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)

DSC2		location ⇒	6:79678460-79678594		CU467049,CH242-141H18,6:79678045-79684707 (Clone quality: bE141H18 on chr=6; Num_of_Contigs=2; )
DSCAM		ENSSSCG00000012073	13:143489169-143526691
DSCAM		location ⇒	13:143410227-143410470		CU466295,CH242-435N8,13:143399819-143422550 (Clone quality: bE435N8 on chr=13; Num_of_Contigs=14; )
DSCAM		location ⇒	13:6344780-6345255		CU469358,CH242-90C11,13:6344208-6347294 (Clone quality: bE90C11 on chr=13; Num_of_Contigs=22; )
DSCAML1		ENSSSCG00000015082	9:43788632-43803862		FP015807,CH242-92G3,9:43785980-43827240 (Clone quality: bE92G3 on chr=9; Num_of_Contigs=2; )
DSCAML1		ENSSSCG00000015081	9:43718204-43770926
DSCAML1		location ⇒	13:143410533-143410348		CU466295,CH242-435N8,13:143399819-143422550 (Clone quality: bE435N8 on chr=13; Num_of_Contigs=14; )
DSCAML1		location ⇒	13:143412543-143412346		CU466295,CH242-435N8,13:143399819-143422550 (Clone quality: bE435N8 on chr=13; Num_of_Contigs=14; )
DSCAML1		location ⇒	13:143420878-143420728		CU466295,CH242-435N8,13:143399819-143422550 (Clone quality: bE435N8 on chr=13; Num_of_Contigs=14; )
DSCAML1		location ⇒	13:143425462-143425359		CU466295,CH242-435N8,13:143422651-143439290 (Clone quality: bE435N8 on chr=13; Num_of_Contigs=14; )
DSCC1		ENSSSCG00000005999	4:18852487-18866495		CU326377,CH242-479G1,4:18779959-18866922 (Clone quality: bE479G1 on chr=4; Num_of_Contigs=8; )
DSCR1		ENSSSCG00000012050	13:139886822-139896139		CU856466,CH242-288N3,13:139835411-139917533 (Clone quality: bE288N3 on chr=13; Num_of_Contigs=3; )
DSCR3		ENSSSCG00000012063	13:141182680-141384994
DSCR6		ENSSSCG00000012060	13:140939654-140948451		CU861931,CH242-165C23,13:140913334-140950293 (Clone quality: bE165C23 on chr=13; Num_of_Contigs=3; )
DSE		ENSSSCG00000004441	1:86070669-86083149		FP090887,CH242-516G1,1:86069922-86107955 (Clone quality: bE516G1 on chr=1; Num_of_Contigs=10; )
DSP		ENSSSCG00000001025	7:4895003-4947068
DSPP		ENSSSCG00000009221	8:112817595-112825331		CU627975,CH242-146A20,8:112817048-112831362 (Clone quality: bE146A20 on chr=8; Num_of_Contigs=6; )
DSPP		location ⇒	8:1075852-1075945		FP003581,CH242-174O3,8:1074156-1077916 (Clone quality: bE174O3 on chr=8; Num_of_Contigs=8; )
DSPP		location ⇒	8:20613484-20613557		FP102197,CH242-520G24,8:20610880-20615785 (Clone quality: bE520G24 on chr=8; Num_of_Contigs=7; )
DSPP		location ⇒	8:2762351-2762444
DSPP		location ⇒	8:5711006-5710889		CU695146,CH242-303G5,8:5705492-5725136 (Clone quality: bE303G5 on chr=8; Num_of_Contigs=7; )
DST		ENSSSCG00000001499	7:33330244-33706764
DST		location ⇒	7:33698887-33699007	CU571137,CH242-40D15,7:33635770-33779210 (Clone quality: bE40D15 on chr=7; Num_of_Contigs=14; )
DST		location ⇒	7:33701161-33701361	CU571137,CH242-40D15,7:33635770-33779210 (Clone quality: bE40D15 on chr=7; Num_of_Contigs=14; )
DST		location ⇒	7:33704810-33704935	CU571137,CH242-40D15,7:33635770-33779210 (Clone quality: bE40D15 on chr=7; Num_of_Contigs=14; )
DST		location ⇒	7:33706342-33706648	CU571137,CH242-40D15,7:33635770-33779210 (Clone quality: bE40D15 on chr=7; Num_of_Contigs=14; )
DSTN		ENSSSCG00000007085	17:26665438-26672558
DSTYK		ENSSSCG00000015286	9:63047063-63081788
DTD1		ENSSSCG00000007098	17:27602731-27721837
DTL		ENSSSCG00000015600	9:123699760-123748223
DTNB		ENSSSCG00000008576	3:105800333-105904523		CU896542,CH242-167I24,3:105793258-105908464 (Clone quality: bE167I24 on chr=3; Num_of_Contigs=4; )
DTNBP1		ENSSSCG00000001062	7:12005701-12123657
DTR		ENSSSCG00000006204	4:70266873-70308578
DTWD2		ENSSSCG00000014225	2:111256448-111382229
DTX1		ENSSSCG00000009873	14:38915894-38952993
DTX2		ENSSSCG00000007696	3:8607444-8619890
DTX3		ENSSSCG00000000449	5:21960121-21963009		CU914582,CH242-235E14,5:21960088-21963229 (Clone quality: bE235E14 on chr=5; Num_of_Contigs=33; )
DTX3L		ENSSSCG00000011876	13:103893450-103901772
DTX4		ENSSSCG00000013145	2:10287122-10321542		CU467529,CH242-205D7,2:10254345-10366022 (Clone quality: bE205D7 on chr=2; Num_of_Contigs=2; )
DULLARD		ENSSSCG00000017935	12:49749479-49755426
DUOX1		ENSSSCG00000004675	1:132322192-132387898
DUOX1		location ⇒	1:132322608-132322240		CU062525,CH242-125K20,1:132198699-132329693 (Clone quality: bE125K20 on chr=1; Num_of_Contigs=2; )
DUOX1		location ⇒	1:132325748-132325512		CU062525,CH242-125K20,1:132198699-132329693 (Clone quality: bE125K20 on chr=1; Num_of_Contigs=2; )
DUOX1		location ⇒	1:132368515-132368285		CU459107,CH242-257E14,1:132366575-132383725 (Clone quality: bE257E14 on chr=1; Num_of_Contigs=5; )
DUOX1		location ⇒	1:132373211-132372982		CU459107,CH242-257E14,1:132366575-132383725 (Clone quality: bE257E14 on chr=1; Num_of_Contigs=5; )
DUOX2		ENSSSCG00000004678	1:132406448-132428074		CU459107,CH242-257E14,1:132383826-132520076 (Clone quality: bE257E14 on chr=1; Num_of_Contigs=5; )
DUOX2		location ⇒	1:132373211-132372982		CU459107,CH242-257E14,1:132366575-132383725 (Clone quality: bE257E14 on chr=1; Num_of_Contigs=5; )
DUOX2		location ⇒	1:132417666-132417895		CU459107,CH242-257E14,1:132383826-132520076 (Clone quality: bE257E14 on chr=1; Num_of_Contigs=5; )
DUOX2		location ⇒	1:132425766-132426001		CU459107,CH242-257E14,1:132383826-132520076 (Clone quality: bE257E14 on chr=1; Num_of_Contigs=5; )
DUOX2		location ⇒	1:132427459-132428930		CU459107,CH242-257E14,1:132383826-132520076 (Clone quality: bE257E14 on chr=1; Num_of_Contigs=5; )

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, 751-16

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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).