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)

CNR1		ENSSSCG00000004309	1:59197960-59199378		CU041250,CH242-413G10,1:59191669-59220084 (Clone quality: bE413G10 on chr=1; Num_of_Contigs=3; )
CNR1		location ⇒	15:94752752-94751893		CU694717,CH242-333N16,15:94748967-94763904 (Clone quality: bE333N16 on chr=15; Num_of_Contigs=10; )
CNRIP1		ENSSSCG00000008349	3:67914323-67938436
CNTD2		ENSSSCG00000002990	6:33567315-33570567		FP102369,CH242-128M4,6:33567029-33575618 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CNTF		ENSSSCG00000013154	2:10604681-10606545		CU929527,CH242-208E7,2:10603479-10641058 (Clone quality: bE208E7 on chr=2; Num_of_Contigs=8; )
CNTFR		location ⇒	10:30664007-30663893		CU928717,CH242-142N10,10:30648624-30667274 (Clone quality: bE142N10 on chr=10; Num_of_Contigs=7; )
CNTFR		location ⇒	10:30681063-30680829		CU928717,CH242-142N10,10:30667375-30714234 (Clone quality: bE142N10 on chr=10; Num_of_Contigs=7; )
CNTFR		location ⇒	10:30689444-30689348		CU928717,CH242-142N10,10:30667375-30714234 (Clone quality: bE142N10 on chr=10; Num_of_Contigs=7; )
CNTFR		location ⇒	10:30796432-30796666		CU571264,CH242-10D18,10:30778361-30801430 (Clone quality: bE10D18 on chr=10; Num_of_Contigs=8; )
CNTLN		ENSSSCG00000005178	1:214264832-214450132
CNTN1		location ⇒	5:68632955-68632515		CU914199,CH242-282N16,5:68625417-68686461 (Clone quality: bE282N16 on chr=5; Num_of_Contigs=1; )
CNTN1		location ⇒	5:68658804-68658642		CU914199,CH242-282N16,5:68625417-68686461 (Clone quality: bE282N16 on chr=5; Num_of_Contigs=1; )
CNTN1		location ⇒	5:68659692-68659577		CU914199,CH242-282N16,5:68625417-68686461 (Clone quality: bE282N16 on chr=5; Num_of_Contigs=1; )
CNTN1		location ⇒	5:68662222-68662140		CU914199,CH242-282N16,5:68625417-68686461 (Clone quality: bE282N16 on chr=5; Num_of_Contigs=1; )
CNTN3		ENSSSCG00000011522	13:47203381-47293508
CNTN3		location ⇒	13:47203540-47203646		FP085479,CH242-132G16,13:47186417-47234157 (Clone quality: bE132G16 on chr=13; Num_of_Contigs=6; )
CNTN3		location ⇒	13:47205870-47206038		FP085479,CH242-132G16,13:47186417-47234157 (Clone quality: bE132G16 on chr=13; Num_of_Contigs=6; )
CNTN3		location ⇒	13:47207168-47207282		FP085479,CH242-132G16,13:47186417-47234157 (Clone quality: bE132G16 on chr=13; Num_of_Contigs=6; )
CNTN3		location ⇒	13:47220992-47221141		FP085479,CH242-132G16,13:47186417-47234157 (Clone quality: bE132G16 on chr=13; Num_of_Contigs=6; )
CNTN4		ENSSSCG00000011527	13:50005585-50199487
CNTN4		location ⇒	13:49806460-49806657		FP236701,CH242-208L22,13:49774553-49814146 (Clone quality: bE208L22 on chr=13; Num_of_Contigs=8; )
CNTN4		location ⇒	13:49870783-49870919		CU464152,CH242-23K12,13:49814147-49998505 (Clone quality: bE23K12 on chr=13; Num_of_Contigs=1; )
CNTN4		location ⇒	13:49878115-49878292		CU464152,CH242-23K12,13:49814147-49998505 (Clone quality: bE23K12 on chr=13; Num_of_Contigs=1; )
CNTN4		location ⇒	13:49957821-49959145		CU464152,CH242-23K12,13:49814147-49998505 (Clone quality: bE23K12 on chr=13; Num_of_Contigs=1; )
CNTN5		ENSSSCG00000014975	9:30901742-31339970
CNTN5		location ⇒	9:30979466-30979556		CU856300,CH242-117F18,9:30975408-30989361 (Clone quality: bE117F18 on chr=9; Num_of_Contigs=9; )
CNTN5		location ⇒	9:31018810-31019018		CU856300,CH242-117F18,9:30989462-31075892 (Clone quality: bE117F18 on chr=9; Num_of_Contigs=9; )
CNTN5		location ⇒	9:31049544-31049647		CU856300,CH242-117F18,9:30989462-31075892 (Clone quality: bE117F18 on chr=9; Num_of_Contigs=9; )
CNTN5		location ⇒	9:31085750-31085931		CU463821,CH242-472H10,9:31075893-31259709 (Clone quality: bE472H10 on chr=9; Num_of_Contigs=1; )
CNTN6		ENSSSCG00000011526	13:48776113-48800941
CNTN6		location ⇒	13:48759829-48759692		CU914399,CH242-123I22,13:48756880-48761391 (Clone quality: bE123I22 on chr=13; Num_of_Contigs=11; )
CNTN6		location ⇒	13:48786767-48786883		CU463264,CH242-212I11,13:48780514-48967199 (Clone quality: bE212I11 on chr=13; Num_of_Contigs=1; )
CNTN6		location ⇒	13:48788141-48788329		CU463264,CH242-212I11,13:48780514-48967199 (Clone quality: bE212I11 on chr=13; Num_of_Contigs=1; )
CNTN6		location ⇒	13:48799605-48799742		CU463264,CH242-212I11,13:48780514-48967199 (Clone quality: bE212I11 on chr=13; Num_of_Contigs=1; )
CNTNAP1		location ⇒	12:17725744-17725869		CU928483,CH242-17I6,12:17706452-17731169 (Clone quality: bE17I6 on chr=12; Num_of_Contigs=8; )
CNTNAP1		location ⇒	12:17726463-17726648		CU928483,CH242-17I6,12:17706452-17731169 (Clone quality: bE17I6 on chr=12; Num_of_Contigs=8; )
CNTNAP1		location ⇒	12:17727157-17727303		CU928483,CH242-17I6,12:17706452-17731169 (Clone quality: bE17I6 on chr=12; Num_of_Contigs=8; )
CNTNAP1		location ⇒	12:17728119-17728214		CU928483,CH242-17I6,12:17706452-17731169 (Clone quality: bE17I6 on chr=12; Num_of_Contigs=8; )
CNTNAP2		ENSSSCG00000015461	9:103588911-103598013		CU928674,CH242-509J10,9:103580756-103606953 (Clone quality: bE509J10 on chr=9; Num_of_Contigs=7; )
CNTNAP2		location ⇒	9:102341614-102341373		CU928439,CH242-395F22,9:102317790-102353628 (Clone quality: bE395F22 on chr=9; Num_of_Contigs=1; )
CNTNAP2		location ⇒	9:102377488-102377384		CU928439,CH242-395F22,9:102353729-102410155 (Clone quality: bE395F22 on chr=9; Num_of_Contigs=1; )
CNTNAP4		location ⇒	6:8130074-8129879		FP015886,CH242-157P8,6:8114431-8216154 (Clone quality: bE157P8 on chr=6; Num_of_Contigs=3; )
CNTNAP4		location ⇒	6:8182943-8182852		FP015886,CH242-157P8,6:8114431-8216154 (Clone quality: bE157P8 on chr=6; Num_of_Contigs=3; )
CNTNAP4		location ⇒	6:8218473-8218345		FP015886,CH242-157P8,6:8216255-8220500 (Clone quality: bE157P8 on chr=6; Num_of_Contigs=3; )
CNTNAP4		location ⇒	6:8218800-8218686		FP015886,CH242-157P8,6:8216255-8220500 (Clone quality: bE157P8 on chr=6; Num_of_Contigs=3; )
CNTNAP5		location ⇒	15:25262707-25262774		CU856257,CH242-116G4,15:25150410-25332167 (Clone quality: bE116G4 on chr=15; Num_of_Contigs=1; )
CNTNAP5		location ⇒	15:25634590-25634419		CU571099,CH242-125N14,15:25589730-25669429 (Clone quality: bE125N14 on chr=15; Num_of_Contigs=4; )
CNTNAP5		location ⇒	15:25658988-25658726		CU571099,CH242-125N14,15:25589730-25669429 (Clone quality: bE125N14 on chr=15; Num_of_Contigs=4; )
CNTNAP5		location ⇒	15:26188048-26187745		CU571193,CH242-158F4,15:26010452-26191819 (Clone quality: bE158F4 on chr=15; Num_of_Contigs=1; )
CNTNAP5a		location ⇒	15:25257009-25256791		CU856257,CH242-116G4,15:25150410-25332167 (Clone quality: bE116G4 on chr=15; Num_of_Contigs=1; )

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).