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)

SLCO1A26579		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
SLCO1C1		ENSSSCG00000000585	5:50249353-50313886
SLCO2A1		ENSSSCG00000011641	13:61551165-61561230
SLCO2B1		ENSSSCG00000014851	9:9179857-9211105		CU655994,CH242-280C8,9:9168027-9211748 (Clone quality: bE280C8 on chr=9; Num_of_Contigs=8; )
SLCO2B1		location ⇒	9:9178336-9178233		CU655994,CH242-280C8,9:9168027-9211748 (Clone quality: bE280C8 on chr=9; Num_of_Contigs=8; )
SLCO2B1		location ⇒	9:9188335-9188097		CU655994,CH242-280C8,9:9168027-9211748 (Clone quality: bE280C8 on chr=9; Num_of_Contigs=8; )
SLCO2B1		location ⇒	9:9201612-9201428		CU655994,CH242-280C8,9:9168027-9211748 (Clone quality: bE280C8 on chr=9; Num_of_Contigs=8; )
SLCO2B1		location ⇒	9:9209884-9209748		CU655994,CH242-280C8,9:9168027-9211748 (Clone quality: bE280C8 on chr=9; Num_of_Contigs=8; )
SLCO3A1		ENSSSCG00000002263	7:95127584-95461543
SLCO4C1		ENSSSCG00000014182	2:97104196-97173621
SLCO5A1		ENSSSCG00000006196	4:67622110-67623120		CU469122,CH242-149H11,4:67565490-67670950 (Clone quality: bE149H11 on chr=4; Num_of_Contigs=3; )
SLCO6A1		ENSSSCG00000014183	2:97208582-97304608		CU468184,CH242-358L10,2:97161075-97360084 (Clone quality: bE358L10 on chr=2; Num_of_Contigs=1; )
SLFN14		ENSSSCG00000017714	12:37759442-37763843		CU927946,CH242-204J8,12:37724810-37778976 (Clone quality: bE204J8 on chr=12; Num_of_Contigs=6; )
SLFNL1		ENSSSCG00000003972	6:121590069-121593877		FP016067,CH242-126M8,6:121551012-121676967 (Clone quality: bE126M8 on chr=6; Num_of_Contigs=2; )
SLIT1		ENSSSCG00000010512	14:113517455-113533607
SLIT2		ENSSSCG00000008749	8:11826140-12034965
SLIT2		ENSSSCG00000017012	16:52336708-52500738
SLIT3		ENSSSCG00000017012	16:52336708-52500738
SLITRK1		ENSSSCG00000009485	11:54663728-54665815		CU076063,CH242-147M6,11:54628405-54818872 (Clone quality: bE147M6 on chr=11; Num_of_Contigs=1; )
SLITRK2		ENSSSCG00000012724	X:117051445-117053994		FP236785,CH242-290N8,X:117047570-117079327 (Clone quality: bE290N8 on chr=X; Num_of_Contigs=3; )
SLITRK3		ENSSSCG00000011736	13:80533004-80535943		CU466936,CH242-212H8,13:80516212-80655818 (Clone quality: bE212H8 on chr=13; Num_of_Contigs=1; )
SLITRK5		ENSSSCG00000009488	11:57924059-57926890
SLITRK6		ENSSSCG00000009486	11:56414187-56416715		CU466998,CH242-71N16,11:56411659-56425726 (Clone quality: bE71N16 on chr=11; Num_of_Contigs=7; )
SLK		ENSSSCG00000010606	14:120006006-120060599		CT737145,CH242-23L13,14:119925154-120085579 (Clone quality: bE23L13 on chr=14; Num_of_Contigs=1; )
SLMAP		ENSSSCG00000011468	13:33188707-33331374
SLMO2		ENSSSCG00000007525	17:61793431-61801869	CR956646,CH242-247L10,17:61655968-61825296 (No clone quality info on bE247L10)
SLN		location ⇒	9:35785404-35784805		CU928597,CH242-212P11,9:35781186-35790454 (Clone quality: bE212P11 on chr=9; Num_of_Contigs=11; )
SLPI		ENSSSCG00000007394	17:49485071-49487656		CU606979,CH242-291J7,17:49482658-49489853 (Clone quality: bE291J7 on chr=17; Num_of_Contigs=31; )
SLPI		ENSSSCG00000007388	17:49357587-49360172		CU606931,CH242-44K10,17:49351128-49369311 (Clone quality: bE44K10 on chr=17; Num_of_Contigs=16; )
SLPI		location ⇒	17:10864619-10864546		CU607010,CH242-309J7,17:10853516-10883354 (Clone quality: bE309J7 on chr=17; Num_of_Contigs=6; )
SLPI		location ⇒	17:27548795-27548851		FP102111,CH242-215E20,17:27539304-27587727 (Clone quality: bE215E20 on chr=17; Num_of_Contigs=2; )
SLPI		location ⇒	17:39203446-39203555		CU407167,CH242-230G19,17:39200054-39238164 (Clone quality: bE230G19 on chr=17; Num_of_Contigs=9; )
SLPI		location ⇒	17:6883046-6882934		CU861958,CH242-252F14,17:6864603-6915949 (Clone quality: bE252F14 on chr=17; Num_of_Contigs=5; )
SLU7		ENSSSCG00000017033	16:60585639-60726327
SMAD1		ENSSSCG00000009040	8:71566227-71612707
SMAD1		ENSSSCG00000016677	18:40739502-40779080
SMAD2		ENSSSCG00000004505	1:101093768-101104311		CU062588,CH242-5J4,1:101076578-101106690 (Clone quality: bE5J4 on chr=1; Num_of_Contigs=16; )
SMAD3		ENSSSCG00000004952	1:172341003-172364322
SMAD3		location ⇒	1:172214109-172214316		FP085473,CH242-111C11,1:172213183-172219464 (Clone quality: bE111C11 on chr=1; Num_of_Contigs=22; )
SMAD3		location ⇒	1:172340933-172340076		FP236622,CH242-20C24,1:172335527-172359216 (Clone quality: bE20C24 on chr=1; Num_of_Contigs=3; )
SMAD3		location ⇒	1:172349256-172349042		FP236622,CH242-20C24,1:172335527-172359216 (Clone quality: bE20C24 on chr=1; Num_of_Contigs=3; )
SMAD3		location ⇒	1:172364284-172364088		FP236622,CH242-20C24,1:172359317-172381276 (Clone quality: bE20C24 on chr=1; Num_of_Contigs=3; )
SMAD4		ENSSSCG00000004524	1:103812352-103866422
SMAD4		location ⇒	1:103828241-103828622		CU457710,CH242-73M15,1:103813127-103936868 (Clone quality: bE73M15 on chr=1; Num_of_Contigs=3; )
SMAD4		location ⇒	1:103835854-103836069		CU457710,CH242-73M15,1:103813127-103936868 (Clone quality: bE73M15 on chr=1; Num_of_Contigs=3; )
SMAD4		location ⇒	1:103850225-103850411		CU457710,CH242-73M15,1:103813127-103936868 (Clone quality: bE73M15 on chr=1; Num_of_Contigs=3; )
SMAD4		location ⇒	1:103864896-103866422		CU457710,CH242-73M15,1:103813127-103936868 (Clone quality: bE73M15 on chr=1; Num_of_Contigs=3; )
SMAD5		ENSSSCG00000014319	2:125760025-125790324		FP102024,CH242-162I22,2:125759713-125801286 (Clone quality: bE162I22 on chr=2; Num_of_Contigs=10; )
SMAD6		ENSSSCG00000004948	1:171829965-171907925
SMAD6		location ⇒	1:12545-12464		CU570732,CH242-271M12,1:1-31034 (Clone quality: bE271M12 on chr=1; Num_of_Contigs=7; )

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).