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)

ASTN1		location ⇒	9:111559330-111559075		FP090898,CH242-188I21,9:111556970-111561724 (Clone quality: bE188I21 on chr=9; Num_of_Contigs=4; )
ASTN1		location ⇒	9:111599872-111599959		FP090898,CH242-188I21,9:111593216-111605875 (Clone quality: bE188I21 on chr=9; Num_of_Contigs=4; )
ASTN1		location ⇒	9:111667105-111666919		FP090898,CH242-188I21,9:111665000-111681072 (Clone quality: bE188I21 on chr=9; Num_of_Contigs=4; )
ASTN1		location ⇒	9:111832673-111832487		CU928937,CH242-5B23,9:111831457-111844874 (Clone quality: bE5B23 on chr=9; Num_of_Contigs=4; )
ASTN2		ENSSSCG00000005502	1:270408190-271210716
ASXL1		ENSSSCG00000007248	17:38069036-38078072		CU075917,CH242-158M7,17:38014651-38109830 (Clone quality: bE158M7 on chr=17; Num_of_Contigs=7; )
ASXL2		ENSSSCG00000008575	3:105630977-105725398
ASXL3		ENSSSCG00000003736	6:81424600-81574531
ASZ1		ENSSSCG00000016627	18:27360547-27412030
ATAD1		ENSSSCG00000010438	14:104672485-104741774
ATAD2		ENSSSCG00000005983	4:15590532-15657584
ATBF1		ENSSSCG00000002752	6:11156755-11256719
ATE1		ENSSSCG00000010699	14:137754459-137916665
ATF1		ENSSSCG00000016847	16:20441100-20441582		CU633723,CH242-522B12,16:20437423-20444873 (Clone quality: bE522B12 on chr=16; Num_of_Contigs=19; )
ATF1		location ⇒	5:15101976-15101873		CU457435,CH242-196H9,5:15100122-15104315 (Clone quality: bE196H9 on chr=5; Num_of_Contigs=21; )
ATF1		location ⇒	5:15115201-15115302		CU457435,CH242-196H9,5:15114631-15118953 (Clone quality: bE196H9 on chr=5; Num_of_Contigs=21; )
ATF2		ENSSSCG00000016847	16:20441100-20441582		CU633723,CH242-522B12,16:20437423-20444873 (Clone quality: bE522B12 on chr=16; Num_of_Contigs=19; )
ATF2		ENSSSCG00000015972	15:75905746-76025052
ATF2		location ⇒	15:75906169-75905617		FP015759,CH242-149L11,15:75875101-75913722 (Clone quality: bE149L11 on chr=15; Num_of_Contigs=3; )
ATF2		location ⇒	15:75923027-75922820		FP015759,CH242-149L11,15:75913823-75932069 (Clone quality: bE149L11 on chr=15; Num_of_Contigs=3; )
ATF2		location ⇒	15:76008000-76007947		CU694603,CH242-31D5,15:75991346-76011973 (Clone quality: bE31D5 on chr=15; Num_of_Contigs=5; )
ATF2		location ⇒	15:76025061-76024989		CU694603,CH242-31D5,15:76024022-76113924 (Clone quality: bE31D5 on chr=15; Num_of_Contigs=5; )
ATF3		ENSSSCG00000015595	9:123225230-123237460
ATF3		location ⇒	9:123224345-123224149		CU928715,CH242-114L21,9:123222733-123226496 (Clone quality: bE114L21 on chr=9; Num_of_Contigs=13; )
ATF4		ENSSSCG00000000084	5:5062591-5064668		CU424445,CH242-128A11,5:5029969-5093393 (Clone quality: bE128A11 on chr=5; Num_of_Contigs=8; )
ATF4		location ⇒	5:5063492-5062593		CU424445,CH242-128A11,5:5029969-5093393 (Clone quality: bE128A11 on chr=5; Num_of_Contigs=8; )
ATF4		location ⇒	5:5063905-5063588		CU424445,CH242-128A11,5:5029969-5093393 (Clone quality: bE128A11 on chr=5; Num_of_Contigs=8; )
ATF4		location ⇒	5:5064668-5064477		CU424445,CH242-128A11,5:5029969-5093393 (Clone quality: bE128A11 on chr=5; Num_of_Contigs=8; )
ATF5		ENSSSCG00000003201	6:38624735-38627251		CU464193,CH242-278I19,6:38623409-38646899 (Clone quality: bE278I19 on chr=6; Num_of_Contigs=12; )
ATF6		ENSSSCG00000006346	4:92291550-92486277
ATF6		location ⇒	4:77533525-77533437	CU151871,CH242-290E19,4:77372663-77578094 (Clone quality: bE290E19 on chr=4; Num_of_Contigs=5; )
ATF6		location ⇒	4:97197180-97197092		FP102690,CH242-379E5,4:97171793-97207767 (Clone quality: bE379E5 on chr=4; Num_of_Contigs=15; )
ATF6		location ⇒	4:97468461-97468373		CU633176,CH242-238D11,4:97443546-97499073 (Clone quality: bE238D11 on chr=4; Num_of_Contigs=11; )
ATF6		location ⇒	4:98586657-98586581		CU469433,CH242-42F16,4:98584345-98587087 (Clone quality: bE42F16 on chr=4; Num_of_Contigs=13; )
ATF7		ENSSSCG00000000278	5:17282499-17306281		CU928648,CH242-523B11,5:17274658-17333972 (Clone quality: bE523B11 on chr=5; Num_of_Contigs=8; )
ATF7		location ⇒	5:17291845-17291954		CU928648,CH242-523B11,5:17274658-17333972 (Clone quality: bE523B11 on chr=5; Num_of_Contigs=8; )
ATF7		location ⇒	5:17293839-17294000		CU928648,CH242-523B11,5:17274658-17333972 (Clone quality: bE523B11 on chr=5; Num_of_Contigs=8; )
ATF7		location ⇒	5:17296112-17296251		CU928648,CH242-523B11,5:17274658-17333972 (Clone quality: bE523B11 on chr=5; Num_of_Contigs=8; )
ATF7		location ⇒	5:17301967-17302080		CU928648,CH242-523B11,5:17274658-17333972 (Clone quality: bE523B11 on chr=5; Num_of_Contigs=8; )
ATF7IP		ENSSSCG00000000612	5:55106636-55171022
ATG12		ENSSSCG00000014220	2:108684028-108700206
ATG12		location ⇒	2:108683616-108683552		FP017291,CH242-139C12,2:108594376-108687090 (Clone quality: bE139C12 on chr=2; Num_of_Contigs=3; )
ATG12		location ⇒	2:108684586-108684523		FP017291,CH242-139C12,2:108594376-108687090 (Clone quality: bE139C12 on chr=2; Num_of_Contigs=3; )
ATG12		location ⇒	2:108685561-108685498		FP017291,CH242-139C12,2:108594376-108687090 (Clone quality: bE139C12 on chr=2; Num_of_Contigs=3; )
ATG12		location ⇒	2:108690266-108690141		FP017291,CH242-139C12,2:108687191-108705806 (Clone quality: bE139C12 on chr=2; Num_of_Contigs=3; )
ATG16L1		ENSSSCG00000016300	15:126228103-126270179
ATG16L2		ENSSSCG00000014819	9:6979934-6993398		CU694608,CH242-349P16,9:6959324-7004274 (Clone quality: bE349P16 on chr=9; Num_of_Contigs=4; )
ATG2B		ENSSSCG00000002502	7:126444772-126524372		CU633930,CH242-67N6,7:126414601-126572725 (Clone quality: bE67N6 on chr=7; Num_of_Contigs=2; )
ATG3		ENSSSCG00000011930	13:109888655-109918847
ATG4A		ENSSSCG00000012569	X:86724128-86904448

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).