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)

DAAM1		ENSSSCG00000005078	1:197289158-197399635
DAAM2		ENSSSCG00000001595	7:40300869-40354344
DAB1		ENSSSCG00000003833	6:110066302-110217991
DAB2		ENSSSCG00000016857	16:21934596-22030455
DAB2IP		ENSSSCG00000005524	1:275494746-275509005		CU915410,CH242-31P10,1:275494128-275511355 (Clone quality: bE31P10 on chr=1; Num_of_Contigs=8; )
DACH1		ENSSSCG00000009457	11:43155733-43392023
DACH2		ENSSSCG00000012464	X:68342129-68792554
DAD1		ENSSSCG00000002050	7:82682146-82707576		CU407030,CH242-171E18,7:82670262-82752637 (Clone quality: bE171E18 on chr=7; Num_of_Contigs=3; )
DAD1		location ⇒	7:82682389-82682152		CU407030,CH242-171E18,7:82670262-82752637 (Clone quality: bE171E18 on chr=7; Num_of_Contigs=3; )
DAD1		location ⇒	7:82693796-82693619		CU407030,CH242-171E18,7:82670262-82752637 (Clone quality: bE171E18 on chr=7; Num_of_Contigs=3; )
DAD1		location ⇒	7:82707515-82707247		CU407030,CH242-171E18,7:82670262-82752637 (Clone quality: bE171E18 on chr=7; Num_of_Contigs=3; )
DAG1		location ⇒	13:26937249-26939523		CU607087,CH242-156N21,13:26933686-26939588 (Clone quality: bE156N21 on chr=13; Num_of_Contigs=29; )
DAGLA		ENSSSCG00000013079	2:8056543-8079221
DAK		ENSSSCG00000013087	2:8464593-8477980
DALRD3		ENSSSCG00000011370	13:26601027-26606452		CU466318,CH242-524L17,13:26598779-26606793 (Clone quality: bE524L17 on chr=13; Num_of_Contigs=16; )
DAND5		ENSSSCG00000013741	2:56138308-56142589		CU463133,CH242-121E19,2:56137209-56155099 (Clone quality: bE121E19 on chr=2; Num_of_Contigs=6; )
DAO		ENSSSCG00000009942	14:42186035-42205117		CT954284,CH242-241M1,14:42019840-42206297 (Clone quality: bE241M1 on chr=14; Num_of_Contigs=1; )
DAP3		ENSSSCG00000006507	4:98171360-98372776
DAP3		location ⇒	4:98201686-98201848		CU469043,CH242-496F19,4:98185715-98237957 (Clone quality: bE496F19 on chr=4; Num_of_Contigs=6; )
DAP3		location ⇒	4:98206188-98206572		CU469043,CH242-496F19,4:98185715-98237957 (Clone quality: bE496F19 on chr=4; Num_of_Contigs=6; )
DAP3		location ⇒	4:98367886-98368048		CU856060,CH242-59F12,4:98333076-98417281 (Clone quality: bE59F12 on chr=4; Num_of_Contigs=5; )
DAP3		location ⇒	4:98372388-98372772		CU856060,CH242-59F12,4:98333076-98417281 (Clone quality: bE59F12 on chr=4; Num_of_Contigs=5; )
DAPK1		ENSSSCG00000010949	10:26963449-27001282
DAPK1		location ⇒	10:182124-182201		CU929008,CH242-207N16,10:137774-191372 (Clone quality: bE207N16 on chr=10; Num_of_Contigs=6; )
DAPK1		location ⇒	10:1883738-1883811		CU929963,CH242-60P14,10:1841357-1915446 (Clone quality: bE60P14 on chr=10; Num_of_Contigs=3; )
DAPK1		location ⇒	10:1942018-1942095		CU929963,CH242-60P14,10:1915547-1996138 (Clone quality: bE60P14 on chr=10; Num_of_Contigs=3; )
DAPK1		location ⇒	10:31757-31834		CU929008,CH242-207N16,10:1-36781 (Clone quality: bE207N16 on chr=10; Num_of_Contigs=6; )
DAPK2		ENSSSCG00000004560	1:111424027-111462238
DAPL1		ENSSSCG00000013810	2:59018449-59019336		FP102498,CH242-323J5,2:59014071-59094738 (Clone quality: bE323J5 on chr=2; Num_of_Contigs=2; )
DAPP1		ENSSSCG00000009175	8:103264180-103289427		FP089503,CH242-496N9,8:103261529-103367524 (Clone quality: bE496N9 on chr=8; Num_of_Contigs=4; )
DAPP1		location ⇒	8:103264207-103264343		FP089503,CH242-496N9,8:103261529-103367524 (Clone quality: bE496N9 on chr=8; Num_of_Contigs=4; )
DAPP1		location ⇒	8:103276723-103276856		FP089503,CH242-496N9,8:103261529-103367524 (Clone quality: bE496N9 on chr=8; Num_of_Contigs=4; )
DAPP1		location ⇒	8:103415583-103415792		FP089503,CH242-496N9,8:103413316-103430320 (Clone quality: bE496N9 on chr=8; Num_of_Contigs=4; )
DAPP1		location ⇒	8:103441538-103441661		FP089503,CH242-496N9,8:103430421-103442786 (Clone quality: bE496N9 on chr=8; Num_of_Contigs=4; )
DARC		ENSSSCG00000006416	4:94777387-94778855		CU462834,CH242-199I10,4:94761474-94795889 (Clone quality: bE199I10 on chr=4; Num_of_Contigs=5; )
DARC		location ⇒	4:94777954-94777336		CU462834,CH242-199I10,4:94761474-94795889 (Clone quality: bE199I10 on chr=4; Num_of_Contigs=5; )
DARS		ENSSSCG00000015689	15:14296947-14371534
DARS2		ENSSSCG00000015495	9:108999478-109014067
DATF1		location ⇒	1:47366890-47366768		CU928313,CH242-267E23,1:47362231-47380980 (Clone quality: bE267E23 on chr=1; Num_of_Contigs=5; )
DAXX		ENSSSCG00000001509	7:34084220-34087457	CU607018,CH242-138E20,7:33930957-34116846 (Clone quality: bE138E20 on chr=7; Num_of_Contigs=1; )
DAXX		location ⇒	7:34086134-34085997	CU607018,CH242-138E20,7:33930957-34116846 (Clone quality: bE138E20 on chr=7; Num_of_Contigs=1; )
DAXX		location ⇒	7:34086705-34086250	CU607018,CH242-138E20,7:33930957-34116846 (Clone quality: bE138E20 on chr=7; Num_of_Contigs=1; )
DAZAP2		location ⇒	5:15204939-15203740		CU694522,CH242-54E2,5:15201806-15208003 (Clone quality: bE54E2 on chr=5; Num_of_Contigs=10; )
DAZAP2		location ⇒	5:15207667-15207612		CU694522,CH242-54E2,5:15201806-15208003 (Clone quality: bE54E2 on chr=5; Num_of_Contigs=10; )
DAZAP2		location ⇒	5:15405581-15404382		CU694837,CH242-191H6,5:15374884-15408249 (Clone quality: bE191H6 on chr=5; Num_of_Contigs=5; )
DAZAP2		location ⇒	5:15409256-15409201		CU694837,CH242-191H6,5:15408350-15439182 (Clone quality: bE191H6 on chr=5; Num_of_Contigs=5; )
DBC1		ENSSSCG00000005504	1:272897185-273000755
DBH		ENSSSCG00000005742	1:288513844-288532154
DBH		ENSSSCG00000004191	1:32774124-32858596

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).