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)

ARHGAP9		ENSSSCG00000000438	5:21735933-21741811		CU896550,CH242-139E23,5:21710330-21749924 (Clone quality: bE139E23 on chr=5; Num_of_Contigs=9; )
ARHGDIB		ENSSSCG00000000604	5:54887166-54907197
ARHGDIB		location ⇒	5:54896921-54897104		CU463008,CH242-511E2,5:54879850-54900376 (Clone quality: bE511E2 on chr=5; Num_of_Contigs=3; )
ARHGDIB		location ⇒	5:54897932-54898020		CU463008,CH242-511E2,5:54879850-54900376 (Clone quality: bE511E2 on chr=5; Num_of_Contigs=3; )
ARHGDIB		location ⇒	5:54903834-54903897		CU463008,CH242-511E2,5:54900477-54907507 (Clone quality: bE511E2 on chr=5; Num_of_Contigs=3; )
ARHGDIB		location ⇒	5:54906455-54906726		CU463008,CH242-511E2,5:54900477-54907507 (Clone quality: bE511E2 on chr=5; Num_of_Contigs=3; )
ARHGDIG398		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
ARHGEF1		ENSSSCG00000003040	6:34598042-34612084		FP015926,CH242-183C8,6:34597834-34614592 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
ARHGEF10		location ⇒	6:52472068-52471998		FP103033,CH242-5A4,6:52470097-52496574 (Clone quality: bE5A4 on chr=6; Num_of_Contigs=4; )
ARHGEF10		location ⇒	6:52472874-52472810		FP103033,CH242-5A4,6:52470097-52496574 (Clone quality: bE5A4 on chr=6; Num_of_Contigs=4; )
ARHGEF10L		ENSSSCG00000003486	6:52462643-52540557
ARHGEF11		ENSSSCG00000006461	4:96799050-96852957
ARHGEF12		ENSSSCG00000015129	9:46152246-46228243
ARHGEF17		ENSSSCG00000014822	9:7389362-7392565		FP102302,CH242-226L8,9:7387994-7417357 (Clone quality: bE226L8 on chr=9; Num_of_Contigs=9; )
ARHGEF18		ENSSSCG00000013568	2:50860218-51020099
ARHGEF19		ENSSSCG00000003472	6:51729378-51739595		FP103064,CH242-117J7,6:51686107-51745024 (Clone quality: bE117J7 on chr=6; Num_of_Contigs=6; )
ARHGEF2		ENSSSCG00000006502	4:97995684-98026848		CU151868,CH242-286M6,4:97945564-98074701 (Clone quality: bE286M6 on chr=4; Num_of_Contigs=4; )
ARHGEF4		ENSSSCG00000016390	15:133559290-133560282		CU929673,CH242-75H18,15:133555168-133568456 (Clone quality: bE75H18 on chr=15; Num_of_Contigs=2; )
ARHGEF5		ENSSSCG00000015466	9:106301474-106323349
ARHGEF7		ENSSSCG00000009551	11:77844097-77936464
ARHGEF7		location ⇒	11:77898243-77898390		CU618308,CH242-131L16,11:77876634-77947370 (Clone quality: bE131L16 on chr=11; Num_of_Contigs=5; )
ARHGEF7		location ⇒	11:77900754-77900843		CU618308,CH242-131L16,11:77876634-77947370 (Clone quality: bE131L16 on chr=11; Num_of_Contigs=5; )
ARHGEF7		location ⇒	11:77902936-77903017		CU618308,CH242-131L16,11:77876634-77947370 (Clone quality: bE131L16 on chr=11; Num_of_Contigs=5; )
ARHGEF7		location ⇒	11:77903221-77903363		CU618308,CH242-131L16,11:77876634-77947370 (Clone quality: bE131L16 on chr=11; Num_of_Contigs=5; )
ARHGEF9		ENSSSCG00000012362	X:50306207-50393778
ARID1A		ENSSSCG00000003559	6:57698526-57794429
ARID1B		ENSSSCG00000004064	1:10682232-10723953
ARID2		ENSSSCG00000000805	5:72548767-72548910		CU694768,CH242-151M22,5:72545575-72628205 (Clone quality: bE151M22 on chr=5; Num_of_Contigs=3; )
ARID3A		ENSSSCG00000013414	2:46101495-46418194
ARID3B		ENSSSCG00000001905	7:64435293-64538483
ARID3C		ENSSSCG00000010971	10:30617509-30624046		CU928717,CH242-142N10,10:30613639-30641888 (Clone quality: bE142N10 on chr=10; Num_of_Contigs=7; )
ARID4A		ENSSSCG00000005073	1:196253123-196447019
ARID4B		ENSSSCG00000010156	14:57189425-57285323		CU469165,CH242-48O20,14:57173522-57298970 (Clone quality: bE48O20 on chr=14; Num_of_Contigs=3; )
ARID4B		location ⇒	14:57003008-57002589		CU468332,CH242-22D2,14:57000014-57004336 (Clone quality: bE22D2 on chr=14; Num_of_Contigs=15; )
ARID4B		location ⇒	14:57271848-57272674		CU469165,CH242-48O20,14:57173522-57298970 (Clone quality: bE48O20 on chr=14; Num_of_Contigs=3; )
ARID4B		location ⇒	14:57278388-57278442		CU469165,CH242-48O20,14:57173522-57298970 (Clone quality: bE48O20 on chr=14; Num_of_Contigs=3; )
ARID4B		location ⇒	14:57284912-57286670		CU469165,CH242-48O20,14:57173522-57298970 (Clone quality: bE48O20 on chr=14; Num_of_Contigs=3; )
ARID5A		ENSSSCG00000008123	3:41785350-41789796		FP102745,CH242-70I16,3:41774995-41793825 (Clone quality: bE70I16 on chr=3; Num_of_Contigs=1; )
ARID5B		ENSSSCG00000010219	14:67947025-68183610
ARIH1		ENSSSCG00000001922	7:65974641-66013214		CU571030,CH242-26L13,7:65973790-66032617 (Clone quality: bE26L13 on chr=7; Num_of_Contigs=6; )
ARIH2		ENSSSCG00000011367	13:26494590-26544983
ARL10		ENSSSCG00000014059	2:70507318-70508337	CU993810,CH242-56M9,2:70506299-70646692 (Clone quality: bE56M9 on chr=2; Num_of_Contigs=3; )
ARL11		ENSSSCG00000009394	11:18069454-18069978		CU928475,CH242-205I22,11:18067774-18085527 (Clone quality: bE205I22 on chr=11; Num_of_Contigs=6; )
ARL13A		ENSSSCG00000012488	X:76008436-76020048		FP015894,CH242-19K5,X:75928516-76058542 (Clone quality: bE19K5 on chr=X; Num_of_Contigs=2; )
ARL14		ENSSSCG00000011734	13:78943940-78944518		CU468903,CH242-109N4,13:78936266-78945454 (Clone quality: bE109N4 on chr=13; Num_of_Contigs=22; )
ARL15		ENSSSCG00000016894	16:30466788-30752803
ARL2		ENSSSCG00000013013	2:5558442-5567477	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
ARL2BP		ENSSSCG00000002819	6:20066227-20073125		FP102873,CH242-277I7,6:20046883-20107879 (Clone quality: bE277I7 on chr=6; Num_of_Contigs=4; )
ARL3		ENSSSCG00000010588	14:118692253-118710685
ARL4		location ⇒	9:77038761-77039363		CU972383,CH242-147M18,9:77036567-77045078 (Clone quality: bE147M18 on chr=9; Num_of_Contigs=11; )

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).