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)

SLC25A20		ENSSSCG00000011366	13:26450563-26477969
SLC25A21		ENSSSCG00000001942	7:69194121-69401052
SLC25A22		ENSSSCG00000012844	2:169881-175302
SLC25A23		ENSSSCG00000013550	2:50085747-50092002		CU694937,CH242-71B7,2:50063281-50092112 (Clone quality: bE71B7 on chr=2; Num_of_Contigs=4; )
SLC25A24		ENSSSCG00000006848	4:116055695-116107987		CU633925,CH242-22J10,4:116054791-116156329 (Clone quality: bE22J10 on chr=4; Num_of_Contigs=4; )
SLC25A25		ENSSSCG00000005636	1:283195289-283204931		CU582767,CH242-108E18,1:283176310-283230748 (Clone quality: bE108E18 on chr=1; Num_of_Contigs=5; )
SLC25A26		ENSSSCG00000011498	13:39840338-39891705		CU856505,CH242-79G22,13:39820023-39910707 (Clone quality: bE79G22 on chr=13; Num_of_Contigs=4; )
SLC25A27		ENSSSCG00000001720	7:48833260-48860167		CU607063,CH242-261A14,7:48822490-48862602 (Clone quality: bE261A14 on chr=7; Num_of_Contigs=10; )
SLC25A28		ENSSSCG00000010539	14:115556809-115566817
SLC25A3		ENSSSCG00000000886	5:80802869-80810886		FP102239,CH242-207O15,5:80776802-80905572 (Clone quality: bE207O15 on chr=5; Num_of_Contigs=5; )
SLC25A31		ENSSSCG00000009078	8:83708507-83733073
SLC25A32		ENSSSCG00000006049	4:34075354-34096562
SLC25A33		ENSSSCG00000003392	6:47008315-47042622
SLC25A34		ENSSSCG00000003467	6:51500091-51503295		CU457447,CH242-71A8,6:51494097-51525122 (Clone quality: bE71A8 on chr=6; Num_of_Contigs=17; )
SLC25A36		ENSSSCG00000011669	13:66578427-66616507
SLC25A37		ENSSSCG00000009641	14:7754934-7796658		CU468613,CH242-66C15,14:7703314-7807202 (Clone quality: bE66C15 on chr=14; Num_of_Contigs=6; )
SLC25A4		ENSSSCG00000015790	15:43516897-43521180		CU914478,CH242-188G11,15:43445277-43549419 (Clone quality: bE188G11 on chr=15; Num_of_Contigs=9; )
SLC25A41		ENSSSCG00000013537	2:49786861-49789400		CU929921,CH242-352E11,2:49783544-49791158 (Clone quality: bE352E11 on chr=2; Num_of_Contigs=12; )
SLC25A43		ENSSSCG00000012624	X:96721229-96757893		CU467108,CH242-78C24,X:96710534-96782751 (Clone quality: bE78C24 on chr=X; Num_of_Contigs=9; )
SLC25A44		ENSSSCG00000006494	4:97785378-97803020		CU302298,CH242-261P14,4:97781614-97811997 (Clone quality: bE261P14 on chr=4; Num_of_Contigs=4; )
SLC25A45		ENSSSCG00000012993	2:5252212-5258469
SLC25A46		ENSSSCG00000014197	2:104136684-104159215
SLC25A5		ENSSSCG00000012623	X:96703946-96706861		CU467108,CH242-78C24,X:96695370-96710433 (Clone quality: bE78C24 on chr=X; Num_of_Contigs=9; )
SLC26A2		ENSSSCG00000014439	2:136453337-136642517
SLC26A5		ENSSSCG00000015425	9:96424991-96462847
SLC26A6		ENSSSCG00000011361	13:26245986-26257272		CU633242,CH242-208G16,13:26234913-26263430 (Clone quality: bE208G16 on chr=13; Num_of_Contigs=5; )
SLC26A6		location ⇒	13:26249887-26250054		CU633242,CH242-208G16,13:26234913-26263430 (Clone quality: bE208G16 on chr=13; Num_of_Contigs=5; )
SLC26A6		location ⇒	13:26250241-26250408		CU633242,CH242-208G16,13:26234913-26263430 (Clone quality: bE208G16 on chr=13; Num_of_Contigs=5; )
SLC26A6		location ⇒	13:26255790-26255968		CU633242,CH242-208G16,13:26234913-26263430 (Clone quality: bE208G16 on chr=13; Num_of_Contigs=5; )
SLC26A6		location ⇒	13:26439784-26439951		CU861514,CH242-101J13,13:26438501-26440696 (Clone quality: bE101J13 on chr=13; Num_of_Contigs=18; )
SLC26A7		ENSSSCG00000006116	4:46052620-46169462
SLC26A8		ENSSSCG00000001555	7:36351998-36557126
SLC26A8		location ⇒	7:36378414-36378321		CU469170,CH242-5A18,7:36295488-36385536 (Clone quality: bE5A18 on chr=7; Num_of_Contigs=5; )
SLC26A8		location ⇒	7:36529399-36529250		CU407302,CH242-7K1,7:36528021-36584617 (Clone quality: bE7K1 on chr=7; Num_of_Contigs=2; )
SLC26A8		location ⇒	7:36530545-36530378		CU407302,CH242-7K1,7:36528021-36584617 (Clone quality: bE7K1 on chr=7; Num_of_Contigs=2; )
SLC26A8		location ⇒	7:36534199-36534073		CU407302,CH242-7K1,7:36528021-36584617 (Clone quality: bE7K1 on chr=7; Num_of_Contigs=2; )
SLC27A1		ENSSSCG00000013879	2:61775304-61826241
SLC27A3		ENSSSCG00000006569	4:100042217-100046601		CU137691,CH242-31M11,4:100039316-100046627 (Clone quality: bE31M11 on chr=4; Num_of_Contigs=9; )
SLC27A4		ENSSSCG00000005648	1:283416332-283419533		CU234126,CH242-282L14,1:283270038-283452033 (Clone quality: bE282L14 on chr=1; Num_of_Contigs=4; )
SLC27A6		ENSSSCG00000014257	2:119506838-119578839
SLC28A1		ENSSSCG00000002632	7:136241229-136287618
SLC28A2		ENSSSCG00000004673	1:132223667-132246863		CU062525,CH242-125K20,1:132198699-132329693 (Clone quality: bE125K20 on chr=1; Num_of_Contigs=2; )
SLC28A3		ENSSSCG00000010960	10:29581160-29615091
SLC29A1		ENSSSCG00000001700	7:45745500-45754441	CT009542,CH242-272H8,7:45714746-45890644 (Clone quality: bE272H8 on chr=7; Num_of_Contigs=13; )
SLC29A2		ENSSSCG00000012941	2:4242570-4250198		CU928034,CH242-426E24,2:4224713-4259422 (Clone quality: bE426E24 on chr=2; Num_of_Contigs=5; )
SLC29A3		ENSSSCG00000010277	14:77405063-77447879		CT737334,CH242-135I3,14:77326635-77536814 (Clone quality: bE135I3 on chr=14; Num_of_Contigs=1; )
SLC29A4		ENSSSCG00000007579	3:3476353-3650128
SLC2A10		ENSSSCG00000007451	17:50933043-50939068		CU640476,CH242-377A5,17:50932850-50948895 (Clone quality: bE377A5 on chr=17; Num_of_Contigs=17; )
SLC2A11		ENSSSCG00000010068	14:50860397-50877629		CU570757,CH242-95E4,14:50714738-50917166 (Clone quality: bE95E4 on chr=14; Num_of_Contigs=1; )
SLC2A12		ENSSSCG00000004172	1:31276107-31319205

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).