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)

ATG4C		ENSSSCG00000003816	6:105495136-105577945		CU467524,CH242-188P17,6:105489671-105579164 (Clone quality: bE188P17 on chr=6; Num_of_Contigs=6; )
ATG4D		ENSSSCG00000013645	2:52961252-52969079		CU993813,CH242-86K24,2:52943491-52988729 (Clone quality: bE86K24 on chr=2; Num_of_Contigs=13; )
ATG5		ENSSSCG00000004370	1:75884869-75910222
ATG7		ENSSSCG00000011575	13:56032507-56080590		CU915532,CH242-98O11,13:56030144-56092732 (Clone quality: bE98O11 on chr=13; Num_of_Contigs=3; )
ATG9A		ENSSSCG00000016211	15:114251285-114260087
ATHL1		ENSSSCG00000014562	2:139903415-139909011		CU928488,CH242-163I11,2:139819049-139956868 (Clone quality: bE163I11 on chr=2; Num_of_Contigs=2; )
ATIC		ENSSSCG00000016173	15:110700540-110931082
ATL2		ENSSSCG00000008487	3:94935004-95028975
ATL3		ENSSSCG00000013054	2:6895331-6936849
ATM		ENSSSCG00000010489	14:111712241-111714699		CU392852,CH242-517O10,14:111696262-111826906 (Clone quality: bE517O10 on chr=14; Num_of_Contigs=2; )
ATM		ENSSSCG00000015007	9:35998717-36015437		CU464170,CH242-497A10,9:35993120-36064035 (Clone quality: bE497A10 on chr=9; Num_of_Contigs=4; )
ATM		location ⇒	9:36003222-36003290		CU464170,CH242-497A10,9:35993120-36064035 (Clone quality: bE497A10 on chr=9; Num_of_Contigs=4; )
ATM		location ⇒	9:36009874-36009981		CU464170,CH242-497A10,9:35993120-36064035 (Clone quality: bE497A10 on chr=9; Num_of_Contigs=4; )
ATM		location ⇒	9:36011011-36011078		CU464170,CH242-497A10,9:35993120-36064035 (Clone quality: bE497A10 on chr=9; Num_of_Contigs=4; )
ATM		location ⇒	9:36015010-36015148		CU464170,CH242-497A10,9:35993120-36064035 (Clone quality: bE497A10 on chr=9; Num_of_Contigs=4; )
ATOH1		ENSSSCG00000009196	8:107872512-107873573		CU464003,CH242-220H23,8:107843572-107959060 (Clone quality: bE220H23 on chr=8; Num_of_Contigs=3; )
ATOH8		ENSSSCG00000008230	3:54029193-54040001		CU928286,CH242-219K12,3:54011146-54043118 (Clone quality: bE219K12 on chr=3; Num_of_Contigs=4; )
ATP10A		ENSSSCG00000004830	1:149061228-149111747
ATP10B		ENSSSCG00000017031	16:60420254-60438902
ATP10D		ENSSSCG00000008812	8:32122853-32198678
ATP11C		ENSSSCG00000012713	X:112382382-112478082		CU582842,CH242-1I19,X:112356591-112507809 (Clone quality: bE1I19 on chr=X; Num_of_Contigs=2; )
ATP12A		ENSSSCG00000009577	11:79781734-79795640
ATP13A1		ENSSSCG00000013930	2:63356154-63376247
ATP13A2		ENSSSCG00000003480	6:52086112-52115649
ATP13A3		ENSSSCG00000011825	13:98954433-99035987
ATP13A4		ENSSSCG00000011821	13:98611342-98681842
ATP1A1		ENSSSCG00000006740	4:108659640-108679554		CU302284,CH242-488D4,4:108656809-108684101 (Clone quality: bE488D4 on chr=4; Num_of_Contigs=9; )
ATP1A1		location ⇒	4:108674080-108673807		CU302284,CH242-488D4,4:108656809-108684101 (Clone quality: bE488D4 on chr=4; Num_of_Contigs=9; )
ATP1A1		location ⇒	4:93747677-93747603	CU138477,CH242-105O19,4:93708821-93889364 (Clone quality: bE105O19 on chr=4; Num_of_Contigs=5; )
ATP1A1		location ⇒	4:93758240-93758161	CU138477,CH242-105O19,4:93708821-93889364 (Clone quality: bE105O19 on chr=4; Num_of_Contigs=5; )
ATP1A1		location ⇒	4:93801979-93801912	CU138477,CH242-105O19,4:93708821-93889364 (Clone quality: bE105O19 on chr=4; Num_of_Contigs=5; )
ATP1A2		ENSSSCG00000006391	4:93788196-93812587	CU138477,CH242-105O19,4:93708821-93889364 (Clone quality: bE105O19 on chr=4; Num_of_Contigs=5; )
ATP1A3		ENSSSCG00000003045	6:34648631-34665650		FP015926,CH242-183C8,6:34644556-34665777 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
ATP1B1		ENSSSCG00000006296	4:85270018-85293969
ATP1B2		ENSSSCG00000017951	12:50007012-50011730	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
ATP1B3		location ⇒	9:14890199-14891472		CU951454,CH242-289A19,9:14871744-14899943 (Clone quality: bE289A19 on chr=9; Num_of_Contigs=1; )
ATP1B4		ENSSSCG00000012606	X:95914706-96018092
ATP2A1		ENSSSCG00000007805	3:16659991-16680428
ATP2A2		ENSSSCG00000009819	14:31714261-31775391
ATP2A2		location ⇒	14:31758654-31759118		CT737366,CH242-196F5,14:31617728-31761686 (Clone quality: bE196F5 on chr=14; Num_of_Contigs=2; )
ATP2A2		location ⇒	14:31771758-31771979		CU467926,CH242-205M8,14:31771027-31793371 (Clone quality: bE205M8 on chr=14; Num_of_Contigs=11; )
ATP2A2		location ⇒	14:31772387-31772592		CU467926,CH242-205M8,14:31771027-31793371 (Clone quality: bE205M8 on chr=14; Num_of_Contigs=11; )
ATP2A2		location ⇒	14:31775122-31776222		CU467926,CH242-205M8,14:31771027-31793371 (Clone quality: bE205M8 on chr=14; Num_of_Contigs=11; )
ATP2A3		ENSSSCG00000017874	12:47316615-47326109		CU655866,CH242-344D10,12:47312999-47327464 (Clone quality: bE344D10 on chr=12; Num_of_Contigs=11; )
ATP2A3		location ⇒	3:16677124-16677195		CU928476,CH242-24P1,3:16664467-16683188 (Clone quality: bE24P1 on chr=3; Num_of_Contigs=5; )
ATP2B1		ENSSSCG00000000921	5:87958687-87973227		CU457444,CH242-365K13,5:87952870-87991764 (Clone quality: bE365K13 on chr=5; Num_of_Contigs=4; )
ATP2B1		location ⇒	5:87958696-87958889		CU457444,CH242-365K13,5:87952870-87991764 (Clone quality: bE365K13 on chr=5; Num_of_Contigs=4; )
ATP2B1		location ⇒	5:87959098-87959312		CU457444,CH242-365K13,5:87952870-87991764 (Clone quality: bE365K13 on chr=5; Num_of_Contigs=4; )
ATP2B1		location ⇒	5:87959757-87959969		CU457444,CH242-365K13,5:87952870-87991764 (Clone quality: bE365K13 on chr=5; Num_of_Contigs=4; )
ATP2B1		location ⇒	5:87972761-87973222		CU457444,CH242-365K13,5:87952870-87991764 (Clone quality: bE365K13 on chr=5; Num_of_Contigs=4; )

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).