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)

SPIRE1		ENSSSCG00000003675	6:66406497-66420890
SPIRE2		ENSSSCG00000002635	6:36752-392496
SPN		ENSSSCG00000012850	2:238775-261809		FP015900,CH242-40P17,2:201823-266668 (Clone quality: bE40P17 on chr=2; Num_of_Contigs=6; )
SPN		ENSSSCG00000017584	12:24727275-24742760
SPNS1		ENSSSCG00000007809	3:16742604-16878319
SPNS2		ENSSSCG00000017879	12:47634040-47663202		CU929689,CH242-152D18,12:47633596-47731471 (Clone quality: bE152D18 on chr=12; Num_of_Contigs=5; )
SPNS3		ENSSSCG00000017880	12:47672232-47728171		CU929689,CH242-152D18,12:47633596-47731471 (Clone quality: bE152D18 on chr=12; Num_of_Contigs=5; )
SPO11		ENSSSCG00000007502	17:60266160-60281288	CR956362,CH242-98D1,17:60206269-60416771 (No clone quality info on bE98D1)
SPOCD1		ENSSSCG00000003606	6:60701999-60726958
SPOCK		ENSSSCG00000014320	2:126314111-126493184
SPOCK		location ⇒	2:126485565-126485628		CU929032,CH242-420A20,2:126471474-126493862 (Clone quality: bE420A20 on chr=2; Num_of_Contigs=14; )
SPOCK		location ⇒	2:126493070-126493185		CU929032,CH242-420A20,2:126471474-126493862 (Clone quality: bE420A20 on chr=2; Num_of_Contigs=14; )
SPOCK1		ENSSSCG00000014320	2:126314111-126493184
SPOCK2		ENSSSCG00000010283	14:78123712-78133143		CU469117,CH242-331I9,14:78120132-78134401 (Clone quality: bE331I9 on chr=14; Num_of_Contigs=11; )
SPOCK3		ENSSSCG00000009722	14:21490946-21857061
SPON1		ENSSSCG00000013393	2:41893073-41915049		CU457766,CH242-56H24,2:41886980-41993443 (Clone quality: bE56H24 on chr=2; Num_of_Contigs=26; )
SPON1		location ⇒	2:41893364-41893101		CU457766,CH242-56H24,2:41886980-41993443 (Clone quality: bE56H24 on chr=2; Num_of_Contigs=26; )
SPON1		location ⇒	2:41895514-41895250		CU457766,CH242-56H24,2:41886980-41993443 (Clone quality: bE56H24 on chr=2; Num_of_Contigs=26; )
SPON1		location ⇒	2:41897613-41897449		CU457766,CH242-56H24,2:41886980-41993443 (Clone quality: bE56H24 on chr=2; Num_of_Contigs=26; )
SPON1		location ⇒	2:41898636-41898469		CU457766,CH242-56H24,2:41886980-41993443 (Clone quality: bE56H24 on chr=2; Num_of_Contigs=26; )
SPOP		ENSSSCG00000017547	12:22922300-22932267		FP015993,CH242-478C13,12:22918428-22950747 (Clone quality: bE478C13 on chr=12; Num_of_Contigs=11; )
SPOPL		ENSSSCG00000015683	15:11661951-11681654
SPP1		ENSSSCG00000004517	1:102963474-102968962		CU914451,CH242-152J17,1:102889373-103019647 (Clone quality: bE152J17 on chr=1; Num_of_Contigs=3; )
SPP1		ENSSSCG00000005111	1:203357008-203366758		CU618319,CH242-25H18,1:203352954-203375604 (Clone quality: bE25H18 on chr=1; Num_of_Contigs=12; )
SPP1		ENSSSCG00000009216	8:112396255-112600779
SPP1		location ⇒	8:112397066-112396326		CU928800,CH242-113D13,8:112377370-112413435 (Clone quality: bE113D13 on chr=8; Num_of_Contigs=8; )
SPP1		location ⇒	8:112397066-112396326		CU928800,CH242-113D13,8:112377370-112413435 (Clone quality: bE113D13 on chr=8; Num_of_Contigs=8; )
SPP1		location ⇒	8:112594084-112593344	CU856168,CH242-97B16,8:112550233-112746938 (Clone quality: bE97B16 on chr=8; Num_of_Contigs=1; )
SPP1		location ⇒	8:112594084-112593344	CU856168,CH242-97B16,8:112550233-112746938 (Clone quality: bE97B16 on chr=8; Num_of_Contigs=1; )
SPP2		ENSSSCG00000016315	15:127041085-127186101
SPR		ENSSSCG00000008309	3:64096794-64101838
SPRED1		ENSSSCG00000004793	1:139642786-139697760
SPRED1		location ⇒	1:139641401-139640404		CU855961,CH242-128P7,1:139622685-139647220 (Clone quality: bE128P7 on chr=1; Num_of_Contigs=7; )
SPRED1		location ⇒	1:139643437-139641923		CU855961,CH242-128P7,1:139622685-139647220 (Clone quality: bE128P7 on chr=1; Num_of_Contigs=7; )
SPRED1		location ⇒	1:139676024-139675854		CU855961,CH242-128P7,1:139672810-139694493 (Clone quality: bE128P7 on chr=1; Num_of_Contigs=7; )
SPRED1		location ⇒	1:139697490-139697314		CU855961,CH242-128P7,1:139694594-139733012 (Clone quality: bE128P7 on chr=1; Num_of_Contigs=7; )
SPRED2		ENSSSCG00000008357	3:70488199-70520381
SPRED3		ENSSSCG00000002958	6:32512365-32517595		FP236590,CH242-507G2,6:32461085-32547641 (Clone quality: bE507G2 on chr=6; Num_of_Contigs=4; )
SPRR1_PIG		ENSSSCG00000006593	4:100427656-100451675
SPRY1		ENSSSCG00000009083	8:86572288-86573247		CU627982,CH242-25A12,8:86564543-86578966 (Clone quality: bE25A12 on chr=8; Num_of_Contigs=11; )
SPRY2		ENSSSCG00000009482	11:51317395-51318342		CU019591,CH242-459E17,11:51316658-51335285 (Clone quality: bE459E17 on chr=11; Num_of_Contigs=7; )
SPRY3		ENSSSCG00000012805	X:123095372-123096238	CU914687,CH242-92A22,X:123079486-123279612 (Clone quality: bE92A22 on chr=X; Num_of_Contigs=11; )
SPRY4		ENSSSCG00000014397	2:130591626-130592525		FP085601,CH242-263D23,2:130537541-130689057 (Clone quality: bE263D23 on chr=2; Num_of_Contigs=3; )
SPRYD3		ENSSSCG00000000262	5:16969902-16984781
SPRYD4		ENSSSCG00000000404	5:20979495-20990348
SPSB3		ENSSSCG00000008015	3:35885199-35921315
SPTA1		ENSSSCG00000006431	4:95123703-95187441
SPTAN1		ENSSSCG00000005654	1:283617055-283683474
SPTAN1		location ⇒	1:283677916-283678214		CU862000,CH242-4D17,1:283660123-283729806 (Clone quality: bE4D17 on chr=1; Num_of_Contigs=2; )
SPTAN1		location ⇒	1:283681746-283681943		CU862000,CH242-4D17,1:283660123-283729806 (Clone quality: bE4D17 on chr=1; Num_of_Contigs=2; )

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).