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)

MTF1		ENSSSCG00000011837	13:100347976-100371822
MTF2		ENSSSCG00000006898	4:128265386-128380927
MTFMT		ENSSSCG00000004543	1:110126651-110157133		CU929866,CH242-13A12,1:110100332-110200592 (Clone quality: bE13A12 on chr=1; Num_of_Contigs=4; )
MTFR1		ENSSSCG00000006219	4:71483869-71549801
MTHFD1		ENSSSCG00000002269	7:96824007-96886357		CU914661,CH242-30K16,7:96812121-96912476 (Clone quality: bE30K16 on chr=7; Num_of_Contigs=3; )
MTHFD2		ENSSSCG00000008289	3:63363672-63372417		CU929887,CH242-215C22,3:63336671-63373209 (Clone quality: bE215C22 on chr=3; Num_of_Contigs=7; )
MTHFD2L		ENSSSCG00000008961	8:59550947-59595287
MTHFR		ENSSSCG00000003428	6:48740047-48751964
MTHFR		location ⇒	6:48740536-48740344		CU855519,CH242-273H12,6:48734866-48744156 (Clone quality: bE273H12 on chr=6; Num_of_Contigs=13; )
MTHFR		location ⇒	6:48743595-48743412		CU855519,CH242-273H12,6:48734866-48744156 (Clone quality: bE273H12 on chr=6; Num_of_Contigs=13; )
MTHFR		location ⇒	6:48744871-48744617		CU695168,CH242-2E14,6:48744157-48789117 (Clone quality: bE2E14 on chr=6; Num_of_Contigs=4; )
MTHFR		location ⇒	6:48750200-48749960		CU695168,CH242-2E14,6:48744157-48789117 (Clone quality: bE2E14 on chr=6; Num_of_Contigs=4; )
MTHFS		ENSSSCG00000001777	7:54854569-54854802		CT842517,CH242-259J18,7:54687428-54857965 (Clone quality: bE259J18 on chr=7; Num_of_Contigs=2; )
MTHFSD		ENSSSCG00000002660	6:1383572-1399454		FP102684,CH242-354G10,6:1372429-1414131 (Clone quality: bE354G10 on chr=6; Num_of_Contigs=3; )
MTIF2		ENSSSCG00000008404	3:79887805-79920488
MTL5		ENSSSCG00000012882	2:2540801-2641517
MTM1		ENSSSCG00000012742	X:120415921-120533332
MTMR1		ENSSSCG00000012743	X:120549903-120608925		CU694277,CH242-322P18,X:120431922-120621889 (Clone quality: bE322P18 on chr=X; Num_of_Contigs=2; )
MTMR10		ENSSSCG00000004844	1:151507679-151555129
MTMR11		ENSSSCG00000006664	4:103126034-103133640		CU468464,CH242-21F2,4:103092969-103158703 (Clone quality: bE21F2 on chr=4; Num_of_Contigs=8; )
MTMR12		ENSSSCG00000016812	16:16214327-16219323		CU914459,CH242-229A22,16:16213354-16225682 (Clone quality: bE229A22 on chr=16; Num_of_Contigs=24; )
MTMR14		ENSSSCG00000011546	13:55142055-55188251
MTMR15		ENSSSCG00000004845	1:151559662-151600352
MTMR2		ENSSSCG00000014970	9:28416282-28512003
MTMR3		ENSSSCG00000009994	14:47647544-47794758
MTMR4		ENSSSCG00000017642	12:32766260-32785441		CU681830,CH242-364G8,12:32658530-32786323 (Clone quality: bE364G8 on chr=12; Num_of_Contigs=5; )
MTMR7		ENSSSCG00000006985	17:4750010-4874897
MTMR9		ENSSSCG00000003615	6:60897236-60898387		FP102820,CH242-217B19,6:60895272-60899183 (Clone quality: bE217B19 on chr=6; Num_of_Contigs=18; )
MTNR1A		ENSSSCG00000007002	17:8308257-8328863		CU606872,CH242-268J1,17:8303505-8350153 (Clone quality: bE268J1 on chr=17; Num_of_Contigs=4; )
MTNR1B		ENSSSCG00000014939	9:25929751-25941910		FP102140,CH242-226D15,9:25929221-25942611 (Clone quality: bE226D15 on chr=9; Num_of_Contigs=12; )
MTO1		ENSSSCG00000004487	1:97530735-97556060		FP102323,CH242-235J13,1:97526792-97569279 (Clone quality: bE235J13 on chr=1; Num_of_Contigs=2; )
MTOR		ENSSSCG00000003413	6:48053956-48175042
MTP18		ENSSSCG00000010007	14:48201842-48205269		CT956025,CH242-69C12,14:48142322-48239134 (Clone quality: bE69C12 on chr=14; Num_of_Contigs=15; )
MTPN		ENSSSCG00000016525	18:11748094-11786584
MTR		ENSSSCG00000010143	14:55696635-55813207
MTRF1		ENSSSCG00000009436	11:24578630-24613800
MTRR		ENSSSCG00000017100	16:71437908-71462478		CU695161,CH242-40A14,16:71420211-71475456 (Clone quality: bE40A14 on chr=16; Num_of_Contigs=8; )
MTSS1		ENSSSCG00000005975	4:14812757-14844479		CU468433,CH242-46N16,4:14812256-14877054 (Clone quality: bE46N16 on chr=4; Num_of_Contigs=6; )
MTSS1		ENSSSCG00000002726	6:9833484-9835275		CU915803,CH242-220M7,6:9833159-9836034 (Clone quality: bE220M7 on chr=6; Num_of_Contigs=25; )
MTSS1		location ⇒	4:14846725-14845847		CU468433,CH242-46N16,4:14812256-14877054 (Clone quality: bE46N16 on chr=4; Num_of_Contigs=6; )
MTSS1L		ENSSSCG00000002726	6:9833484-9835275		CU915803,CH242-220M7,6:9833159-9836034 (Clone quality: bE220M7 on chr=6; Num_of_Contigs=25; )
MTTP		ENSSSCG00000009179	8:103485922-103536558
MTUS1		ENSSSCG00000006989	17:5189223-5334179
MTX1		ENSSSCG00000006523	4:98685371-98690530
MTX3		ENSSSCG00000014116	2:77838051-77846965		CU914717,CH242-399K18,2:77815512-77849586 (Clone quality: bE399K18 on chr=2; Num_of_Contigs=12; )
MUC-24		ENSSSCG00000004414	1:80531982-80546382		CU075452,CH242-39D23,1:80450203-80633251 (Clone quality: bE39D23 on chr=1; Num_of_Contigs=2; )
MUC1		ENSSSCG00000006525	4:98706988-98710064		CU179666,CH242-242M24,4:98705913-98751478 (Clone quality: bE242M24 on chr=4; Num_of_Contigs=7; )
MUC1		location ⇒	4:98708065-98708198		CU179666,CH242-242M24,4:98705913-98751478 (Clone quality: bE242M24 on chr=4; Num_of_Contigs=7; )
MUC1		location ⇒	4:98708345-98708468		CU179666,CH242-242M24,4:98705913-98751478 (Clone quality: bE242M24 on chr=4; Num_of_Contigs=7; )
MUC1		location ⇒	4:98708550-98708702		CU179666,CH242-242M24,4:98705913-98751478 (Clone quality: bE242M24 on chr=4; Num_of_Contigs=7; )

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).