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)

ERBB2		ENSSSCG00000008515	3:100804030-100918000
ERBB2		ENSSSCG00000016953	16:41795660-41883604
ERBB2		ENSSSCG00000017497	12:20557656-20578620
ERBB2		ENSSSCG00000017502	12:20622594-20637983		CU640399,CH242-251F23,12:20578579-20644206 (Clone quality: bE251F23 on chr=12; Num_of_Contigs=5; )
ERBB2		ENSSSCG00000017558	12:23906392-23910614
ERBB2		location ⇒	7:116609-116670		CU657920,CH242-367F14,7:95842-128080 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
ERBB2		location ⇒	7:161183-161122		CU657920,CH242-367F14,7:155481-179062 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
ERBB2		location ⇒	7:262868-262937		CU467789,CH242-514I8,7:246590-284983 (Clone quality: bE514I8 on chr=7; Num_of_Contigs=7; )
ERBB2		location ⇒	7:526691-526760		CU855572,CH242-50N10,7:524294-532582 (Clone quality: bE50N10 on chr=7; Num_of_Contigs=30; )
ERBB2IP		ENSSSCG00000016953	16:41795660-41883604
ERBB2IP		location ⇒	16:41829218-41829020		CU466255,CH242-441J5,16:41827755-41836193 (Clone quality: bE441J5 on chr=16; Num_of_Contigs=10; )
ERBB2IP		location ⇒	16:41835305-41835185		CU466255,CH242-441J5,16:41827755-41836193 (Clone quality: bE441J5 on chr=16; Num_of_Contigs=10; )
ERBB2IP		location ⇒	16:41845897-41845808		CU466255,CH242-441J5,16:41836294-41858417 (Clone quality: bE441J5 on chr=16; Num_of_Contigs=10; )
ERBB2IP		location ⇒	16:41858815-41858765		CU466255,CH242-441J5,16:41858518-41883254 (Clone quality: bE441J5 on chr=16; Num_of_Contigs=10; )
ERBB3		ENSSSCG00000000377	5:20410544-20452691
ERBB3		ENSSSCG00000000372	5:20325539-20460307
ERBB3		location ⇒	5:20372849-20373057		CU457395,CH242-13B13,5:20372409-20376786 (Clone quality: bE13B13 on chr=5; Num_of_Contigs=23; )
ERBB3		location ⇒	5:20376489-20376643		CU457395,CH242-13B13,5:20372409-20376786 (Clone quality: bE13B13 on chr=5; Num_of_Contigs=23; )
ERBB4		ENSSSCG00000016160	15:107147960-107599764
ERBB4		location ⇒	15:107142265-107140139		CU466976,CH242-503F7,15:107071140-107195673 (Clone quality: bE503F7 on chr=15; Num_of_Contigs=2; )
ERBB4		location ⇒	15:107146935-107146229		CU466976,CH242-503F7,15:107071140-107195673 (Clone quality: bE503F7 on chr=15; Num_of_Contigs=2; )
ERBB4		location ⇒	15:107147544-107147482		CU466976,CH242-503F7,15:107071140-107195673 (Clone quality: bE503F7 on chr=15; Num_of_Contigs=2; )
ERBB4		location ⇒	15:107148404-107147660		CU466976,CH242-503F7,15:107071140-107195673 (Clone quality: bE503F7 on chr=15; Num_of_Contigs=2; )
ERC1		ENSSSCG00000000755	5:64007172-64357042
ERCC3		ENSSSCG00000015722	15:23896682-23899474		FP102347,CH242-133M6,15:23895305-23900287 (Clone quality: bE133M6 on chr=15; Num_of_Contigs=4; )
ERCC4		ENSSSCG00000007881	3:26683951-26720087		CU915697,CH242-447C18,3:26680940-26779917 (Clone quality: bE447C18 on chr=3; Num_of_Contigs=5; )
ERCC5		ENSSSCG00000009533	11:72024509-72035383
ERCC6		ENSSSCG00000010391	14:93841276-93912229
ERCC8		ENSSSCG00000016934	16:37767354-37833053
EREG		ENSSSCG00000008962	8:59653735-59668303
EREG		location ⇒	8:35666841-35666765		FP015961,CH242-68J9,8:35666593-35707684 (Clone quality: bE68J9 on chr=8; Num_of_Contigs=5; )
EREG		location ⇒	8:59666689-59666776		FP236682,CH242-469E11,8:59664524-59668354 (Clone quality: bE469E11 on chr=8; Num_of_Contigs=18; )
EREG		location ⇒	8:59668177-59668304		FP236682,CH242-469E11,8:59664524-59668354 (Clone quality: bE469E11 on chr=8; Num_of_Contigs=18; )
EREG		location ⇒	8:59786373-59786122		FP236682,CH242-469E11,8:59782718-59792773 (Clone quality: bE469E11 on chr=8; Num_of_Contigs=18; )
ERF		ENSSSCG00000003034	6:34363446-34365614		FP102858,CH242-504I8,6:34362915-34392170 (Clone quality: bE504I8 on chr=6; Num_of_Contigs=13; )
ERG		ENSSSCG00000016448	18:5361066-5376452
ERGIC1		ENSSSCG00000016988	16:48644987-48667333
ERGIC2		ENSSSCG00000000536	5:42802321-42849718
ERH		ENSSSCG00000002307	7:101463797-101479517		CU468204,CH242-522C13,7:101443320-101498848 (Clone quality: bE522C13 on chr=7; Num_of_Contigs=8; )
ERI2		ENSSSCG00000007856	3:22856855-22865191		FP016068,CH242-129A5,3:22846362-22866918 (Clone quality: bE129A5 on chr=3; Num_of_Contigs=8; )
ERI3		ENSSSCG00000003935	6:119803887-119847184		CU929772,CH242-330I2,6:119756449-119866672 (Clone quality: bE330I2 on chr=6; Num_of_Contigs=19; )
ERLIN1		ENSSSCG00000010547	14:116037716-116072802		CT868715,CH242-513L2,14:116015867-116113953 (Clone quality: bE513L2 on chr=14; Num_of_Contigs=23; )
ERLIN2		ENSSSCG00000015827	15:46144169-46159127		FP236525,CH242-315C20,15:46063691-46179411 (Clone quality: bE315C20 on chr=15; Num_of_Contigs=4; )
ERMP1		ENSSSCG00000005207	1:226224429-226287788
ERN1		ENSSSCG00000017279	12:12476768-12508945		CU694679,CH242-184I12,12:12462076-12561338 (Clone quality: bE184I12 on chr=12; Num_of_Contigs=5; )
ERO1L		ENSSSCG00000005037	1:190632580-190785319
ERO1LB		ENSSSCG00000010148	14:56264356-56327610
ERP27		ENSSSCG00000000605	5:54909804-54936073		CU463008,CH242-511E2,5:54907608-54936373 (Clone quality: bE511E2 on chr=5; Num_of_Contigs=3; )
ERP29		ENSSSCG00000009888	14:39733860-39742358		CU469371,CH242-288I9,14:39698665-39792017 (Clone quality: bE288I9 on chr=14; Num_of_Contigs=6; )
ERP44		ENSSSCG00000005387	1:253440127-253538508

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, 651-29

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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).