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)

SRF		ENSSSCG00000001674	7:44482572-44490295		CU633197,CH242-208A12,7:44468928-44491614 (Clone quality: bE208A12 on chr=7; Num_of_Contigs=8; )
SRF		ENSSSCG00000003881	6:116750667-116836008
SRGAP1		ENSSSCG00000000463	5:28242156-28250371		CU463965,CH242-324I12,5:28139329-28252131 (Clone quality: bE324I12 on chr=5; Num_of_Contigs=2; )
SRGAP2		ENSSSCG00000000463	5:28242156-28250371		CU463965,CH242-324I12,5:28139329-28252131 (Clone quality: bE324I12 on chr=5; Num_of_Contigs=2; )
SRGAP2		location ⇒	9:131371039-131370714		FP102405,CH242-268I11,9:131368851-131377378 (Clone quality: bE268I11 on chr=9; Num_of_Contigs=3; )
SRGAP2		location ⇒	9:131382379-131383074
SRGAP2		location ⇒	9:131383121-131383940		FP102872,CH242-139J15,9:131382379-131386418 (Clone quality: bE139J15 on chr=9; Num_of_Contigs=9; )
SRGAP2		location ⇒	9:131384512-131385617		FP102872,CH242-139J15,9:131382379-131386418 (Clone quality: bE139J15 on chr=9; Num_of_Contigs=9; )
SRGAP3		location ⇒	13:54618410-54618610		CU928436,CH242-299D23,13:54602943-54690385 (Clone quality: bE299D23 on chr=13; Num_of_Contigs=8; )
SRGAP3		location ⇒	13:54618782-54619128		CU928436,CH242-299D23,13:54602943-54690385 (Clone quality: bE299D23 on chr=13; Num_of_Contigs=8; )
SRGAP3		location ⇒	13:54743652-54743847		CU928436,CH242-299D23,13:54733914-54752453 (Clone quality: bE299D23 on chr=13; Num_of_Contigs=8; )
SRGAP3		location ⇒	13:54755407-54755245		CU928436,CH242-299D23,13:54752554-54766606 (Clone quality: bE299D23 on chr=13; Num_of_Contigs=8; )
SRGN		ENSSSCG00000010249	14:75329507-75346802
SRGN		location ⇒	14:75343776-75343882		CT737222,CH242-62M1,14:75343233-75510707 (Clone quality: bE62M1 on chr=14; Num_of_Contigs=1; )
SRGN		location ⇒	14:75347339-75347448		CT737222,CH242-62M1,14:75343233-75510707 (Clone quality: bE62M1 on chr=14; Num_of_Contigs=1; )
SRI		ENSSSCG00000015298	9:63887349-63902649		CU695059,CH242-345H3,9:63879805-64040257 (Clone quality: bE345H3 on chr=9; Num_of_Contigs=1; )
SRL		ENSSSCG00000007949	3:34146708-34157800		FP089483,CH242-216B18,3:34139809-34181580 (Clone quality: bE216B18 on chr=3; Num_of_Contigs=4; )
SRM		ENSSSCG00000003411	6:48024205-48027317
SRP19		ENSSSCG00000014206	2:105620817-105628084		CU856120,CH242-510G20,2:105607531-105633212 (Clone quality: bE510G20 on chr=2; Num_of_Contigs=10; )
SRP54		ENSSSCG00000001955	7:70619949-70668714
SRP68		ENSSSCG00000017191	12:3726699-3760988
SRP72		ENSSSCG00000008900	8:47111232-47142651		CU606852,CH242-220F7,8:47084665-47178142 (Clone quality: bE220F7 on chr=8; Num_of_Contigs=9; )
SRPK1		ENSSSCG00000001554	7:36268680-36330279
SRPRB		ENSSSCG00000011639	13:61486750-61519167		CU633685,CH242-265M20,13:61378623-61549248 (Clone quality: bE265M20 on chr=13; Num_of_Contigs=2; )
SRPX		ENSSSCG00000012234	X:33531792-33650133
SRPX		location ⇒	X:33532327-33531832	CU207420,CH242-423B7,X:33462829-33637204 (Clone quality: bE423B7 on chr=X; Num_of_Contigs=5; )
SRPX		location ⇒	X:33546912-33546787	CU207420,CH242-423B7,X:33462829-33637204 (Clone quality: bE423B7 on chr=X; Num_of_Contigs=5; )
SRPX		location ⇒	X:33557297-33557161	CU207420,CH242-423B7,X:33462829-33637204 (Clone quality: bE423B7 on chr=X; Num_of_Contigs=5; )
SRPX2		ENSSSCG00000012482	X:75680819-75707940		CU207261,CH242-166I17,X:75651367-75713469 (Clone quality: bE166I17 on chr=X; Num_of_Contigs=6; )
SRP_euk_arch		ENSSSCG00000018426	13:76081109-76081407		CU466509,CH242-517N1,13:76026848-76122515 (Clone quality: bE517N1 on chr=13; Num_of_Contigs=3; )
SRP_euk_arch		ENSSSCG00000018788	1:187872885-187873181		CU633502,CH242-240C20,1:187832890-187878221 (Clone quality: bE240C20 on chr=1; Num_of_Contigs=4; )
SRP_euk_arch		ENSSSCG00000018901	1:228874107-228874403		CU618324,CH242-276M24,1:228857825-228880847 (Clone quality: bE276M24 on chr=1; Num_of_Contigs=4; )
SRP_euk_arch		ENSSSCG00000019545	5:81985086-81985364		FP102267,CH242-81I11,5:81855271-82016430 (Clone quality: bE81I11 on chr=5; Num_of_Contigs=1; )
SRP_euk_arch		ENSSSCG00000018176	3:93758083-93758381
SRP_euk_arch		ENSSSCG00000019995	1:188087244-188087540		CU606975,CH242-251A8,1:188036812-188088768 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
SRP_euk_arch		ENSSSCG00000019736	7:24236112-24236406	FP085562,CH242-160O9,7:24118819-24263585 (Clone quality: bE160O9 on chr=7; Num_of_Contigs=12; )
SRP_euk_arch		ENSSSCG00000019855	9:105844955-105845260		CU693385,CH242-143F22,9:105742784-105878546 (Clone quality: bE143F22 on chr=9; Num_of_Contigs=2; )
SRP_euk_arch		ENSSSCG00000019407	1:188101726-188102022		CU606975,CH242-251A8,1:188088869-188146416 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
SRP_euk_arch		ENSSSCG00000019100	5:82105518-82105796		CU457471,CH242-277A17,5:82103159-82108485 (Clone quality: bE277A17 on chr=5; Num_of_Contigs=4; )
SRP_euk_arch		ENSSSCG00000019312	8:35666766-35667061		FP015961,CH242-68J9,8:35666593-35707684 (Clone quality: bE68J9 on chr=8; Num_of_Contigs=5; )
SRP_euk_arch		ENSSSCG00000019622	13:28805793-28806089		CU914695,CH242-195P19,13:28772257-28826761 (Clone quality: bE195P19 on chr=13; Num_of_Contigs=14; )
SRR		ENSSSCG00000017827	12:45848928-45855592		CU640470,CH242-300A22,12:45800890-45898822 (Clone quality: bE300A22 on chr=12; Num_of_Contigs=5; )
SRRD		ENSSSCG00000009961	14:44815970-44838730
SRRM1		ENSSSCG00000003545	6:56792395-56826807
SRRM4		ENSSSCG00000009846	14:33901249-33912313		CU856553,CH242-13D3,14:33898331-33916043 (Clone quality: bE13D3 on chr=14; Num_of_Contigs=22; )
SRRM5		ENSSSCG00000003060	6:34955504-34957372		FP102604,CH242-184P4,6:34931170-34967938 (No clone quality info on )
SS18		ENSSSCG00000003716	6:76243402-76320545
SS18L2		ENSSSCG00000011283	13:21979641-21982806		CU928031,CH242-357P22,13:21974185-22006928 (Clone quality: bE357P22 on chr=13; Num_of_Contigs=3; )
SSA1		ENSSSCG00000014780	9:5122888-5130672		CU915729,CH242-257A21,9:5115921-5135602 (Clone quality: bE257A21 on chr=9; Num_of_Contigs=10; )
SSA1		location ⇒	9:132302086-132301994		CU633410,CH242-391L17,9:132252384-132466044 (Clone quality: bE391L17 on chr=9; 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

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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).