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)

ALG12		ENSSSCG00000000980	5:100004911-100009405		FP102108,CH242-165O15,5:99992574-100011326 (Clone quality: bE165O15 on chr=5; Num_of_Contigs=15; )
ALG13		ENSSSCG00000012586	X:89541558-89605612
ALG14		ENSSSCG00000006885	4:126917074-127023023
ALG2		ENSSSCG00000005383	1:252552067-252557275		CU861555,CH242-297P22,1:252535523-252612502 (Clone quality: bE297P22 on chr=1; Num_of_Contigs=1; )
ALG5		ENSSSCG00000009360	11:12367075-12402691
ALG6		ENSSSCG00000003815	6:105122528-105174005
ALG8		ENSSSCG00000014887	9:12358172-12431972
ALG9		location ⇒	9:38469717-38469583		CU928661,CH242-297D12,9:38467581-38485059 (Clone quality: bE297D12 on chr=9; Num_of_Contigs=9; )
ALG9		location ⇒	9:38470926-38470792		CU928661,CH242-297D12,9:38467581-38485059 (Clone quality: bE297D12 on chr=9; Num_of_Contigs=9; )
ALG9		location ⇒	9:38579435-38579590		CU928661,CH242-297D12,9:38573805-38587933 (Clone quality: bE297D12 on chr=9; Num_of_Contigs=9; )
ALG9		location ⇒	9:38583221-38583357		CU928661,CH242-297D12,9:38573805-38587933 (Clone quality: bE297D12 on chr=9; Num_of_Contigs=9; )
ALK		ENSSSCG00000000232	5:15977317-15991021
ALK		ENSSSCG00000017148	12:1118815-1161509
ALK		ENSSSCG00000016565	18:16959707-16972262
ALK		ENSSSCG00000015874	15:60075213-60214837
ALK		ENSSSCG00000015873	15:59787229-59823186
ALK		ENSSSCG00000008533	3:103131578-103185564
ALK		ENSSSCG00000005382	1:252432143-252486884
ALK		ENSSSCG00000000233	5:16023608-16057075		CU606912,CH242-90A20,5:16023396-16077450 (Clone quality: bE90A20 on chr=5; Num_of_Contigs=3; )
ALK		location ⇒	3:103141655-103141335		CU468318,CH242-184D1,3:103097547-103173415 (Clone quality: bE184D1 on chr=3; Num_of_Contigs=6; )
ALK		location ⇒	3:103144165-103144014		CU468318,CH242-184D1,3:103097547-103173415 (Clone quality: bE184D1 on chr=3; Num_of_Contigs=6; )
ALK		location ⇒	3:103146488-103146280		CU468318,CH242-184D1,3:103097547-103173415 (Clone quality: bE184D1 on chr=3; Num_of_Contigs=6; )
ALK-5		ENSSSCG00000005382	1:252432143-252486884
ALK-5		location ⇒	1:252461625-252461873		CU571046,CH242-46J18,1:252437834-252466458 (Clone quality: bE46J18 on chr=1; Num_of_Contigs=4; )
ALK-5		location ⇒	1:252465705-252465949		CU571046,CH242-46J18,1:252437834-252466458 (Clone quality: bE46J18 on chr=1; Num_of_Contigs=4; )
ALK-5		location ⇒	1:252472358-252472586		CU861555,CH242-297P22,1:252469152-252535422 (Clone quality: bE297P22 on chr=1; Num_of_Contigs=1; )
ALK-5		location ⇒	1:252486338-252486632		CU861555,CH242-297P22,1:252469152-252535422 (Clone quality: bE297P22 on chr=1; Num_of_Contigs=1; )
ALKBH1		ENSSSCG00000002407	7:108768108-108770184		CU468695,CH242-190O3,7:108763563-108772619 (Clone quality: bE190O3 on chr=7; Num_of_Contigs=13; )
ALKBH2		ENSSSCG00000009939	14:42038720-42043216		CT954284,CH242-241M1,14:42019840-42206297 (Clone quality: bE241M1 on chr=14; Num_of_Contigs=1; )
ALKBH4		ENSSSCG00000007686	3:8208703-8215978		CU861964,CH242-275K10,3:8193129-8225131 (Clone quality: bE275K10 on chr=3; Num_of_Contigs=9; )
ALKBH6		ENSSSCG00000002910	6:30377775-30380613		CU466979,CH242-510C11,6:30377195-30398733 (Clone quality: bE510C11 on chr=6; Num_of_Contigs=10; )
ALKBH7		ENSSSCG00000013541	2:49836372-49838405		CU929921,CH242-352E11,2:49825944-49850143 (Clone quality: bE352E11 on chr=2; Num_of_Contigs=12; )
ALLC		ENSSSCG00000008650	3:120328665-120346596
ALMS1		ENSSSCG00000008295	3:63621567-63633520		CU463123,CH242-385I3,3:63620104-63635885 (Clone quality: bE385I3 on chr=3; Num_of_Contigs=11; )
ALOX12		ENSSSCG00000017930	12:49583096-49596090
ALOX12		location ⇒	12:49583601-49583098		CU914703,CH242-254H21,12:49564591-49589172 (Clone quality: bE254H21 on chr=12; Num_of_Contigs=9; )
ALOX12		location ⇒	12:49583897-49583721		CU914703,CH242-254H21,12:49564591-49589172 (Clone quality: bE254H21 on chr=12; Num_of_Contigs=9; )
ALOX12		location ⇒	12:49584118-49584016		CU914703,CH242-254H21,12:49564591-49589172 (Clone quality: bE254H21 on chr=12; Num_of_Contigs=9; )
ALOX12		location ⇒	12:49586806-49586744		CU914703,CH242-254H21,12:49564591-49589172 (Clone quality: bE254H21 on chr=12; Num_of_Contigs=9; )
ALOX12B		ENSSSCG00000017980	12:50514484-50524502		CU914306,CH242-98O15,12:50484156-50527029 (Clone quality: bE98O15 on chr=12; Num_of_Contigs=9; )
ALOX15		ENSSSCG00000017923	12:49494286-49503043
ALOX15		location ⇒	12:49496205-49496411		CU972403,CH242-271B3,12:49488831-49496492 (Clone quality: bE271B3 on chr=12; Num_of_Contigs=15; )
ALOX15		location ⇒	12:49499431-49499645		CU972403,CH242-271B3,12:49496593-49528528 (Clone quality: bE271B3 on chr=12; Num_of_Contigs=15; )
ALOX15		location ⇒	12:49500445-49500617		CU972403,CH242-271B3,12:49496593-49528528 (Clone quality: bE271B3 on chr=12; Num_of_Contigs=15; )
ALOX15		location ⇒	12:49501967-49502932		CU972403,CH242-271B3,12:49496593-49528528 (Clone quality: bE271B3 on chr=12; Num_of_Contigs=15; )
ALOX15B		ENSSSCG00000017978	12:50493830-50502854		CU914306,CH242-98O15,12:50484156-50527029 (Clone quality: bE98O15 on chr=12; Num_of_Contigs=9; )
ALOX5		location ⇒	14:94886098-94885976		CU468425,CH242-390A15,14:94808687-94931541 (Clone quality: bE390A15 on chr=14; Num_of_Contigs=2; )
ALOX5		location ⇒	14:94886679-94886404		CU468425,CH242-390A15,14:94808687-94931541 (Clone quality: bE390A15 on chr=14; Num_of_Contigs=2; )
ALOX5		location ⇒	14:95058719-95058994		CU468617,CH242-8J14,14:95054768-95064537 (Clone quality: bE8J14 on chr=14; Num_of_Contigs=13; )
ALOX5		location ⇒	14:95059300-95059422		CU468617,CH242-8J14,14:95054768-95064537 (Clone quality: bE8J14 on chr=14; Num_of_Contigs=13; )

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, 751-800, 801-850, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-32

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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).