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)

SMAD6		location ⇒	1:12582-12465		CU570732,CH242-271M12,1:1-31034 (Clone quality: bE271M12 on chr=1; Num_of_Contigs=7; )
SMAD6		location ⇒	1:2756-2837		CU570732,CH242-271M12,1:1-31034 (Clone quality: bE271M12 on chr=1; Num_of_Contigs=7; )
SMAD6		location ⇒	1:2836-2763		CU570732,CH242-271M12,1:1-31034 (Clone quality: bE271M12 on chr=1; Num_of_Contigs=7; )
SMAD7		ENSSSCG00000004507	1:101672864-101700903		CU062441,CH242-143B15,1:101658147-101702023 (Clone quality: bE143B15 on chr=1; Num_of_Contigs=3; )
SMAD9		ENSSSCG00000009357	11:12164136-12268651
SMAGP		ENSSSCG00000000224	5:15383458-15403175		CU694837,CH242-191H6,5:15374884-15408249 (Clone quality: bE191H6 on chr=5; Num_of_Contigs=5; )
SMAP1		ENSSSCG00000004276	1:53243221-53352644
SMAP2		ENSSSCG00000003983	6:122137451-122186147		CU694583,CH242-250P22,6:122065497-122229785 (Clone quality: bE250P22 on chr=6; Num_of_Contigs=1; )
SMARCA1		ENSSSCG00000012649	X:104198947-104274523		CU695129,CH242-218P14,X:104175406-104287701 (Clone quality: bE218P14 on chr=X; Num_of_Contigs=6; )
SMARCA2		ENSSSCG00000005232	1:229848236-230024688
SMARCA4		ENSSSCG00000013629	2:52483857-52573498
SMARCA5		ENSSSCG00000009047	8:72649551-72688655
SMARCAD1		ENSSSCG00000009193	8:107465930-107591273
SMARCB1		ENSSSCG00000010070	14:50889446-50920532
SMARCC1		ENSSSCG00000011340	13:25404412-25599338
SMARCC2		ENSSSCG00000000382	5:20482739-20502648		CU694915,CH242-453C18,5:20460687-20504457 (Clone quality: bE453C18 on chr=5; Num_of_Contigs=10; )
SMARCD1		ENSSSCG00000000215	5:14634315-14684388
SMARCD2		ENSSSCG00000017286	12:12665578-12674428
SMARCD3		ENSSSCG00000016435	18:5044751-5054049
SMARCE1		ENSSSCG00000017468	12:19608048-19621464		CU856162,CH242-340B15,12:19607891-19623524 (Clone quality: bE340B15 on chr=12; Num_of_Contigs=24; )
SMC1A		ENSSSCG00000012325	X:45583024-45620710
SMC3		ENSSSCG00000010625	14:126576623-126615913
SMC4		ENSSSCG00000011731	13:78782572-78821617		CU466375,CH242-17F2,13:78718958-78854255 (Clone quality: bE17F2 on chr=13; Num_of_Contigs=7; )
SMC5		ENSSSCG00000005255	1:234143853-234162624		CU074416,CH242-91G16,1:234077167-234163653 (Clone quality: bE91G16 on chr=1; Num_of_Contigs=6; )
SMC6		ENSSSCG00000008614	3:111476924-111549253
SMCP		ENSSSCG00000006594	4:100489890-100537402		CU210949,CH242-471G17,4:100442582-100566951 (Clone quality: bE471G17 on chr=4; Num_of_Contigs=4; )
SMCR7L		ENSSSCG00000000085	5:5070632-5081602		CU424445,CH242-128A11,5:5029969-5093393 (Clone quality: bE128A11 on chr=5; Num_of_Contigs=8; )
SMEK1		ENSSSCG00000002441	7:120955676-120990699		CU302426,CH242-45H24,7:120893357-121059688 (Clone quality: bE45H24 on chr=7; Num_of_Contigs=2; )
SMG5		ENSSSCG00000006490	4:97674150-97704637		CU468654,CH242-228K10,4:97649767-97712830 (Clone quality: bE228K10 on chr=4; Num_of_Contigs=7; )
SMG6		ENSSSCG00000017826	12:45610780-45836519
SMG7		ENSSSCG00000015558	9:117064539-117103942
SMN1		location ⇒	16:45048458-45048557		FP103012,CH242-101B11,16:45040228-45063123 (Clone quality: bE101B11 on chr=16; Num_of_Contigs=2; )
SMN1		location ⇒	16:45064514-45064716		FP103012,CH242-101B11,16:45063224-45090105 (Clone quality: bE101B11 on chr=16; Num_of_Contigs=2; )
SMN1		location ⇒	16:45064858-45065015		FP103012,CH242-101B11,16:45063224-45090105 (Clone quality: bE101B11 on chr=16; Num_of_Contigs=2; )
SMN1		location ⇒	16:45066713-45066763		FP103012,CH242-101B11,16:45063224-45090105 (Clone quality: bE101B11 on chr=16; Num_of_Contigs=2; )
SMNDC1		ENSSSCG00000010623	14:126332835-126343680		CT737363,CH242-181F23,14:126304259-126433090 (Clone quality: bE181F23 on chr=14; Num_of_Contigs=4; )
SMO		ENSSSCG00000016569	18:17609463-17636344		CU638846,CH242-272C14,18:17604734-17699485 (Clone quality: bE272C14 on chr=18; Num_of_Contigs=4; )
SMOC1		ENSSSCG00000002314	7:101933488-102011490		CT943645,CH242-235L8,7:101928117-102040051 (Clone quality: bE235L8 on chr=7; Num_of_Contigs=2; )
SMOC2		ENSSSCG00000004013	1:1240205-1711059
SMOX		ENSSSCG00000007140	17:33110927-33143047
SMPD1		ENSSSCG00000014627	9:2612617-2614989		CU972372,CH242-47M8,9:2612491-2620938 (Clone quality: bE47M8 on chr=9; Num_of_Contigs=7; )
SMPD2		ENSSSCG00000004408	1:80365494-80481222
SMPD3		ENSSSCG00000002764	6:12579098-12590292		CU462933,CH242-310F10,6:12564924-12617393 (Clone quality: bE310F10 on chr=6; Num_of_Contigs=6; )
SMPDL3A		ENSSSCG00000004233	1:41352453-41370661
SMPDL3B		ENSSSCG00000003582	6:58525746-58549905		CU928393,CH242-274K17,6:58465404-58557237 (Clone quality: bE274K17 on chr=6; Num_of_Contigs=5; )
SMS		ENSSSCG00000012166	X:16864438-16893797	CU210923,CH242-498A9,X:16850786-17046971 (Clone quality: bE498A9 on chr=X; Num_of_Contigs=1; )
SMS		ENSSSCG00000011808	13:94724975-94726408		CU466378,CH242-185B2,13:94693645-94764313 (Clone quality: bE185B2 on chr=13; Num_of_Contigs=3; )
SMS1		ENSSSCG00000010433	14:103817282-103909542
SMS1		location ⇒	14:103730594-103729835		CU407016,CH242-121F9,14:103598725-103733348 (Clone quality: bE121F9 on chr=14; Num_of_Contigs=3; )
SMS1		location ⇒	14:103876274-103877125		CU468843,CH242-150G20,14:103816843-103884156 (Clone quality: bE150G20 on chr=14; Num_of_Contigs=6; )

Go to records:
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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).