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)

ANGPT1		location ⇒	4:30025437-30025833
ANGPT1		location ⇒	4:30312770-30313280		CU467718,CH242-27F1,4:30302193-30380282 (Clone quality: bE27F1 on chr=4; Num_of_Contigs=6; )
ANGPT1		location ⇒	4:30315261-30315344		CU467718,CH242-27F1,4:30302193-30380282 (Clone quality: bE27F1 on chr=4; Num_of_Contigs=6; )
ANGPT1		location ⇒	4:30315465-30315552		CU467718,CH242-27F1,4:30302193-30380282 (Clone quality: bE27F1 on chr=4; Num_of_Contigs=6; )
ANGPT2		ENSSSCG00000015753	15:34591356-34702700
ANGPT4		ENSSSCG00000007198	17:36122402-36167016
ANGPTL1		ENSSSCG00000015522	9:113351224-113368504		CU633555,CH242-205J12,9:113348988-113374704 (Clone quality: bE205J12 on chr=9; Num_of_Contigs=9; )
ANGPTL2		ENSSSCG00000005608	1:281992701-282012979		CU570734,CH242-291A18,1:281951292-282025802 (Clone quality: bE291A18 on chr=1; Num_of_Contigs=4; )
ANGPTL3		ENSSSCG00000003819	6:105913737-105923539		CU442730,CH242-139A14,6:105850601-105994617 (Clone quality: bE139A14 on chr=6; Num_of_Contigs=1; )
ANGPTL3		location ⇒	6:105914328-105914103		CU442730,CH242-139A14,6:105850601-105994617 (Clone quality: bE139A14 on chr=6; Num_of_Contigs=1; )
ANGPTL3		location ⇒	6:105914959-105914691		CU442730,CH242-139A14,6:105850601-105994617 (Clone quality: bE139A14 on chr=6; Num_of_Contigs=1; )
ANGPTL3		location ⇒	6:105918040-105917923		CU442730,CH242-139A14,6:105850601-105994617 (Clone quality: bE139A14 on chr=6; Num_of_Contigs=1; )
ANGPTL3		location ⇒	6:105923562-105923045		CU442730,CH242-139A14,6:105850601-105994617 (Clone quality: bE139A14 on chr=6; Num_of_Contigs=1; )
ANGPTL4		ENSSSCG00000013599	2:51661362-51668630		FP090904,CH242-212F1,2:51608045-51700090 (Clone quality: bE212F1 on chr=2; Num_of_Contigs=2; )
ANGPTL4		location ⇒	2:51661504-51661930		FP090904,CH242-212F1,2:51608045-51700090 (Clone quality: bE212F1 on chr=2; Num_of_Contigs=2; )
ANGPTL4		location ⇒	2:51662319-51662441		FP090904,CH242-212F1,2:51608045-51700090 (Clone quality: bE212F1 on chr=2; Num_of_Contigs=2; )
ANGPTL4		location ⇒	2:51666158-51666444		FP090904,CH242-212F1,2:51608045-51700090 (Clone quality: bE212F1 on chr=2; Num_of_Contigs=2; )
ANGPTL4		location ⇒	2:51667960-51668629		FP090904,CH242-212F1,2:51608045-51700090 (Clone quality: bE212F1 on chr=2; Num_of_Contigs=2; )
ANGPTL5		ENSSSCG00000014978	9:32419929-32436878		CU639456,CH242-236M19,9:32375977-32501103 (Clone quality: bE236M19 on chr=9; Num_of_Contigs=2; )
ANGPTL6		ENSSSCG00000013663	2:53410011-53413401		CU462940,CH242-319N14,2:53390856-53454909 (Clone quality: bE319N14 on chr=2; Num_of_Contigs=3; )
ANGPTL7		ENSSSCG00000003414	6:48115411-48121120		CU929865,CH242-128C5,6:48070432-48147672 (Clone quality: bE128C5 on chr=6; Num_of_Contigs=2; )
ANK1		location ⇒	17:10524691-10524776		CU606939,CH242-152E6,17:10516707-10539534 (Clone quality: bE152E6 on chr=17; Num_of_Contigs=8; )
ANK1		location ⇒	17:10556126-10556199		CU606939,CH242-152E6,17:10539635-10615238 (Clone quality: bE152E6 on chr=17; Num_of_Contigs=8; )
ANK1		location ⇒	17:10818921-10819006		CU607010,CH242-309J7,17:10815796-10820625 (Clone quality: bE309J7 on chr=17; Num_of_Contigs=6; )
ANK1		location ⇒	17:10897436-10897351		CU407001,CH242-336P3,17:10883355-10958368 (Clone quality: bE336P3 on chr=17; Num_of_Contigs=6; )
ANK2		ENSSSCG00000009125	8:93935642-94260375
ANK3		ENSSSCG00000010212	14:66043448-66337057
ANKDD1A		ENSSSCG00000004545	1:110257675-110289633
ANKDD1B		ENSSSCG00000014083	2:73478095-73542057
ANKFN1		ENSSSCG00000017609	12:30352923-30616668
ANKFY1		ENSSSCG00000017877	12:47448928-47502467		FP067370,CH242-167N15,12:47435523-47507053 (Clone quality: bE167N15 on chr=12; Num_of_Contigs=3; )
ANKH		ENSSSCG00000016784	16:3367401-3388588		FP016119,CH242-235L15,16:3364905-3405008 (Clone quality: bE235L15 on chr=16; Num_of_Contigs=3; )
ANKHD1		ENSSSCG00000014364	2:129174209-129313297
ANKIB1		ENSSSCG00000015314	9:67732870-67803649
ANKMY1		ENSSSCG00000016365	15:131666942-131700913
ANKMY2		ENSSSCG00000015360	9:80353951-80364012		FP102811,CH242-114K4,9:80349705-80368187 (Clone quality: bE114K4 on chr=9; Num_of_Contigs=4; )
ANKRA2		ENSSSCG00000014070	2:71568269-71581131
ANKRA2		ENSSSCG00000014070	2:71568269-71581131
ANKRD1		ENSSSCG00000010461	14:107545885-107554865		CU468426,CH242-393K2,14:107512155-107560763 (Clone quality: bE393K2 on chr=14; Num_of_Contigs=3; )
ANKRD10		ENSSSCG00000009548	11:77575293-77599887
ANKRD10		location ⇒	11:77585508-77585278		FP016099,CH242-239C16,11:77573093-77591626 (Clone quality: bE239C16 on chr=11; Num_of_Contigs=7; )
ANKRD10		location ⇒	11:77745787-77745662		FP016099,CH242-239C16,11:77739026-77747534 (Clone quality: bE239C16 on chr=11; Num_of_Contigs=7; )
ANKRD11		ENSSSCG00000002641	6:271021-272181		FP102614,CH242-198I21,6:270189-272191 (Clone quality: bE198I21 on chr=6; Num_of_Contigs=22; )
ANKRD12		ENSSSCG00000003682	6:67376351-67467410
ANKRD13C		ENSSSCG00000003790	6:100275112-100379805
ANKRD1523189		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
ANKRD2		ENSSSCG00000010522	14:113787537-113801204		CU407093,CH242-523G22,14:113665116-113843304 (Clone quality: bE523G22 on chr=14; Num_of_Contigs=4; )
ANKRD22		ENSSSCG00000010445	14:105648630-105671648		CU407100,CH242-6G15,14:105633579-105756079 (Clone quality: bE6G15 on chr=14; Num_of_Contigs=2; )
ANKRD23		ENSSSCG00000008200	3:52166600-52171312		FP102744,CH242-70H5,3:52166217-52203121 (Clone quality: bE70H5 on chr=3; Num_of_Contigs=11; )
ANKRD24		ENSSSCG00000013497	2:48395701-48410767		CU929466,CH242-60A20,2:48379010-48440195 (Clone quality: bE60A20 on chr=2; Num_of_Contigs=5; )

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, 1751-32

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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).