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)

SLC17A5		ENSSSCG00000004486	1:97476511-97508094
SLC17A6		ENSSSCG00000013343	2:34487230-34524223	CU928035,CH242-451D16,2:34371290-34570417 (Clone quality: bE451D16 on chr=2; Num_of_Contigs=1; )
SLC17A7		ENSSSCG00000003170	6:38022095-38031264		FP102665,CH242-289C15,6:38017263-38038160 (Clone quality: bE289C15 on chr=6; Num_of_Contigs=6; )
SLC17A8		ENSSSCG00000000876	5:79504847-79560410
SLC17A9		ENSSSCG00000001108	7:21796209-21803042		CT797471,CH242-54M14,7:21795511-21989531 (Clone quality: bE54M14 on chr=7; Num_of_Contigs=1; )
SLC18A1		ENSSSCG00000009601	14:3964476-3991654		CU468169,CH242-117E9,14:3935323-4002125 (Clone quality: bE117E9 on chr=14; Num_of_Contigs=3; )
SLC18A2		ENSSSCG00000010668	14:133222166-133226981		CU468444,CH242-75D17,14:133216687-133236214 (Clone quality: bE75D17 on chr=14; Num_of_Contigs=6; )
SLC19A2		ENSSSCG00000006290	4:84598339-84623218	CU179726,CH242-320P15,4:84431793-84627616 (Clone quality: bE320P15 on chr=4; Num_of_Contigs=2; )
SLC1A1		ENSSSCG00000005222	1:227504516-227581929
SLC1A2		ENSSSCG00000013296	2:24078355-24106165	FP102395,CH242-89L24,2:24070203-24124283 (Clone quality: bE89L24 on chr=2; Num_of_Contigs=2; )
SLC1A3		ENSSSCG00000016841	16:19372955-19456093
SLC1A4		ENSSSCG00000008361	3:70952186-70955390		CU694922,CH242-490O4,3:70949006-70958252 (Clone quality: bE490O4 on chr=3; Num_of_Contigs=11; )
SLC1A5		ENSSSCG00000003105	6:36406154-36419430		FP102520,CH242-105K10,6:36396758-36420546 (Clone quality: bE105K10 on chr=6; Num_of_Contigs=11; )
SLC1A6		ENSSSCG00000013833	2:60093297-60107747		CU915718,CH242-156C19,2:60080233-60146626 (Clone quality: bE156C19 on chr=2; Num_of_Contigs=6; )
SLC1A7		ENSSSCG00000003852	6:113002672-113042034		CU457407,CH242-32C10,6:112971956-113073523 (Clone quality: bE32C10 on chr=6; Num_of_Contigs=4; )
SLC20A1		ENSSSCG00000008093	3:39164471-39178511		CU468646,CH242-150P16,3:39162908-39178589 (Clone quality: bE150P16 on chr=3; Num_of_Contigs=14; )
SLC20A1		location ⇒	3:39164629-39164144		CU468646,CH242-150P16,3:39162908-39178589 (Clone quality: bE150P16 on chr=3; Num_of_Contigs=14; )
SLC20A1		location ⇒	3:39167725-39167169		CU468646,CH242-150P16,3:39162908-39178589 (Clone quality: bE150P16 on chr=3; Num_of_Contigs=14; )
SLC20A1		location ⇒	3:39176589-39176514		CU468646,CH242-150P16,3:39162908-39178589 (Clone quality: bE150P16 on chr=3; Num_of_Contigs=14; )
SLC20A1		location ⇒	3:39178429-39178133		CU468646,CH242-150P16,3:39162908-39178589 (Clone quality: bE150P16 on chr=3; Num_of_Contigs=14; )
SLC20A2		ENSSSCG00000007027	17:11684828-11696169
SLC22A1		ENSSSCG00000004041	1:8342554-8493870
SLC22A10		ENSSSCG00000013058	2:7397900-7414319		CU856126,CH242-83B5,2:7376724-7438568 (Clone quality: bE83B5 on chr=2; Num_of_Contigs=5; )
SLC22A12		ENSSSCG00000013025	2:5956009-5963155		CU468547,CH242-388P19,2:5950754-5963980 (Clone quality: bE388P19 on chr=2; Num_of_Contigs=12; )
SLC22A13		ENSSSCG00000011256	13:19146069-19153361		CU633398,CH242-322L18,13:19047156-19166830 (Clone quality: bE322L18 on chr=13; Num_of_Contigs=3; )
SLC22A14		ENSSSCG00000011255	13:19112438-19141042		CU633398,CH242-322L18,13:19047156-19166830 (Clone quality: bE322L18 on chr=13; Num_of_Contigs=3; )
SLC22A15		ENSSSCG00000006743	4:108983750-109072718
SLC22A16		ENSSSCG00000004399	1:79477108-79519854
SLC22A17		ENSSSCG00000002025	7:82073543-82078995		CU633625,CH242-116C14,7:82041923-82116183 (Clone quality: bE116C14 on chr=7; Num_of_Contigs=8; )
SLC22A18		ENSSSCG00000012855	2:366376-371582		FP102729,CH242-528B20,2:366171-373048 (Clone quality: bE528B20 on chr=2; Num_of_Contigs=10; )
SLC22A2		ENSSSCG00000004040	1:8293987-8324160		CU466379,CH242-186M5,1:8289583-8337882 (Clone quality: bE186M5 on chr=1; Num_of_Contigs=9; )
SLC22A20		ENSSSCG00000012998	2:5378140-5396133	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
SLC22A23		ENSSSCG00000001004	7:2625463-2766959
SLC22A3		ENSSSCG00000004039	1:8129892-8225152	FP085554,CH242-84O6,1:8054542-8235565 (Clone quality: bE84O6 on chr=1; Num_of_Contigs=4; )
SLC22A4		ENSSSCG00000014275	2:122381352-122424998	CU372899,CH242-156J20,2:122331474-122542304 (Clone quality: bE156J20 on chr=2; Num_of_Contigs=2; )
SLC24A1		ENSSSCG00000004937	1:170733645-170834764
SLC24A2		ENSSSCG00000005167	1:211876491-212175784
SLC24A3		ENSSSCG00000007100	17:28607874-28773547
SLC24A4		ENSSSCG00000002450	7:121849046-122023906
SLC24A5		ENSSSCG00000004662	1:128934219-128955897		CU326370,CH242-254D22,1:128907392-129088077 (Clone quality: bE254D22 on chr=1; Num_of_Contigs=1; )
SLC24A6		ENSSSCG00000009880	14:39120072-39135071		CU468469,CH242-242L24,14:39091266-39137232 (Clone quality: bE242L24 on chr=14; Num_of_Contigs=11; )
SLC25A1		ENSSSCG00000010116	14:52085674-52088540		CU618331,CH242-323M12,14:52058244-52088542 (Clone quality: bE323M12 on chr=14; Num_of_Contigs=3; )
SLC25A11		ENSSSCG00000017907	12:49166626-49169716
SLC25A12		ENSSSCG00000015949	15:72982821-73025768
SLC25A13		ENSSSCG00000015336	9:70988862-71236251
SLC25A14		ENSSSCG00000012660	X:104997400-105027407
SLC25A15		ENSSSCG00000009373	11:15446763-15490831		CU633931,CH242-96K7,11:15417255-15552394 (Clone quality: bE96K7 on chr=11; Num_of_Contigs=6; )
SLC25A16		ENSSSCG00000010237	14:74447330-74485061
SLC25A17		ENSSSCG00000000072	5:3885912-3932901
SLC25A19		ENSSSCG00000017208	12:4214992-4226772	CU928991,CH242-32C19,12:4079494-4242296 (Clone quality: bE32C19 on chr=12; Num_of_Contigs=2; )

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).