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)

CHCHD3		ENSSSCG00000016545	18:14416787-14713845
CHCHD4		ENSSSCG00000011604	13:58620612-58631854		CU633560,CH242-223L17,13:58606695-58635414 (Clone quality: bE223L17 on chr=13; Num_of_Contigs=4; )
CHCHD5		ENSSSCG00000008094	3:39228065-39233621		CU468646,CH242-150P16,3:39220626-39238675 (Clone quality: bE150P16 on chr=3; Num_of_Contigs=14; )
CHCHD7		ENSSSCG00000006246	4:78537159-78539793		CU462960,CH242-392H23,4:78478849-78542797 (Clone quality: bE392H23 on chr=4; Num_of_Contigs=4; )
CHCHD8		ENSSSCG00000014830	9:7961136-7961390		CU855642,CH242-23A3,9:7946296-8000820 (Clone quality: bE23A3 on chr=9; Num_of_Contigs=4; )
CHD1		ENSSSCG00000014177	2:94230594-94317877
CHD1L		ENSSSCG00000006701	4:104380357-104431888		CU462855,CH242-55M18,4:104356215-104442546 (Clone quality: bE55M18 on chr=4; Num_of_Contigs=3; )
CHD1L		location ⇒	4:104391543-104391489		CU462855,CH242-55M18,4:104356215-104442546 (Clone quality: bE55M18 on chr=4; Num_of_Contigs=3; )
CHD1L		location ⇒	4:104392505-104392355		CU462855,CH242-55M18,4:104356215-104442546 (Clone quality: bE55M18 on chr=4; Num_of_Contigs=3; )
CHD1L		location ⇒	4:104412855-104412697		CU462855,CH242-55M18,4:104356215-104442546 (Clone quality: bE55M18 on chr=4; Num_of_Contigs=3; )
CHD1L		location ⇒	4:104414750-104414585		CU462855,CH242-55M18,4:104356215-104442546 (Clone quality: bE55M18 on chr=4; Num_of_Contigs=3; )
CHD2		ENSSSCG00000002266	7:96129112-96309994
CHD3		ENSSSCG00000017976	12:50303676-50325223
CHD4		ENSSSCG00000000697	5:60075744-60108307
CHD5		ENSSSCG00000003366	6:45332620-45728863
CHD6		ENSSSCG00000007360	17:46158657-46392227
CHD7		ENSSSCG00000006231	4:75164367-75284941		CU179734,CH242-121P2,4:75134250-75287035 (Clone quality: bE121P2 on chr=4; Num_of_Contigs=1; )
CHD8		ENSSSCG00000002116	7:84151689-84178473
CHDH		ENSSSCG00000011456	13:30150698-30160652		CU466421,CH242-96K10,13:30111067-30195183 (Clone quality: bE96K10 on chr=13; Num_of_Contigs=2; )
CHEK1		ENSSSCG00000015215	9:51316196-51347188		CU694782,CH242-247G18,9:51267226-51364229 (Clone quality: bE247G18 on chr=9; Num_of_Contigs=6; )
CHERP		ENSSSCG00000013860	2:61080544-61096211
CHESS1		location ⇒	7:118914812-118914434		CT737419,CH242-216C24,7:118868952-118963392 (Clone quality: bE216C24 on chr=7; Num_of_Contigs=2; )
CHESS1		location ⇒	7:118915559-118915135		CT737419,CH242-216C24,7:118868952-118963392 (Clone quality: bE216C24 on chr=7; Num_of_Contigs=2; )
CHESS1		location ⇒	7:118916265-118915629		CT737419,CH242-216C24,7:118868952-118963392 (Clone quality: bE216C24 on chr=7; Num_of_Contigs=2; )
CHESS1		location ⇒	7:119148435-119147876		CT824637,CH242-207I17,7:119143221-119152105 (Clone quality: bE207I17 on chr=7; Num_of_Contigs=3; )
CHFR		ENSSSCG00000009732	14:22393578-22422399		CU468405,CH242-25J16,14:22359876-22472183 (Clone quality: bE25J16 on chr=14; Num_of_Contigs=2; )
CHGA		ENSSSCG00000002456	7:122483936-122496243		CU468886,CH242-145B2,7:122436020-122571421 (Clone quality: bE145B2 on chr=7; Num_of_Contigs=2; )
CHGA		location ⇒	7:122483963-122484171		CU468886,CH242-145B2,7:122436020-122571421 (Clone quality: bE145B2 on chr=7; Num_of_Contigs=2; )
CHGA		location ⇒	7:122487386-122487481		CU468886,CH242-145B2,7:122436020-122571421 (Clone quality: bE145B2 on chr=7; Num_of_Contigs=2; )
CHGA		location ⇒	7:122663783-122663991		CU407295,CH242-521B20,7:122649219-122733151 (Clone quality: bE521B20 on chr=7; Num_of_Contigs=24; )
CHGA		location ⇒	7:122667206-122667301		CU407295,CH242-521B20,7:122649219-122733151 (Clone quality: bE521B20 on chr=7; Num_of_Contigs=24; )
CHGB		ENSSSCG00000007045	17:13888688-13898657
CHGB		location ⇒	17:13883998-13883849		CU469266,CH242-271I11,17:13879445-13888410 (Clone quality: bE271I11 on chr=17; Num_of_Contigs=11; )
CHGB		location ⇒	17:13889175-13889271		CU469266,CH242-271I11,17:13888511-13889407 (Clone quality: bE271I11 on chr=17; Num_of_Contigs=11; )
CHGB		location ⇒	17:13894619-13896354		CU311185,CH242-222G18,17:13889408-14007446 (Clone quality: bE222G18 on chr=17; Num_of_Contigs=4; )
CHGB		location ⇒	17:13898259-13898651		CU311185,CH242-222G18,17:13889408-14007446 (Clone quality: bE222G18 on chr=17; Num_of_Contigs=4; )
CHI3L1		ENSSSCG00000015476	9:106887764-106897180
CHI3L1		location ⇒	9:106888404-106887765		CU928698,CH242-36A5,9:106880618-106891574 (Clone quality: bE36A5 on chr=9; Num_of_Contigs=1; )
CHI3L1		location ⇒	9:106889628-106889446		CU928698,CH242-36A5,9:106880618-106891574 (Clone quality: bE36A5 on chr=9; Num_of_Contigs=1; )
CHI3L1		location ⇒	9:106894030-106893877		CU928698,CH242-36A5,9:106891675-106913585 (Clone quality: bE36A5 on chr=9; Num_of_Contigs=1; )
CHI3L1		location ⇒	9:106895524-106895322		CU928698,CH242-36A5,9:106891675-106913585 (Clone quality: bE36A5 on chr=9; Num_of_Contigs=1; )
CHI3L2		ENSSSCG00000006796	4:113510807-113527330		CU468595,CH242-175A23,4:113445124-113550429 (Clone quality: bE175A23 on chr=4; Num_of_Contigs=4; )
CHIA		location ⇒	4:113388917-113388560		CU469152,CH242-313G11,4:113381697-113391527 (Clone quality: bE313G11 on chr=4; Num_of_Contigs=7; )
CHIA		location ⇒	4:113429705-113429647		CU469152,CH242-313G11,4:113414355-113438519 (Clone quality: bE313G11 on chr=4; Num_of_Contigs=7; )
CHIA		location ⇒	4:113463860-113463503		CU468595,CH242-175A23,4:113445124-113550429 (Clone quality: bE175A23 on chr=4; Num_of_Contigs=4; )
CHIA		location ⇒	4:113481863-113481805		CU468595,CH242-175A23,4:113445124-113550429 (Clone quality: bE175A23 on chr=4; Num_of_Contigs=4; )
CHIC1		ENSSSCG00000012416	X:58506025-58542220		CU855548,CH242-76N16,X:58454852-58549293 (Clone quality: bE76N16 on chr=X; Num_of_Contigs=6; )
CHIC2		ENSSSCG00000008839	8:35088374-35142023
CHID1		ENSSSCG00000012837	2:95868-114388		CU928976,CH242-144M19,2:43742-170991 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
CHIT1		ENSSSCG00000015477	9:106930090-106943581		CU928698,CH242-36A5,9:106913686-107009377 (Clone quality: bE36A5 on chr=9; 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).