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)

ST8SIA4		location ⇒	2:95985750-95983716		CU468503,CH242-522P4,2:95977434-96060564 (Clone quality: bE522P4 on chr=2; Num_of_Contigs=4; )
ST8SIA4		location ⇒	2:95986712-95985817		CU468503,CH242-522P4,2:95977434-96060564 (Clone quality: bE522P4 on chr=2; Num_of_Contigs=4; )
ST8SIA4		location ⇒	2:95987678-95986772		CU468503,CH242-522P4,2:95977434-96060564 (Clone quality: bE522P4 on chr=2; Num_of_Contigs=4; )
ST8SIA4		location ⇒	2:96075674-96075273		CU468503,CH242-522P4,2:96060665-96094415 (Clone quality: bE522P4 on chr=2; Num_of_Contigs=4; )
ST8SIA6		ENSSSCG00000011034	10:41881976-41954472		CU570641,CH242-190K24,10:41813007-41971567 (Clone quality: bE190K24 on chr=10; Num_of_Contigs=3; )
STA5A_PIG		ENSSSCG00000017402	12:17923290-17946321
STAB1		ENSSSCG00000011443	13:29246750-29272576
STAB1		location ⇒	13:29267970-29268120		CU550676,CH242-330J9,13:29135788-29268883 (Clone quality: bE330J9 on chr=13; Num_of_Contigs=4; )
STAB1		location ⇒	13:29268452-29268594		CU550676,CH242-330J9,13:29135788-29268883 (Clone quality: bE330J9 on chr=13; Num_of_Contigs=4; )
STAB1		location ⇒	13:29268696-29268756		CU550676,CH242-330J9,13:29135788-29268883 (Clone quality: bE330J9 on chr=13; Num_of_Contigs=4; )
STAB2		ENSSSCG00000000852	5:75832573-75857396
STAB2		ENSSSCG00000000854	5:75973930-76000503
STAB2		location ⇒	5:75954436-75954319		FP016116,CH242-81J1,5:75937545-75968591 (Clone quality: bE81J1 on chr=5; Num_of_Contigs=3; )
STAB2		location ⇒	5:75956213-75956114		FP016116,CH242-81J1,5:75937545-75968591 (Clone quality: bE81J1 on chr=5; Num_of_Contigs=3; )
STAB2		location ⇒	5:75961236-75961078		FP016116,CH242-81J1,5:75937545-75968591 (Clone quality: bE81J1 on chr=5; Num_of_Contigs=3; )
STAB2		location ⇒	5:75962892-75962581		FP016116,CH242-81J1,5:75937545-75968591 (Clone quality: bE81J1 on chr=5; Num_of_Contigs=3; )
STAC2		ENSSSCG00000017508	12:21054363-21060781		FP085518,CH242-274F4,12:21003722-21101963 (Clone quality: bE274F4 on chr=12; Num_of_Contigs=3; )
STAG1		ENSSSCG00000011652	13:63425369-63603141
STAG2		ENSSSCG00000012642	X:99287973-99372629
STAG2		location ⇒	X:99288032-99288082		CU463995,CH242-82J8,X:99286822-99321274 (Clone quality: bE82J8 on chr=X; Num_of_Contigs=8; )
STAG2		location ⇒	X:99310896-99311102		CU463995,CH242-82J8,X:99286822-99321274 (Clone quality: bE82J8 on chr=X; Num_of_Contigs=8; )
STAG2		location ⇒	X:99334216-99334422	CU467914,CH242-238F10,X:99330376-99533514 (Clone quality: bE238F10 on chr=X; Num_of_Contigs=6; )
STAG2		location ⇒	X:99372318-99374301	CU467914,CH242-238F10,X:99330376-99533514 (Clone quality: bE238F10 on chr=X; Num_of_Contigs=6; )
STAG3		ENSSSCG00000007650	3:6425709-6461066		CU694680,CH242-187A15,3:6349164-6471889 (Clone quality: bE187A15 on chr=3; Num_of_Contigs=2; )
STAM		ENSSSCG00000011036	10:42205139-42266121
STAM2		ENSSSCG00000016399	15:134202826-134217916
STAMBP		ENSSSCG00000008300	3:63698796-63728520
STAMBPL1		ENSSSCG00000010446	14:105697409-105758894
STAP1		ENSSSCG00000008923	8:56305819-56328081
STAP2		ENSSSCG00000013506	2:48557847-48566922		CU972396,CH242-401E10,2:48541506-48658119 (Clone quality: bE401E10 on chr=2; Num_of_Contigs=4; )
STARD10		ENSSSCG00000014818	9:6935386-6969829
STARD13		ENSSSCG00000009348	11:9393429-9416560		CU407200,CH242-321D19,11:9389573-9416609 (Clone quality: bE321D19 on chr=11; Num_of_Contigs=12; )
STARD3		ENSSSCG00000017499	12:20587727-20613581		CU640399,CH242-251F23,12:20578579-20644206 (Clone quality: bE251F23 on chr=12; Num_of_Contigs=5; )
STARD4		ENSSSCG00000014202	2:104840795-104856025
STARD5		ENSSSCG00000001788	7:56244425-56255579		CT954232,CH242-235B20,7:56145412-56302593 (Clone quality: bE235B20 on chr=7; Num_of_Contigs=2; )
STARD6		ENSSSCG00000004530	1:106693181-106718548		CU694517,CH242-313D11,1:106640135-106799320 (Clone quality: bE313D11 on chr=1; Num_of_Contigs=2; )
STARD7		ENSSSCG00000008132	3:42095144-42118620
STARD8		ENSSSCG00000012828	X:123890666-123903745
STAT1		ENSSSCG00000016057	15:90083773-90118570
STAT1		ENSSSCG00000000481	5:31794327-31799589		CU694828,CH242-167J2,5:31764796-31807287 (Clone quality: bE167J2 on chr=5; Num_of_Contigs=11; )
STAT1		ENSSSCG00000009997	14:48017985-48020973	CT827833,CH242-227A13,14:47931258-48074674 (Clone quality: bE227A13 on chr=14; Num_of_Contigs=2; )
STAT1		ENSSSCG00000014626	9:2597412-2606196		CU972372,CH242-47M8,9:2582658-2612390 (Clone quality: bE47M8 on chr=9; Num_of_Contigs=7; )
STAT1		ENSSSCG00000016916	16:32637552-32684001
STAT1		location ⇒	15:90090714-90090528		CU550692,CH242-85L23,15:90078832-90097389 (Clone quality: bE85L23 on chr=15; Num_of_Contigs=15; )
STAT1		location ⇒	15:90092635-90092489		CU550692,CH242-85L23,15:90078832-90097389 (Clone quality: bE85L23 on chr=15; Num_of_Contigs=15; )
STAT1		location ⇒	15:90106136-90105981		CU550692,CH242-85L23,15:90104981-90107838 (Clone quality: bE85L23 on chr=15; Num_of_Contigs=15; )
STAT1		location ⇒	15:90117725-90117579		CU550692,CH242-85L23,15:90107939-90118894 (Clone quality: bE85L23 on chr=15; Num_of_Contigs=15; )
STAT2		ENSSSCG00000000396	5:20723188-20737703
STAT2		location ⇒	5:16062216-16062293		CU606912,CH242-90A20,5:16023396-16077450 (Clone quality: bE90A20 on chr=5; Num_of_Contigs=3; )
STAT2		location ⇒	5:3534366-3534275		CU633382,CH242-275I12,5:3532673-3536452 (Clone quality: bE275I12 on chr=5; Num_of_Contigs=9; )

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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).