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)

SCUBE3		ENSSSCG00000001536	7:35596571-35617151
SCUBE3		location ⇒	7:35597002-35596723		CU468855,CH242-522A1,7:35589363-35613107 (Clone quality: bE522A1 on chr=7; Num_of_Contigs=14; )
SCUBE3		location ⇒	7:35599136-35599055		CU468855,CH242-522A1,7:35589363-35613107 (Clone quality: bE522A1 on chr=7; Num_of_Contigs=14; )
SCUBE3		location ⇒	7:35599401-35599249		CU468855,CH242-522A1,7:35589363-35613107 (Clone quality: bE522A1 on chr=7; Num_of_Contigs=14; )
SCUBE3		location ⇒	7:35599982-35599867		CU468855,CH242-522A1,7:35589363-35613107 (Clone quality: bE522A1 on chr=7; Num_of_Contigs=14; )
SCYL1		ENSSSCG00000012984	2:5053264-5066070
SCYL2		ENSSSCG00000000877	5:79573719-79612876
SCYL3		ENSSSCG00000006283	4:84225205-84266389
SDAD1		ENSSSCG00000008974	8:60999255-61117935
SDC1		ENSSSCG00000008601	3:109603804-109608153		CU856117,CH242-479B3,3:109586437-109610385 (Clone quality: bE479B3 on chr=3; Num_of_Contigs=16; )
SDC1		location ⇒	3:109605346-109604881		CU856117,CH242-479B3,3:109586437-109610385 (Clone quality: bE479B3 on chr=3; Num_of_Contigs=16; )
SDC1		location ⇒	3:109607086-109607001		CU856117,CH242-479B3,3:109586437-109610385 (Clone quality: bE479B3 on chr=3; Num_of_Contigs=16; )
SDC2		ENSSSCG00000006088	4:40347854-40472312
SDC2		location ⇒	4:40348178-40347012		CU468314,CH242-153B17,4:40308041-40388872 (Clone quality: bE153B17 on chr=4; Num_of_Contigs=4; )
SDC2		location ⇒	4:40348456-40348209		CU468314,CH242-153B17,4:40308041-40388872 (Clone quality: bE153B17 on chr=4; Num_of_Contigs=4; )
SDC2		location ⇒	4:40471936-40471757		CU856032,CH242-278K7,4:40453075-40583544 (Clone quality: bE278K7 on chr=4; Num_of_Contigs=5; )
SDC2		location ⇒	4:40472265-40471991		CU856032,CH242-278K7,4:40453075-40583544 (Clone quality: bE278K7 on chr=4; Num_of_Contigs=5; )
SDC3		ENSSSCG00000003592	6:59860661-59869360
SDC3		location ⇒	6:59864185-59864368		CU928875,CH242-220B22,6:59862047-59864459 (Clone quality: bE220B22 on chr=6; Num_of_Contigs=16; )
SDC3		location ⇒	6:59865556-59865858		CU928875,CH242-220B22,6:59864560-59882262 (Clone quality: bE220B22 on chr=6; Num_of_Contigs=16; )
SDC3		location ⇒	6:59869004-59869330		CU928875,CH242-220B22,6:59864560-59882262 (Clone quality: bE220B22 on chr=6; Num_of_Contigs=16; )
SDC4		ENSSSCG00000007401	17:49658654-49678806		CU606851,CH242-219J22,17:49636607-49702762 (Clone quality: bE219J22 on chr=17; Num_of_Contigs=12; )
SDC4		location ⇒	17:49537512-49537313		CU606979,CH242-291J7,17:49534403-49550932 (Clone quality: bE291J7 on chr=17; Num_of_Contigs=31; )
SDC4		location ⇒	17:49540281-49540142		CU606979,CH242-291J7,17:49534403-49550932 (Clone quality: bE291J7 on chr=17; Num_of_Contigs=31; )
SDC4		location ⇒	17:49658977-49658699		CU606851,CH242-219J22,17:49636607-49702762 (Clone quality: bE219J22 on chr=17; Num_of_Contigs=12; )
SDC4		location ⇒	17:49663083-49662884		CU606851,CH242-219J22,17:49636607-49702762 (Clone quality: bE219J22 on chr=17; Num_of_Contigs=12; )
SDCBP		ENSSSCG00000006237	4:77126612-77158781		CU582808,CH242-379F13,4:77090955-77172237 (Clone quality: bE379F13 on chr=4; Num_of_Contigs=8; )
SDCBP		location ⇒	4:77126746-77126104		CU582808,CH242-379F13,4:77090955-77172237 (Clone quality: bE379F13 on chr=4; Num_of_Contigs=8; )
SDCBP		location ⇒	4:77127275-77126772		CU582808,CH242-379F13,4:77090955-77172237 (Clone quality: bE379F13 on chr=4; Num_of_Contigs=8; )
SDCBP		location ⇒	4:77130762-77130586		CU582808,CH242-379F13,4:77090955-77172237 (Clone quality: bE379F13 on chr=4; Num_of_Contigs=8; )
SDCBP		location ⇒	4:77132677-77132514		CU582808,CH242-379F13,4:77090955-77172237 (Clone quality: bE379F13 on chr=4; Num_of_Contigs=8; )
SDCBP2		ENSSSCG00000007189	17:35664033-35681873		CU638675,CH242-204E6,17:35560423-35742963 (Clone quality: bE204E6 on chr=17; Num_of_Contigs=1; )
SDCCAG1		ENSSSCG00000005011	1:188039752-188086473		CU606975,CH242-251A8,1:188036812-188088768 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
SDCCAG8		ENSSSCG00000010871	10:15855296-15928953		CU571098,CH242-123F14,10:15850724-15932846 (Clone quality: bE123F14 on chr=10; Num_of_Contigs=5; )
SDCCAG8		location ⇒	10:15906261-15906482		CU571098,CH242-123F14,10:15850724-15932846 (Clone quality: bE123F14 on chr=10; Num_of_Contigs=5; )
SDCCAG8		location ⇒	10:15908823-15908963		CU571098,CH242-123F14,10:15850724-15932846 (Clone quality: bE123F14 on chr=10; Num_of_Contigs=5; )
SDCCAG8		location ⇒	10:15925834-15925970		CU571098,CH242-123F14,10:15850724-15932846 (Clone quality: bE123F14 on chr=10; Num_of_Contigs=5; )
SDCCAG8		location ⇒	10:16113029-16113370		CU570926,CH242-205H3,10:16016755-16179951 (Clone quality: bE205H3 on chr=10; Num_of_Contigs=1; )
SDF2		ENSSSCG00000017772	12:42673824-42683966
SDF2L1		ENSSSCG00000010085	14:51323339-51325336		CU633431,CH242-79C11,14:51180713-51414471 (Clone quality: bE79C11 on chr=14; Num_of_Contigs=4; )
SDF4		ENSSSCG00000003332	6:42800941-42811060		FP102596,CH242-173K23,6:42793613-42821104 (Clone quality: bE173K23 on chr=6; Num_of_Contigs=10; )
SDHAF2		ENSSSCG00000013082	2:8382171-8394994		CU896534,CH242-169N17,2:8375072-8412883 (Clone quality: bE169N17 on chr=2; Num_of_Contigs=6; )
SDHC		location ⇒	9:5978706-5978643		CU855587,CH242-289J23,9:5968658-6025382 (Clone quality: bE289J23 on chr=9; Num_of_Contigs=8; )
SDK1		ENSSSCG00000007574	3:2606911-2734825
SDK2		ENSSSCG00000017244	12:5527833-5644640	CU928109,CH242-415P4,12:5525126-5703603 (Clone quality: bE415P4 on chr=12; Num_of_Contigs=6; )
SDK2		location ⇒	12:5624549-5624675	CU928109,CH242-415P4,12:5525126-5703603 (Clone quality: bE415P4 on chr=12; Num_of_Contigs=6; )
SDK2		location ⇒	12:5707458-5707584	CU929672,CH242-62J22,12:5703604-5857364 (Clone quality: bE62J22 on chr=12; Num_of_Contigs=4; )
SDPR		ENSSSCG00000016063	15:90975204-90986922		CU855682,CH242-93G4,15:90925045-90992881 (No clone quality info on )
SDR16C5		ENSSSCG00000006245	4:78483102-78495726		CU462960,CH242-392H23,4:78478849-78542797 (Clone quality: bE392H23 on chr=4; Num_of_Contigs=4; )
SDR16C6		ENSSSCG00000006244	4:78450443-78475768

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, 2601-16

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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).