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)

SLC5A12		ENSSSCG00000013338	2:31544295-31593706	CU468572,CH242-524G2,2:31513128-31727078 (Clone quality: bE524G2 on chr=2; Num_of_Contigs=6; )
SLC5A4		ENSSSCG00000010039	14:49670401-49703815		CU468977,CH242-158O5,14:49653560-49846294 (Clone quality: bE158O5 on chr=14; Num_of_Contigs=1; )
SLC5A5		ENSSSCG00000013890	2:62125473-62141196		CU463003,CH242-317A24,2:62084905-62151709 (Clone quality: bE317A24 on chr=2; Num_of_Contigs=2; )
SLC5A6		ENSSSCG00000008550	3:104359765-104366796		CU896571,CH242-143O19,3:104350462-104376227 (Clone quality: bE143O19 on chr=3; Num_of_Contigs=6; )
SLC5A7		ENSSSCG00000008140	3:43066041-43089484		CU469416,CH242-209K6,3:43058692-43135972 (Clone quality: bE209K6 on chr=3; Num_of_Contigs=7; )
SLC5A9		ENSSSCG00000003882	6:116965263-116976571
SLC6A1		ENSSSCG00000011577	13:56263117-56280465		CU633270,CH242-296G12,13:56249224-56284781 (Clone quality: bE296G12 on chr=13; Num_of_Contigs=16; )
SLC6A12		ENSSSCG00000000749	5:63418324-63553345
SLC6A126539		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
SLC6A15		ENSSSCG00000000936	5:92051099-92076522
SLC6A17		ENSSSCG00000006811	4:114370350-114521126
SLC6A17		location ⇒	4:114370717-114370338		CU302283,CH242-482I14,4:114369965-114381523 (Clone quality: bE482I14 on chr=4; Num_of_Contigs=20; )
SLC6A17		location ⇒	4:114374709-114374515		CU302283,CH242-482I14,4:114369965-114381523 (Clone quality: bE482I14 on chr=4; Num_of_Contigs=20; )
SLC6A17		location ⇒	4:114377403-114377153		CU302283,CH242-482I14,4:114369965-114381523 (Clone quality: bE482I14 on chr=4; Num_of_Contigs=20; )
SLC6A17		location ⇒	4:114399139-114398763		CU137690,CH242-29J13,4:114381524-114421060 (Clone quality: bE29J13 on chr=4; Num_of_Contigs=7; )
SLC6A18		ENSSSCG00000017117	16:76728665-76737159		FP236205,CH242-148J9,16:76728115-76737983 (Clone quality: bE148J9 on chr=16; Num_of_Contigs=7; )
SLC6A19		ENSSSCG00000017120	16:76870469-76879899
SLC6A2		ENSSSCG00000002827	6:20697214-20742549
SLC6A2		location ⇒	6:20711205-20711677		CU694664,CH242-101O9,6:20659655-20726218 (Clone quality: bE101O9 on chr=6; Num_of_Contigs=8; )
SLC6A3		ENSSSCG00000017121	16:76880421-76905242
SLC6A4		ENSSSCG00000017797	12:44316246-44341563
SLC6A5		ENSSSCG00000013346	2:36165220-36215222
SLC6A6		ENSSSCG00000011600	13:58354069-58386637		CU633920,CH242-163H4,13:58353853-58390772 (Clone quality: bE163H4 on chr=13; Num_of_Contigs=6; )
SLC6A8		ENSSSCG00000012771	X:122474553-122477223		FP245398,CH242-390A7,X:122474466-122509200 (Clone quality: bE390A7 on chr=X; Num_of_Contigs=13; )
SLC7A1		ENSSSCG00000009324	11:6079920-6092468
SLC7A10		ENSSSCG00000002864	6:28694053-28708979		CU638683,CH242-3F10,6:28679939-28721948 (Clone quality: bE3F10 on chr=6; Num_of_Contigs=8; )
SLC7A11		location ⇒	1:187872885-187872956		CU633502,CH242-240C20,1:187832890-187878221 (Clone quality: bE240C20 on chr=1; Num_of_Contigs=4; )
SLC7A11		location ⇒	1:188087540-188087469		CU606975,CH242-251A8,1:188036812-188088768 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
SLC7A11		location ⇒	1:188102022-188101951		CU606975,CH242-251A8,1:188088869-188146416 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
SLC7A11		location ⇒	1:228874404-228874332		CU618324,CH242-276M24,1:228857825-228880847 (Clone quality: bE276M24 on chr=1; Num_of_Contigs=4; )
SLC7A14		ENSSSCG00000011748	13:83158119-83211761		CU928383,CH242-276A6,13:83144715-83238970 (Clone quality: bE276A6 on chr=13; Num_of_Contigs=3; )
SLC7A2		ENSSSCG00000006987	17:5032161-5053065		CU682348,CH242-166L11,17:5021825-5054296 (Clone quality: bE166L11 on chr=17; Num_of_Contigs=5; )
SLC7A4		ENSSSCG00000010102	14:51729892-51989336
SLC7A5		location ⇒	12:51338941-51338917		CU656027,CH242-486K1,12:51336011-51368008 (Clone quality: bE486K1 on chr=12; Num_of_Contigs=10; )
SLC7A6OS		ENSSSCG00000002766	6:12771811-12772415		CU929721,CH242-222H7,6:12770760-12775439 (Clone quality: bE222H7 on chr=6; Num_of_Contigs=27; )
SLC7A7		ENSSSCG00000002041	7:82432218-82469416		CT737318,CH242-17H24,7:82408265-82613937 (Clone quality: bE17H24 on chr=7; Num_of_Contigs=1; )
SLC7A8		ENSSSCG00000002032	7:82233276-82298502
SLC8A2		ENSSSCG00000003117	6:37015039-37017329	FP104555,CH242-158J7,6:37001645-37018015 (Clone quality: bE158J7 on chr=6; Num_of_Contigs=11; )
SLC8A3		ENSSSCG00000002315	7:102030197-102160111
SLC9A1		ENSSSCG00000003569	6:58042526-58095232		FP067355,CH242-106I19,6:57995161-58172236 (Clone quality: bE106I19 on chr=6; Num_of_Contigs=1; )
SLC9A11		ENSSSCG00000015489	9:108751341-108776682
SLC9A2		ENSSSCG00000008152	3:46980500-46997106		CU928772,CH242-100B10,3:46950462-47008341 (Clone quality: bE100B10 on chr=3; Num_of_Contigs=3; )
SLC9A3R1		ENSSSCG00000017232	12:4689210-4706638	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
SLC9A3R2		ENSSSCG00000008038	3:36396774-36407197
SLC9A4		ENSSSCG00000008155	3:47236978-47299269
SLC9A5		ENSSSCG00000002783	6:13311218-13329653		CU929920,CH242-351A16,6:13258514-13336829 (Clone quality: bE351A16 on chr=6; Num_of_Contigs=8; )
SLC9A6		ENSSSCG00000012698	X:109312988-109367081
SLC9A8		ENSSSCG00000007466	17:53559298-53649678
SLC9A9		ENSSSCG00000011686	13:68693577-69014869
SLCO1A2		ENSSSCG00000000584	5:50079369-50104219

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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).