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)

MARCH2		location ⇒	2:51712027-51712084		FP090904,CH242-212F1,2:51700191-51798128 (Clone quality: bE212F1 on chr=2; Num_of_Contigs=2; )
MARCH3		ENSSSCG00000014249	2:117577326-117634797
MARCH4		ENSSSCG00000016176	15:111713998-111737042		CU855571,CH242-469L1,15:111696360-111744157 (Clone quality: bE469L1 on chr=15; Num_of_Contigs=2; )
MARCH5		ENSSSCG00000010469	14:108991016-109041755		CT827946,CH242-224C6,14:108973964-109064597 (Clone quality: bE224C6 on chr=14; Num_of_Contigs=3; )
MARCH6		ENSSSCG00000017094	16:69470363-69526693
MARCH7		ENSSSCG00000015883	15:62044511-62138745
MARCH8		ENSSSCG00000010403	14:94749760-94875780
MARCH9		ENSSSCG00000000448	5:21956856-21959987
MARCKS		ENSSSCG00000003614	6:60871315-60873228		FP102820,CH242-217B19,6:60862663-60883389 (Clone quality: bE217B19 on chr=6; Num_of_Contigs=18; )
MARCKS		ENSSSCG00000004431	1:83523072-83526428
MARCKSL1		ENSSSCG00000003614	6:60871315-60873228		FP102820,CH242-217B19,6:60862663-60883389 (Clone quality: bE217B19 on chr=6; Num_of_Contigs=18; )
MARCO		ENSSSCG00000015716	15:23171216-23209712
MARCO		location ⇒	15:23195294-23195395		CU694946,CH242-90M4,15:23148607-23195588 (Clone quality: bE90M4 on chr=15; Num_of_Contigs=2; )
MARCO		location ⇒	15:23195484-23195550		CU694946,CH242-90M4,15:23148607-23195588 (Clone quality: bE90M4 on chr=15; Num_of_Contigs=2; )
MARCO		location ⇒	15:23206608-23206712		CU694946,CH242-90M4,15:23201455-23249008 (Clone quality: bE90M4 on chr=15; Num_of_Contigs=2; )
MARCO		location ⇒	15:23208082-23208262		CU694946,CH242-90M4,15:23201455-23249008 (Clone quality: bE90M4 on chr=15; Num_of_Contigs=2; )
MARK1		ENSSSCG00000010825	10:10027493-10062023		CU861957,CH242-244D10,10:10024403-10093658 (Clone quality: bE244D10 on chr=10; Num_of_Contigs=6; )
MARK2		ENSSSCG00000013050	2:6599544-6605759		CU928683,CH242-160D10,2:6599491-6606989 (Clone quality: bE160D10 on chr=2; Num_of_Contigs=16; )
MARS		ENSSSCG00000007321	17:42164310-42187808		CU607085,CH242-137E1,17:42127348-42190090 (Clone quality: bE137E1 on chr=17; Num_of_Contigs=8; )
MARS		location ⇒	5:21619772-21619683		CU896550,CH242-139E23,5:21612989-21627956 (Clone quality: bE139E23 on chr=5; Num_of_Contigs=9; )
MARS		location ⇒	5:21622114-21621898		CU896550,CH242-139E23,5:21612989-21627956 (Clone quality: bE139E23 on chr=5; Num_of_Contigs=9; )
MARS		location ⇒	5:21633755-21633548		CU896550,CH242-139E23,5:21628057-21640744 (Clone quality: bE139E23 on chr=5; Num_of_Contigs=9; )
MARS		location ⇒	5:21640524-21640448		CU896550,CH242-139E23,5:21628057-21640744 (Clone quality: bE139E23 on chr=5; Num_of_Contigs=9; )
MARS2		ENSSSCG00000016081	15:95061179-95062960		CU693402,CH242-237H6,15:95024381-95096225 (Clone quality: bE237H6 on chr=15; Num_of_Contigs=7; )
MARVELD2		ENSSSCG00000016959	16:44683865-44698029
MARVELD3		ENSSSCG00000002734	6:10275561-10288669
MAS1		ENSSSCG00000004045	1:8656260-8657237	CU855864,CH242-178J19,1:8528462-8661814 (Clone quality: bE178J19 on chr=1; Num_of_Contigs=11; )
MASP1		ENSSSCG00000011806	13:94375011-94422595		CU466303,CH242-512J18,13:94239314-94474859 (Clone quality: bE512J18 on chr=13; Num_of_Contigs=1; )
MASP1		location ⇒	13:94391815-94391617		CU466303,CH242-512J18,13:94239314-94474859 (Clone quality: bE512J18 on chr=13; Num_of_Contigs=1; )
MASP1		location ⇒	13:94394102-94393970		CU466303,CH242-512J18,13:94239314-94474859 (Clone quality: bE512J18 on chr=13; Num_of_Contigs=1; )
MASP1		location ⇒	13:94395905-94395725		CU466303,CH242-512J18,13:94239314-94474859 (Clone quality: bE512J18 on chr=13; Num_of_Contigs=1; )
MASP1		location ⇒	13:94415284-94415049		CU466303,CH242-512J18,13:94239314-94474859 (Clone quality: bE512J18 on chr=13; Num_of_Contigs=1; )
MASP2		ENSSSCG00000003410	6:48012243-48015116		CU694468,CH242-449E16,6:48008138-48016683 (Clone quality: bE449E16 on chr=6; Num_of_Contigs=13; )
MAST2		ENSSSCG00000003913	6:118496579-118603481		CU442756,CH242-95G1,6:118479333-118621567 (Clone quality: bE95G1 on chr=6; Num_of_Contigs=2; )
MAST2		location ⇒	6:118507295-118507211		CU442756,CH242-95G1,6:118479333-118621567 (Clone quality: bE95G1 on chr=6; Num_of_Contigs=2; )
MAST2		location ⇒	6:118507615-118507559		CU442756,CH242-95G1,6:118479333-118621567 (Clone quality: bE95G1 on chr=6; Num_of_Contigs=2; )
MAST2		location ⇒	6:118518017-118517945		CU442756,CH242-95G1,6:118479333-118621567 (Clone quality: bE95G1 on chr=6; Num_of_Contigs=2; )
MAST2		location ⇒	6:118668042-118668112		CU655893,CH242-136J6,6:118667815-118683273 (Clone quality: bE136J6 on chr=6; Num_of_Contigs=10; )
MAST3		ENSSSCG00000013895	2:62305425-62341749
MAST4		ENSSSCG00000016956	16:42947267-43030554
MASTL		ENSSSCG00000011065	10:47090268-47111012		FP016148,CH242-23C20,10:47072290-47111751 (Clone quality: bE23C20 on chr=10; Num_of_Contigs=4; )
MAT1A		ENSSSCG00000010337	14:85592979-85608224		CU469045,CH242-504L17,14:85591107-85617057 (Clone quality: bE504L17 on chr=14; Num_of_Contigs=9; )
MATK		ENSSSCG00000013494	2:48277326-48285156		FP102497,CH242-307J7,2:48199823-48346436 (Clone quality: bE307J7 on chr=2; Num_of_Contigs=2; )
MATK		location ⇒	2:48277777-48277327		FP102497,CH242-307J7,2:48199823-48346436 (Clone quality: bE307J7 on chr=2; Num_of_Contigs=2; )
MATK		location ⇒	2:48278508-48278313		FP102497,CH242-307J7,2:48199823-48346436 (Clone quality: bE307J7 on chr=2; Num_of_Contigs=2; )
MATK		location ⇒	2:48282978-48282759		FP102497,CH242-307J7,2:48199823-48346436 (Clone quality: bE307J7 on chr=2; Num_of_Contigs=2; )
MATK		location ⇒	2:48285154-48285026		FP102497,CH242-307J7,2:48199823-48346436 (Clone quality: bE307J7 on chr=2; Num_of_Contigs=2; )
MATN2		ENSSSCG00000006082	4:38948540-39076509
MATN3		ENSSSCG00000008603	3:109776929-109797255
MATN4		ENSSSCG00000007391	17:49415549-49425725

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, 1401-46

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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).