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)

SCD		location ⇒	14:160008-160085		CU571022,CH242-21I12,14:8902-208834 (Clone quality: bE21I12 on chr=14; Num_of_Contigs=5; )
SCD		location ⇒	14:49731-49840		CU571022,CH242-21I12,14:8902-208834 (Clone quality: bE21I12 on chr=14; Num_of_Contigs=5; )
SCD5		ENSSSCG00000009245	8:116649525-116752791
SCEL		ENSSSCG00000009474	11:48596276-48660061
SCFD1		ENSSSCG00000001973	7:74865939-74935765
SCFD2		ENSSSCG00000008836	8:34531882-34540031
SCG3		ENSSSCG00000004630	1:125063510-125106124		CU019579,CH242-2K4,1:124966545-125142351 (Clone quality: bE2K4 on chr=1; Num_of_Contigs=2; )
SCG5		ENSSSCG00000004807	1:144186182-144203289
SCGB1A1		ENSSSCG00000013060	2:7463684-7468478		FP102338,CH242-94E13,2:7461354-7473580 (Clone quality: bE94E13 on chr=2; Num_of_Contigs=10; )
SCGB1A1		location ⇒	2:1460986-1461070		CU469203,CH242-236K15,2:1460963-1466566 (Clone quality: bE236K15 on chr=2; Num_of_Contigs=23; )
SCGB1A1		location ⇒	2:2052525-2052622		CU657972,CH242-48M13,2:2043925-2053185 (Clone quality: bE48M13 on chr=2; Num_of_Contigs=8; )
SCGB1A1		location ⇒	2:2116762-2116653		CU657972,CH242-48M13,2:2115323-2118592 (Clone quality: bE48M13 on chr=2; Num_of_Contigs=8; )
SCGB1A1		location ⇒	2:2272144-2272241		CU463344,CH242-408M2,2:2253075-2296687 (Clone quality: bE408M2 on chr=2; Num_of_Contigs=8; )
SCGB1C1		ENSSSCG00000014554	2:139823526-139824983		CU928488,CH242-163I11,2:139819049-139956868 (Clone quality: bE163I11 on chr=2; Num_of_Contigs=2; )
SCGB3A1		ENSSSCG00000014008	2:67351168-67353012		CU928737,CH242-57D18,2:67309708-67370688 (Clone quality: bE57D18 on chr=2; Num_of_Contigs=12; )
SCGN		ENSSSCG00000001101	7:21572868-21616489
SCIN		ENSSSCG00000015353	9:77079774-77108450
SCLT1		ENSSSCG00000009070	8:82526329-82719351
SCLY		ENSSSCG00000016334	15:130132812-130168731
SCMH1		ENSSSCG00000003971	6:121556505-121584304		FP016067,CH242-126M8,6:121551012-121676967 (Clone quality: bE126M8 on chr=6; Num_of_Contigs=2; )
SCML1		ENSSSCG00000012152	X:13745957-13756300	CU207277,CH242-186H22,X:13637952-13829937 (Clone quality: bE186H22 on chr=X; Num_of_Contigs=1; )
SCML2		ENSSSCG00000012155	X:14338937-14442071
SCML4		ENSSSCG00000004380	1:77418742-77434193
SCN1B		ENSSSCG00000002878	6:29833496-29835363		FP102631,CH242-21N23,6:29833359-29835772 (Clone quality: bE21N23 on chr=6; Num_of_Contigs=2; )
SCN2A		ENSSSCG00000015905	15:67147950-67223934
SCN2B		ENSSSCG00000015088	9:44374321-44383848		FP102383,CH242-195F19,9:44362091-44419833 (Clone quality: bE195F19 on chr=9; Num_of_Contigs=1; )
SCN4A		ENSSSCG00000017282	12:12591089-12619924		CU466386,CH242-271O11,12:12583385-12667411 (Clone quality: bE271O11 on chr=12; Num_of_Contigs=5; )
SCN4B		ENSSSCG00000015087	9:44341689-44361448
SCN5A		ENSSSCG00000011259	13:19268539-19355430
SCN8A		ENSSSCG00000000228	5:15775900-15830824
SCN9A		ENSSSCG00000015913	15:68206582-68283686
SCN9A		location ⇒	15:66839181-66839265		CU571037,CH242-288H22,15:66835046-66846113 (Clone quality: bE288H22 on chr=15; Num_of_Contigs=8; )
SCN9A		location ⇒	15:67859298-67859355		CU928376,CH242-445M1,15:67825792-67860474 (Clone quality: bE445M1 on chr=15; Num_of_Contigs=9; )
SCN9A		location ⇒	15:67917409-67917513		FP236152,CH242-525O14,15:67912869-67918885 (Clone quality: bE525O14 on chr=15; Num_of_Contigs=17; )
SCN9A		location ⇒	15:68082348-68082244		CU468079,CH242-521F2,15:68077344-68084587 (Clone quality: bE521F2 on chr=15; Num_of_Contigs=9; )
SCNM1		ENSSSCG00000006632	4:102034145-102036663	CU138569,CH242-265M12,4:101911025-102092543 (Clone quality: bE265M12 on chr=4; Num_of_Contigs=8; )
SCNN1B		ENSSSCG00000007835	3:20951250-20999609
SCNN1D		ENSSSCG00000003328	6:42772991-42868583
SCNN1G		ENSSSCG00000007836	3:21061701-21092136		FP016036,CH242-110N18,3:21035624-21151631 (Clone quality: bE110N18 on chr=3; Num_of_Contigs=6; )
SCO1		ENSSSCG00000018008	12:52478379-52492918		CU856557,CH242-14N5,12:52466634-52504582 (Clone quality: bE14N5 on chr=12; Num_of_Contigs=6; )
SCO2		ENSSSCG00000000966	5:99709550-99710350		CU929756,CH242-288F8,5:99690941-99727774 (Clone quality: bE288F8 on chr=5; Num_of_Contigs=8; )
SCOC		ENSSSCG00000005653	1:283607936-283608280		CU862000,CH242-4D17,1:283577364-283612638 (Clone quality: bE4D17 on chr=1; Num_of_Contigs=2; )
SCP2		ENSSSCG00000003853	6:113080671-113203294
SCPEP1		ENSSSCG00000017617	12:31074498-31102483
SCRN1		ENSSSCG00000016684	18:41319073-41376514
SCRN2		ENSSSCG00000017521	12:21600831-21605247		CU655852,CH242-166I5,12:21573723-21615705 (Clone quality: bE166I5 on chr=12; Num_of_Contigs=13; )
SCRN3		ENSSSCG00000015964	15:75237237-75244760		CU694548,CH242-149L4,15:75228809-75244820 (Clone quality: bE149L4 on chr=15; Num_of_Contigs=10; )
SCRT1		ENSSSCG00000005919	4:695854-696813		FP085492,CH242-176F2,4:677220-697185 (Clone quality: bE176F2 on chr=4; Num_of_Contigs=15; )
SCTR		ENSSSCG00000015739	15:29214256-29228212
SCUBE2		ENSSSCG00000014575	9:399189-442728		CU695192,CH242-65G4,9:386580-488562 (Clone quality: bE65G4 on chr=9; 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

Report problems to zhu

iastate.edu

$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).