	1:289443302-289443358		FP016072,CH242-144F6,1:289443189-289450815 (Clone quality: bE144F6 on chr=1; Num_of_Contigs=5; )
COL5A1		location ⇒	1:289471409-289471359		FP016072,CH242-144F6,1:289453212-289481674 (Clone quality: bE144F6 on chr=1; Num_of_Contigs=5; )
COL5A1		location ⇒	1:289615742-289615687		FP016072,CH242-144F6,1:289607290-289615782 (Clone quality: bE144F6 on chr=1; Num_of_Contigs=5; )
COL5A1		location ⇒	1:289633282-289633230		FP016072,CH242-144F6,1:289628444-289633282 (Clone quality: bE144F6 on chr=1; Num_of_Contigs=5; )
COL5A2		ENSSSCG00000016035	15:88097765-88149761		CU467671,CH242-14N12,15:88029080-88150714 (Clone quality: bE14N12 on chr=15; Num_of_Contigs=4; )
COL5A2		location ⇒	15:88098306-88097562		CU467671,CH242-14N12,15:88029080-88150714 (Clone quality: bE14N12 on chr=15; Num_of_Contigs=4; )
COL5A2		location ⇒	15:88099223-88098982		CU467671,CH242-14N12,15:88029080-88150714 (Clone quality: bE14N12 on chr=15; Num_of_Contigs=4; )
COL5A2		location ⇒	15:88102026-88101838		CU467671,CH242-14N12,15:88029080-88150714 (Clone quality: bE14N12 on chr=15; Num_of_Contigs=4; )
COL5A2		location ⇒	15:88103901-88103601		CU467671,CH242-14N12,15:88029080-88150714 (Clone quality: bE14N12 on chr=15; Num_of_Contigs=4; )
COL5A3		ENSSSCG00000013667	2:53494963-53531846
COL5A3		location ⇒	2:53495072-53495233		CU694567,CH242-210G21,2:53494964-53520973 (Clone quality: bE210G21 on chr=2; Num_of_Contigs=8; )
COL5A3		location ⇒	2:53525359-53525567		CU694567,CH242-210G21,2:53521074-53557390 (Clone quality: bE210G21 on chr=2; Num_of_Contigs=8; )
COL5A3		location ⇒	2:53530882-53531123		CU694567,CH242-210G21,2:53521074-53557390 (Clone quality: bE210G21 on chr=2; Num_of_Contigs=8; )
COL5A3		location ⇒	2:53531216-53531846		CU694567,CH242-210G21,2:53521074-53557390 (Clone quality: bE210G21 on chr=2; Num_of_Contigs=8; )
COL6A3		location ⇒	15:129497298-129496644		CU570741,CH242-330M24,15:129495865-129527332 (Clone quality: bE330M24 on chr=15; Num_of_Contigs=4; )
COL6A3		location ⇒	15:129509438-129509174		CU570741,CH242-330M24,15:129495865-129527332 (Clone quality: bE330M24 on chr=15; Num_of_Contigs=4; )
COL6A3		location ⇒	15:129511287-129510890		CU570741,CH242-330M24,15:129495865-129527332 (Clone quality: bE330M24 on chr=15; Num_of_Contigs=4; )
COL6A3		location ⇒	15:129515948-129515408		CU570741,CH242-330M24,15:129495865-129527332 (Clone quality: bE330M24 on chr=15; Num_of_Contigs=4; )
COL7A1		ENSSSCG00000011355	13:26165472-26197263		CU633242,CH242-208G16,13:26093504-26215489 (Clone quality: bE208G16 on chr=13; Num_of_Contigs=5; )
COL7A1		location ⇒	13:26194819-26194574		CU633242,CH242-208G16,13:26093504-26215489 (Clone quality: bE208G16 on chr=13; Num_of_Contigs=5; )
COL8A1		ENSSSCG00000011973	13:117279151-117464309
COL8A1		location ⇒	13:117279150-117279680		CU463088,CH242-434O16,13:117216921-117333948 (Clone quality: bE434O16 on chr=13; Num_of_Contigs=2; )
COL8A2		ENSSSCG00000003635	6:62572235-62575956
COL9A1		ENSSSCG00000004274	1:52902061-52966690
COL9A1		location ⇒	1:52904842-52904915		FP016097,CH242-222D20,1:52891223-52937884 (Clone quality: bE222D20 on chr=1; Num_of_Contigs=5; )
COL9A1		location ⇒	1:52910039-52910094		FP016097,CH242-222D20,1:52891223-52937884 (Clone quality: bE222D20 on chr=1; Num_of_Contigs=5; )
COL9A1		location ⇒	1:52910197-52910253		FP016097,CH242-222D20,1:52891223-52937884 (Clone quality: bE222D20 on chr=1; Num_of_Contigs=5; )
COL9A1		location ⇒	1:52912982-52913037		FP016097,CH242-222D20,1:52891223-52937884 (Clone quality: bE222D20 on chr=1; Num_of_Contigs=5; )
coll-4		ENSSSCG00000009584	14:1167125-1208885		CU469368,CH242-181M10,14:1134838-1275802 (Clone quality: bE181M10 on chr=14; Num_of_Contigs=3; )
COMMD1		ENSSSCG00000008376	3:73327013-73467229
COMMD10		ENSSSCG00000014223	2:108943224-109132414
COMMD2		ENSSSCG00000011705	13:73279530-73286464		CU915458,CH242-198A13,13:73208094-73314403 (Clone quality: bE198A13 on chr=13; Num_of_Contigs=5; )
COMMD3		ENSSSCG00000011082	10:50114378-50118369		CU855495,CH242-193A5,10:50112956-50191194 (Clone quality: bE193A5 on chr=10; Num_of_Contigs=4; )
COMMD7		ENSSSCG00000007251	17:38216545-38220001		CU469238,CH242-509F7,17:38206321-38220274 (Clone quality: bE509F7 on chr=17; Num_of_Contigs=14; )
COMMD8		ENSSSCG00000008811	8:32051206-32061483		CU469276,CH242-360F6,8:32027914-32071691 (Clone quality: bE360F6 on chr=8; Num_of_Contigs=16; )
COMMD9		ENSSSCG00000013293	2:23470429-23489724	CU928703,CH242-486C6,2:23404536-23611467 (Clone quality: bE486C6 on chr=2; Num_of_Contigs=3; )
COMP		ENSSSCG00000013916	2:62816352-62971603
COMP		location ⇒	2:62818279-62818092		CU914263,CH242-289B6,2:62670241-62856330 (Clone quality: bE289B6 on chr=2; Num_of_Contigs=2; )
COMP		location ⇒	2:62966000-62965813		CU928669,CH242-407A11,2:62947668-62996424 (Clone quality: bE407A11 on chr=2; Num_of_Contigs=14; )
COMP		location ⇒	2:77973710-77973584		CU914717,CH242-399K18,2:77934120-77977420 (Clone quality: bE399K18 on chr=2; Num_of_Contigs=12; )
COMP		location ⇒	2:77985709-77985835		CU929852,CH242-88F3,2:77980519-77993250 (Clone quality: bE88F3 on chr=2; Num_of_Contigs=12; )
COMT		ENSSSCG00000010132	14:52639564-52656710		CT737290,CH242-153A5,14:52550615-52684021 (Clone quality: bE153A5 on chr=14; Num_of_Contigs=5; )
COMTD1		ENSSSCG00000010321	14:81000719-81002728		CU407134,CH242-119B10,14:80999978-81033330 (Clone quality: bE119B10 on chr=14; Num_of_Contigs=8; )
COP1		ENSSSCG00000015509	9:110873524-111071949
COP1		location ⇒	9:110998094-110998018		CU855662,CH242-3H1,9:110982843-111000900 (Clone quality: bE3H1 on chr=9; Num_of_Contigs=5; )
COP1		location ⇒	9:111009155-111009058		CU638728,CH242-5J14,9:111000901-111067851 (Clone quality: bE5J14 on chr=9; Num_of_Contigs=2; )

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).