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)

CLSTN3		ENSSSCG00000000672	5:59690194-59717186		CU929436,CH242-260C21,5:59673769-59719308 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
CLSTN3		location ⇒	5:59706529-59706364		CU929436,CH242-260C21,5:59673769-59719308 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
CLSTN3		location ⇒	5:59709410-59709295		CU929436,CH242-260C21,5:59673769-59719308 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
CLSTN3		location ⇒	5:59710739-59710516		CU929436,CH242-260C21,5:59673769-59719308 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
CLTA		ENSSSCG00000005341	1:248152976-248174769
CLTB		ENSSSCG00000014058	2:70483574-70497728	FP101981,CH242-191F5,2:70304317-70501298 (Clone quality: bE191F5 on chr=2; Num_of_Contigs=3; )
CLTC		ENSSSCG00000017666	12:33985185-34054684
CLU		ENSSSCG00000009668	14:11455355-11469903		CU633626,CH242-119C13,14:11386850-11482027 (Clone quality: bE119C13 on chr=14; Num_of_Contigs=3; )
CLU		location ⇒	14:11455609-11455352		CU633626,CH242-119C13,14:11386850-11482027 (Clone quality: bE119C13 on chr=14; Num_of_Contigs=3; )
CLU		location ⇒	14:11456703-11456469		CU633626,CH242-119C13,14:11386850-11482027 (Clone quality: bE119C13 on chr=14; Num_of_Contigs=3; )
CLU		location ⇒	14:11460711-11460300		CU633626,CH242-119C13,14:11386850-11482027 (Clone quality: bE119C13 on chr=14; Num_of_Contigs=3; )
CLU		location ⇒	14:11461892-11461720		CU633626,CH242-119C13,14:11386850-11482027 (Clone quality: bE119C13 on chr=14; Num_of_Contigs=3; )
CLUAP1		ENSSSCG00000007955	3:34692372-34719552
CLVS1		ENSSSCG00000006230	4:74700637-74837404
CLYBL		ENSSSCG00000009519	11:69608627-69616134		CU019587,CH242-392B6,11:69599884-69619777 (Clone quality: bE392B6 on chr=11; Num_of_Contigs=3; )
CMA1		ENSSSCG00000001982	7:81169720-81170797		CT997804,CH242-280B15,7:81169104-81187111 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
CMA1		location ⇒	7:81081729-81081444		CT997804,CH242-280B15,7:81065282-81125246 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
CMA1		location ⇒	7:81083790-81083637		CT997804,CH242-280B15,7:81065282-81125246 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
CMA1		location ⇒	7:81170678-81170963		CT997804,CH242-280B15,7:81169104-81187111 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
CMA1		location ⇒	7:81188465-81188157		CT997804,CH242-280B15,7:81187212-81281808 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
CMAH		ENSSSCG00000001099	7:20915175-20953635		CT757509,CH242-59J23,7:20849612-20971392 (Clone quality: bE59J23 on chr=7; Num_of_Contigs=2; )
CMAS		ENSSSCG00000000572	5:49578971-49599123		CU928274,CH242-124L20,5:49463010-49625704 (Clone quality: bE124L20 on chr=5; Num_of_Contigs=2; )
CMIP		location ⇒	6:4804405-4804319		CU856256,CH242-10B22,6:4770537-4809533 (Clone quality: bE10B22 on chr=6; Num_of_Contigs=4; )
CMIP		location ⇒	6:4807566-4807495		CU856256,CH242-10B22,6:4770537-4809533 (Clone quality: bE10B22 on chr=6; Num_of_Contigs=4; )
CMIP		location ⇒	6:4839909-4839860		CU498927,CH242-275F15,6:4838469-4859950 (Clone quality: bE275F15 on chr=6; Num_of_Contigs=23; )
CMIP		location ⇒	6:4847692-4847631		CU498927,CH242-275F15,6:4838469-4859950 (Clone quality: bE275F15 on chr=6; Num_of_Contigs=23; )
CMKLR1		ENSSSCG00000009947	14:42651169-42652260		CU468889,CH242-242A7,14:42643147-42658415 (Clone quality: bE242A7 on chr=14; Num_of_Contigs=11; )
CMPK1		ENSSSCG00000003885	6:117488999-117523191
CMPK2		ENSSSCG00000008647	3:118820856-118833508
CMRF35		ENSSSCG00000017237	12:4859156-4867151	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
CMTM3		location ⇒	X:28111864-28111807		CU467916,CH242-260N18,X:28050040-28217566 (Clone quality: bE260N18 on chr=X; Num_of_Contigs=3; )
CMTM4		location ⇒	7:87181457-87180795	CU468857,CH242-57B1,7:87017236-87192934 (Clone quality: bE57B1 on chr=7; Num_of_Contigs=1; )
CMTM4		location ⇒	7:87244706-87245368		CU582814,CH242-47I16,7:87198133-87254080 (Clone quality: bE47I16 on chr=7; Num_of_Contigs=3; )
CMTM4		location ⇒	7:87485667-87486329		CU468947,CH242-254B6,7:87371812-87498069 (Clone quality: bE254B6 on chr=7; Num_of_Contigs=6; )
CMTM5		ENSSSCG00000002028	7:82104640-82107317		CU633625,CH242-116C14,7:82041923-82116183 (Clone quality: bE116C14 on chr=7; Num_of_Contigs=8; )
CMTM5		location ⇒	7:82104991-82104857		CU633625,CH242-116C14,7:82041923-82116183 (Clone quality: bE116C14 on chr=7; Num_of_Contigs=8; )
CMTM5		location ⇒	7:82106124-82105970		CU633625,CH242-116C14,7:82041923-82116183 (Clone quality: bE116C14 on chr=7; Num_of_Contigs=8; )
CMTM5		location ⇒	7:82106640-82106544		CU633625,CH242-116C14,7:82041923-82116183 (Clone quality: bE116C14 on chr=7; Num_of_Contigs=8; )
CMTM5		location ⇒	7:82107310-82107026		CU633625,CH242-116C14,7:82041923-82116183 (Clone quality: bE116C14 on chr=7; Num_of_Contigs=8; )
CMTM6		ENSSSCG00000011232	13:15989159-16011778
CMTM6		location ⇒	13:15993835-15993734		CU695035,CH242-232M3,13:15975852-16010460 (Clone quality: bE232M3 on chr=13; Num_of_Contigs=6; )
CMTM6		location ⇒	13:16001081-16000903		CU695035,CH242-232M3,13:15975852-16010460 (Clone quality: bE232M3 on chr=13; Num_of_Contigs=6; )
CMTM6		location ⇒	13:16011767-16011579		CU695035,CH242-232M3,13:16010561-16074512 (Clone quality: bE232M3 on chr=13; Num_of_Contigs=6; )
CMTM7		ENSSSCG00000011234	13:16094008-16105509		CU695035,CH242-232M3,13:16074613-16112727 (Clone quality: bE232M3 on chr=13; Num_of_Contigs=6; )
CMTM8		location ⇒	13:16142308-16142484		CU695035,CH242-232M3,13:16139966-16170288 (Clone quality: bE232M3 on chr=13; Num_of_Contigs=6; )
CMYA3		ENSSSCG00000015917	15:69280019-69326123
CMYA5		ENSSSCG00000014115	2:77545955-77621724
CNBD1		ENSSSCG00000006133	4:51128333-51287202
CNBD1		location ⇒	4:51130164-51130081		CU137692,CH242-39J21,4:51017862-51180439 (Clone quality: bE39J21 on chr=4; Num_of_Contigs=1; )
CNBD1		location ⇒	4:51479712-51479634		CU571217,CH242-276P1,4:51295015-51486101 (Clone quality: bE276P1 on chr=4; 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).