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)

CDC42BPB		location ⇒	7:130864383-130864275		CT998550,CH242-445C19,7:130850075-130928536 (Clone quality: bE445C19 on chr=7; Num_of_Contigs=6; )
CDC42BPB		location ⇒	7:130864877-130864820		CT998550,CH242-445C19,7:130850075-130928536 (Clone quality: bE445C19 on chr=7; Num_of_Contigs=6; )
CDC42BPG		ENSSSCG00000013018	2:5734333-5752406	FP101995,CH242-228D7,2:5725813-5761270 (Clone quality: bE228D7 on chr=2; Num_of_Contigs=13; )
CDC42EP2		ENSSSCG00000012996	2:5298971-5299615		CU856029,CH242-276E8,2:5292491-5308091 (Clone quality: bE276E8 on chr=2; Num_of_Contigs=9; )
CDC42EP2		location ⇒	2:5299642-5298848		CU856029,CH242-276E8,2:5292491-5308091 (Clone quality: bE276E8 on chr=2; Num_of_Contigs=9; )
CDC42EP3		ENSSSCG00000008490	3:95647554-95648318		CU856694,CH242-232D5,3:95617551-95695660 (Clone quality: bE232D5 on chr=3; Num_of_Contigs=2; )
CDC42EP4		ENSSSCG00000017245	12:5769195-5770268	CU929672,CH242-62J22,12:5703604-5857364 (Clone quality: bE62J22 on chr=12; Num_of_Contigs=4; )
CDC42EP5		ENSSSCG00000003274	6:40729599-40729913		CU914171,CH242-113P17,6:40726223-40729915 (Clone quality: bE113P17 on chr=6; Num_of_Contigs=7; )
CDC42SE1		ENSSSCG00000006638	4:102126950-102133468		CU459198,CH242-258B14,4:102107604-102144873 (Clone quality: bE258B14 on chr=4; Num_of_Contigs=7; )
CDC42SE2		ENSSSCG00000014266	2:121411617-121514265
CDC45L		ENSSSCG00000010122	14:52244529-52269749		CU468637,CH242-526M15,14:52233729-52290922 (Clone quality: bE526M15 on chr=14; Num_of_Contigs=13; )
CDC5L		ENSSSCG00000001708	7:45906188-45949646	CR956370,CH242-181F19,7:45890645-46067290 (No clone quality info on bE181F19)
CDC6		ENSSSCG00000017471	12:19750959-19764757
CDC73		ENSSSCG00000010801	10:1623870-1649597		CU929655,CH242-497M20,10:1621464-1649831 (Clone quality: bE497M20 on chr=10; Num_of_Contigs=12; )
CDCA2		ENSSSCG00000009653	14:9636872-9684424		CU041332,CH242-35P19,14:9599147-9818169 (Clone quality: bE35P19 on chr=14; Num_of_Contigs=1; )
CDCA3		ENSSSCG00000000683	5:59889344-59891707		CU457492,CH242-370K21,5:59880009-59901315 (Clone quality: bE370K21 on chr=5; Num_of_Contigs=10; )
CDCA4		ENSSSCG00000002559	7:133225520-133226158		CU695123,CH242-103I13,7:133218893-133234990 (Clone quality: bE103I13 on chr=7; Num_of_Contigs=13; )
CDCA5		ENSSSCG00000013008	2:5504232-5509330	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
CDCA7		ENSSSCG00000015961	15:74393186-74406634
CDCP1		ENSSSCG00000011298	13:23480639-23512665
CDGAP		ENSSSCG00000011902	13:105601126-105746664
CDH-p		location ⇒	14:35515291-35515327		CU481873,CH242-337G9,14:35514017-35532352 (Clone quality: bE337G9 on chr=14; Num_of_Contigs=15; )
CDH-p		location ⇒	14:35548014-35548050		CT737179,CH242-7H2,14:35543952-35742587 (Clone quality: bE7H2 on chr=14; Num_of_Contigs=1; )
CDH-p		location ⇒	18:5423765-5423813		CU928555,CH242-184M19,18:5412053-5424237 (Clone quality: bE184M19 on chr=18; Num_of_Contigs=14; )
CDH-p		location ⇒	18:5425620-5425665		CU928555,CH242-184M19,18:5424338-5430649 (Clone quality: bE184M19 on chr=18; Num_of_Contigs=14; )
CDH-p		location ⇒	18:5426904-5426998		CU928555,CH242-184M19,18:5424338-5430649 (Clone quality: bE184M19 on chr=18; Num_of_Contigs=14; )
CDH-p		location ⇒	18:5427855-5427907		CU928555,CH242-184M19,18:5424338-5430649 (Clone quality: bE184M19 on chr=18; Num_of_Contigs=14; )
CDH1		location ⇒	6:22651554-22651687		CU457410,CH242-36K11,6:22572591-22709391 (Clone quality: bE36K11 on chr=6; Num_of_Contigs=2; )
CDH10		ENSSSCG00000016802	16:11068482-11179497
CDH10		location ⇒	16:11068752-11068288		FP236489,CH242-276M10,16:10997348-11080311 (Clone quality: bE276M10 on chr=16; Num_of_Contigs=1; )
CDH11		ENSSSCG00000002795	6:14546161-14596703
CDH11		location ⇒	6:14596440-14597167		CU633602,CH242-7C12,6:14592914-14794772 (Clone quality: bE7C12 on chr=6; Num_of_Contigs=1; )
CDH12		ENSSSCG00000016799	16:9383414-9692211
CDH12		location ⇒	16:9383346-9383213		CU929813,CH242-476M21,16:9374112-9401044 (Clone quality: bE476M21 on chr=16; Num_of_Contigs=10; )
CDH12		location ⇒	16:9383787-9383408		CU929813,CH242-476M21,16:9374112-9401044 (Clone quality: bE476M21 on chr=16; Num_of_Contigs=10; )
CDH13		ENSSSCG00000002684	6:3169764-3320214
CDH13		location ⇒	6:3498813-3498659		CU929573,CH242-144O13,6:3468793-3552233 (Clone quality: bE144O13 on chr=6; Num_of_Contigs=3; )
CDH13		location ⇒	6:3619630-3619750		CU657927,CH242-205N21,6:3571216-3634252 (Clone quality: bE205N21 on chr=6; Num_of_Contigs=7; )
CDH13		location ⇒	6:3653759-3653550		CU657927,CH242-205N21,6:3634353-3659664 (Clone quality: bE205N21 on chr=6; Num_of_Contigs=7; )
CDH13		location ⇒	6:4093167-4092998		CU928547,CH242-98E1,6:4090235-4100839 (Clone quality: bE98E1 on chr=6; Num_of_Contigs=9; )
CDH15		ENSSSCG00000002642	6:312204-320834		FP102614,CH242-198I21,6:311914-324297 (Clone quality: bE198I21 on chr=6; Num_of_Contigs=22; )
CDH15		location ⇒	6:319990-320160		FP102614,CH242-198I21,6:311914-324297 (Clone quality: bE198I21 on chr=6; Num_of_Contigs=22; )
CDH15		location ⇒	6:320485-320834		FP102614,CH242-198I21,6:311914-324297 (Clone quality: bE198I21 on chr=6; Num_of_Contigs=22; )
CDH17		ENSSSCG00000006106	4:43120544-43202644
CDH17		location ⇒	4:43148802-43148942		CU407285,CH242-511L5,4:43142016-43234568 (Clone quality: bE511L5 on chr=4; Num_of_Contigs=2; )
CDH17		location ⇒	4:43149813-43149955		CU407285,CH242-511L5,4:43142016-43234568 (Clone quality: bE511L5 on chr=4; Num_of_Contigs=2; )
CDH17		location ⇒	4:43159990-43160152		CU407285,CH242-511L5,4:43142016-43234568 (Clone quality: bE511L5 on chr=4; Num_of_Contigs=2; )
CDH17		location ⇒	4:43160258-43160461		CU407285,CH242-511L5,4:43142016-43234568 (Clone quality: bE511L5 on chr=4; Num_of_Contigs=2; )
CDH18		ENSSSCG00000016797	16:7815329-7816379		CU466489,CH242-446L4,16:7813634-7841882 (Clone quality: bE446L4 on chr=16; Num_of_Contigs=18; )
CDH18		location ⇒	16:7612636-7612072		FP074865,CH242-399A18,16:7601231-7628812 (Clone quality: bE399A18 on chr=16; Num_of_Contigs=11; )

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).