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)

CFD		location ⇒	2:46147751-46147884		FP015903,CH242-504E7,2:46128360-46188530 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
CFDP1		ENSSSCG00000002711	6:8894416-9010084
CFH		ENSSSCG00000010893	10:20931114-21000738
CFH		location ⇒	10:20949337-20949524		CU570835,CH242-258F22,10:20918446-20959904 (Clone quality: bE258F22 on chr=10; Num_of_Contigs=4; )
CFH		location ⇒	10:20956383-20956577		CU570835,CH242-258F22,10:20918446-20959904 (Clone quality: bE258F22 on chr=10; Num_of_Contigs=4; )
CFH		location ⇒	10:20970687-20970876		CU570835,CH242-258F22,10:20960005-21004045 (Clone quality: bE258F22 on chr=10; Num_of_Contigs=4; )
CFH		location ⇒	10:20989857-20990044		CU570835,CH242-258F22,10:20960005-21004045 (Clone quality: bE258F22 on chr=10; Num_of_Contigs=4; )
CFHR3		location ⇒	10:20979296-20979393		CU570835,CH242-258F22,10:20960005-21004045 (Clone quality: bE258F22 on chr=10; Num_of_Contigs=4; )
CFHR4		location ⇒	10:20979237-20979393		CU570835,CH242-258F22,10:20960005-21004045 (Clone quality: bE258F22 on chr=10; Num_of_Contigs=4; )
CFI		ENSSSCG00000009138	8:96596051-96633160		CU463265,CH242-237G17,8:96455649-96640359 (Clone quality: bE237G17 on chr=8; Num_of_Contigs=1; )
CFL1		ENSSSCG00000012974	2:4873775-4876747		CU856129,CH242-95H3,2:4866849-4898129 (Clone quality: bE95H3 on chr=2; Num_of_Contigs=5; )
CFL2		ENSSSCG00000001959	7:70881120-70885365		CT842119,CH242-155B15,7:70879109-70897503 (Clone quality: bE155B15 on chr=7; Num_of_Contigs=2; )
CFLAR		ENSSSCG00000016101	15:98529731-98558003		CU607103,CH242-8O23,15:98528637-98560423 (Clone quality: bE8O23 on chr=15; Num_of_Contigs=7; )
CFLAR		location ⇒	15:98495500-98495833		CU607103,CH242-8O23,15:98494284-98503382 (Clone quality: bE8O23 on chr=15; Num_of_Contigs=7; )
CFLAR		location ⇒	15:98529942-98529835		CU607103,CH242-8O23,15:98528637-98560423 (Clone quality: bE8O23 on chr=15; Num_of_Contigs=7; )
CFLAR		location ⇒	15:98532269-98532132		CU607103,CH242-8O23,15:98528637-98560423 (Clone quality: bE8O23 on chr=15; Num_of_Contigs=7; )
CFLAR		location ⇒	15:98533598-98533269		CU607103,CH242-8O23,15:98528637-98560423 (Clone quality: bE8O23 on chr=15; Num_of_Contigs=7; )
CFP		ENSSSCG00000012278	X:42114188-42120897		FP015952,CH242-69I19,X:42111786-42120976 (Clone quality: bE69I19 on chr=X; Num_of_Contigs=6; )
CFTR		ENSSSCG00000013378	2:38991417-39078510
CFTR		ENSSSCG00000016626	18:27082563-27318358
CFTR		ENSSSCG00000010543	14:115716020-115793964
CFTR		ENSSSCG00000007874	3:25657262-25744405
CFTR		ENSSSCG00000006693	4:103708512-103740596		CU467072,CH242-100P4,4:103582921-103758989 (Clone quality: bE100P4 on chr=4; Num_of_Contigs=2; )
CFTR		ENSSSCG00000004253	1:46179458-46223177		CU694620,CH242-40E16,1:46176101-46306057 (Clone quality: bE40E16 on chr=1; Num_of_Contigs=3; )
CFTR		ENSSSCG00000000575	5:49779572-49787960		CU633289,CH242-396D5,5:49776296-49788272 (Clone quality: bE396D5 on chr=5; Num_of_Contigs=9; )
CFTR		location ⇒	18:27164022-27163767		CU655902,CH242-168J2,18:27158406-27228869 (Clone quality: bE168J2 on chr=18; Num_of_Contigs=6; )
CFTR		location ⇒	18:27196850-27196600		CU655902,CH242-168J2,18:27158406-27228869 (Clone quality: bE168J2 on chr=18; Num_of_Contigs=6; )
CFTR		location ⇒	18:27208094-27207363		CU655902,CH242-168J2,18:27158406-27228869 (Clone quality: bE168J2 on chr=18; Num_of_Contigs=6; )
CFTR		location ⇒	18:27257096-27256849		CU570831,CH242-248P18,18:27255622-27312951 (Clone quality: bE248P18 on chr=18; Num_of_Contigs=3; )
CGA		ENSSSCG00000004297	1:58190063-58192283		CU302429,CH242-523A23,1:58130259-58329718 (Clone quality: bE523A23 on chr=1; Num_of_Contigs=1; )
CGA		ENSSSCG00000002456	7:122483936-122496243		CU468886,CH242-145B2,7:122436020-122571421 (Clone quality: bE145B2 on chr=7; Num_of_Contigs=2; )
CGA		location ⇒	1:58190430-58190351		CU302429,CH242-523A23,1:58130259-58329718 (Clone quality: bE523A23 on chr=1; Num_of_Contigs=1; )
CGA		location ⇒	1:58191067-58190881		CU302429,CH242-523A23,1:58130259-58329718 (Clone quality: bE523A23 on chr=1; Num_of_Contigs=1; )
CGA		location ⇒	1:58192283-58192183		CU302429,CH242-523A23,1:58130259-58329718 (Clone quality: bE523A23 on chr=1; Num_of_Contigs=1; )
CGB		ENSSSCG00000007045	17:13888688-13898657
CGB		location ⇒	6:37754573-37754747		FP102974,CH242-517N5,6:37749269-37760175 (Clone quality: bE517N5 on chr=6; Num_of_Contigs=15; )
CGB		location ⇒	6:37755034-37755277		FP102974,CH242-517N5,6:37749269-37760175 (Clone quality: bE517N5 on chr=6; Num_of_Contigs=15; )
CGN		ENSSSCG00000006621	4:101660178-101678072	CU457720,CH242-246P6,4:101656497-101737893 (Clone quality: bE246P6 on chr=4; Num_of_Contigs=11; )
CGNL1		ENSSSCG00000004599	1:118494279-118605598
CGREF1		ENSSSCG00000008555	3:104442887-104525095
CGRRF1		ENSSSCG00000005049	1:192489460-192490113		CU407279,CH242-502I9,1:192488957-192491048 (Clone quality: bE502I9 on chr=1; Num_of_Contigs=21; )
CH25H		ENSSSCG00000010449	14:106023219-106024031	CT737339,CH242-154E22,14:105909176-106037305 (Clone quality: bE154E22 on chr=14; Num_of_Contigs=1; )
CHAC1		ENSSSCG00000004754	1:136793968-136852983
CHAC2		ENSSSCG00000008416	3:81305159-81315051
CHAD		ENSSSCG00000016689	18:42148455-42150884		CU640410,CH242-280G23,18:42123022-42293146 (Clone quality: bE280G23 on chr=18; Num_of_Contigs=1; )
CHADL		ENSSSCG00000000067	5:3656182-3664850		CU407312,CH242-137N12,5:3622530-3679649 (Clone quality: bE137N12 on chr=5; Num_of_Contigs=3; )
CHAF1A		ENSSSCG00000013509	2:48617722-48648678		CU972396,CH242-401E10,2:48541506-48658119 (Clone quality: bE401E10 on chr=2; Num_of_Contigs=4; )
CHAF1B		ENSSSCG00000012056	13:140478012-140502797
CHAT		ENSSSCG00000010392	14:93957673-94007899		CT990602,CH242-369H2,14:93954050-94016526 (Clone quality: bE369H2 on chr=14; Num_of_Contigs=4; )
CHCHD1		ENSSSCG00000010308	14:79809667-79811230		CT827821,CH242-151I16,14:79768716-79822020 (Clone quality: bE151I16 on chr=14; Num_of_Contigs=5; )

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).