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)

CSF1R		location ⇒	2:136530580-136530435		CU681821,CH242-138G12,2:136481055-136539241 (Clone quality: bE138G12 on chr=2; Num_of_Contigs=10; )
CSF1R		location ⇒	2:136532012-136531881		CU681821,CH242-138G12,2:136481055-136539241 (Clone quality: bE138G12 on chr=2; Num_of_Contigs=10; )
CSF1R		location ⇒	2:136588000-136587947		CU914366,CH242-274B11,2:136584432-136593468 (Clone quality: bE274B11 on chr=2; Num_of_Contigs=10; )
CSF1R		location ⇒	2:136738853-136738771		CU914366,CH242-274B11,2:136737836-136759157 (Clone quality: bE274B11 on chr=2; Num_of_Contigs=10; )
CSF2RB		ENSSSCG00000000136	5:7187547-7201962		CU407327,CH242-127L5,5:7172124-7252136 (Clone quality: bE127L5 on chr=5; Num_of_Contigs=4; )
CSF2RB		location ⇒	5:7194285-7194444		CU407327,CH242-127L5,5:7172124-7252136 (Clone quality: bE127L5 on chr=5; Num_of_Contigs=4; )
CSF2RB		location ⇒	5:7194593-7194733		CU407327,CH242-127L5,5:7172124-7252136 (Clone quality: bE127L5 on chr=5; Num_of_Contigs=4; )
CSF2RB		location ⇒	5:7195287-7195458		CU407327,CH242-127L5,5:7172124-7252136 (Clone quality: bE127L5 on chr=5; Num_of_Contigs=4; )
CSF2RB		location ⇒	5:7195539-7195692		CU407327,CH242-127L5,5:7172124-7252136 (Clone quality: bE127L5 on chr=5; Num_of_Contigs=4; )
CSF3		ENSSSCG00000017482	12:20149317-20151340		CU929462,CH242-284N22,12:20140316-20189597 (Clone quality: bE284N22 on chr=12; Num_of_Contigs=12; )
CSF3		ENSSSCG00000017488	12:20296783-20298339		CU928026,CH242-256H23,12:20268098-20354915 (Clone quality: bE256H23 on chr=12; Num_of_Contigs=2; )
CSF3		location ⇒	12:20149593-20149748		CU929462,CH242-284N22,12:20140316-20189597 (Clone quality: bE284N22 on chr=12; Num_of_Contigs=12; )
CSF3		location ⇒	12:20150818-20151340		CU929462,CH242-284N22,12:20140316-20189597 (Clone quality: bE284N22 on chr=12; Num_of_Contigs=12; )
CSF3		location ⇒	12:20296950-20296430		CU928026,CH242-256H23,12:20268098-20354915 (Clone quality: bE256H23 on chr=12; Num_of_Contigs=2; )
CSF3		location ⇒	12:20298175-20298020		CU928026,CH242-256H23,12:20268098-20354915 (Clone quality: bE256H23 on chr=12; Num_of_Contigs=2; )
CSGALNACT1		ENSSSCG00000007005	17:8991273-9062512
CSGALNACT2		ENSSSCG00000010200	14:63770342-63793948		CT990536,CH242-194C16,14:63711553-63927511 (Clone quality: bE194C16 on chr=14; Num_of_Contigs=1; )
CSGLCA-T		ENSSSCG00000016436	18:5054144-5058667		FP102583,CH242-165F21,18:5049308-5059326 (Clone quality: bE165F21 on chr=18; Num_of_Contigs=16; )
CSK		ENSSSCG00000006154	4:57076596-57096490
CSK		ENSSSCG00000001900	7:64237167-64255644		CU468845,CH242-162A4,7:64176153-64332301 (Clone quality: bE162A4 on chr=7; Num_of_Contigs=2; )
CSK		location ⇒	7:64237769-64237274		CU468845,CH242-162A4,7:64176153-64332301 (Clone quality: bE162A4 on chr=7; Num_of_Contigs=2; )
CSK		location ⇒	7:64238126-64238038		CU468845,CH242-162A4,7:64176153-64332301 (Clone quality: bE162A4 on chr=7; Num_of_Contigs=2; )
CSK		location ⇒	7:64238425-64238230		CU468845,CH242-162A4,7:64176153-64332301 (Clone quality: bE162A4 on chr=7; Num_of_Contigs=2; )
CSK		location ⇒	7:64239142-64239051		CU468845,CH242-162A4,7:64176153-64332301 (Clone quality: bE162A4 on chr=7; Num_of_Contigs=2; )
CSMD1		ENSSSCG00000015748	15:31723440-31811607
CSMD2		ENSSSCG00000003622	6:61287367-61532046
CSMD3		ENSSSCG00000006019	4:25305719-25396681		CU638678,CH242-271I21,4:25305084-25454232 (Clone quality: bE271I21 on chr=4; Num_of_Contigs=1; )
CSN1S1		ENSSSCG00000009262	8:119751674-119768662
CSN2		ENSSSCG00000009261	8:119735253-119743791
CSN3		ENSSSCG00000009267	8:119975507-119979593
CSNK1A1		ENSSSCG00000014435	2:136066674-136114318		FP085505,CH242-216N6,2:136052687-136129050 (Clone quality: bE216N6 on chr=2; Num_of_Contigs=3; )
CSNK1E		ENSSSCG00000000107	5:5954265-5978702
CSNK1G1		ENSSSCG00000004558	1:111204004-111245381		CU302261,CH242-182N21,1:111189543-111264608 (Clone quality: bE182N21 on chr=1; Num_of_Contigs=3; )
CSNK1G2		ENSSSCG00000013445	2:46888727-46912817
CSNK1G3		ENSSSCG00000014240	2:115049275-115124715		CU694501,CH242-152O13,2:115047747-115140453 (Clone quality: bE152O13 on chr=2; Num_of_Contigs=5; )
CSNK1G3		location ⇒	2:115049026-115049453		CU694501,CH242-152O13,2:115047747-115140453 (Clone quality: bE152O13 on chr=2; Num_of_Contigs=5; )
CSNK1G3		location ⇒	2:115079468-115079703		CU694501,CH242-152O13,2:115047747-115140453 (Clone quality: bE152O13 on chr=2; Num_of_Contigs=5; )
CSNK1G3		location ⇒	2:115124661-115126223		CU694501,CH242-152O13,2:115047747-115140453 (Clone quality: bE152O13 on chr=2; Num_of_Contigs=5; )
CSNK1G3		location ⇒	2:115126323-115127051		CU694501,CH242-152O13,2:115047747-115140453 (Clone quality: bE152O13 on chr=2; Num_of_Contigs=5; )
CSNK2A1		ENSSSCG00000007203	17:36504785-36557774
CSNK2A2		ENSSSCG00000002804	6:19556201-19597920
CSNK2B		ENSSSCG00000001414	7:27739874-27744824	CU467793,CH242-60C3,7:27581747-27762222 (Clone quality: bE60C3 on chr=7; Num_of_Contigs=1; )
CSPG2		location ⇒	2:81145665-81145944		CU463168,CH242-402A9,2:81126985-81296405 (Clone quality: bE402A9 on chr=2; Num_of_Contigs=1; )
CSPG5		ENSSSCG00000011339	13:25350196-25396358
CSPP1		ENSSSCG00000006202	4:70108359-70218908
CSPP1		location ⇒	4:70113372-70113293		CU462950,CH242-344F3,4:70071842-70166346 (Clone quality: bE344F3 on chr=4; Num_of_Contigs=2; )
CSPP1		location ⇒	4:70147975-70147917		CU462950,CH242-344F3,4:70071842-70166346 (Clone quality: bE344F3 on chr=4; Num_of_Contigs=2; )
CSPP1		location ⇒	4:70164095-70164032		CU462950,CH242-344F3,4:70071842-70166346 (Clone quality: bE344F3 on chr=4; Num_of_Contigs=2; )
CSPP1		location ⇒	4:70192877-70192450		CU462950,CH242-344F3,4:70166447-70219329 (Clone quality: bE344F3 on chr=4; Num_of_Contigs=2; )
CSRNP1		ENSSSCG00000011264	13:19759626-19770479		CU856480,CH242-203F12,13:19659552-19771103 (Clone quality: bE203F12 on chr=13; Num_of_Contigs=3; )

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).