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)

CD27		ENSSSCG00000000705	5:60215579-60220962		CU633552,CH242-193I18,5:60186767-60298754 (Clone quality: bE193I18 on chr=5; Num_of_Contigs=2; )
CD27		ENSSSCG00000013543	2:49855557-49858531		CU929921,CH242-352E11,2:49850244-49867632 (Clone quality: bE352E11 on chr=2; Num_of_Contigs=12; )
CD27		ENSSSCG00000013548	2:49988613-49991587		CU694937,CH242-71B7,2:49979846-50046985 (Clone quality: bE71B7 on chr=2; Num_of_Contigs=4; )
CD27		location ⇒	5:60216065-60215963		CU633552,CH242-193I18,5:60186767-60298754 (Clone quality: bE193I18 on chr=5; Num_of_Contigs=2; )
CD27		location ⇒	5:60217121-60217026		CU633552,CH242-193I18,5:60186767-60298754 (Clone quality: bE193I18 on chr=5; Num_of_Contigs=2; )
CD27		location ⇒	5:60220269-60220133		CU633552,CH242-193I18,5:60186767-60298754 (Clone quality: bE193I18 on chr=5; Num_of_Contigs=2; )
CD271		ENSSSCG00000017548	12:22987595-23005905
CD274		ENSSSCG00000005211	1:226573119-226592640		CU457399,CH242-185B23,1:226537240-226608332 (Clone quality: bE185B23 on chr=1; Num_of_Contigs=9; )
CD274		location ⇒	1:226574601-226574541		CU457399,CH242-185B23,1:226537240-226608332 (Clone quality: bE185B23 on chr=1; Num_of_Contigs=9; )
CD274		location ⇒	1:226576186-226576082		CU457399,CH242-185B23,1:226537240-226608332 (Clone quality: bE185B23 on chr=1; Num_of_Contigs=9; )
CD274		location ⇒	1:226578387-226578102		CU457399,CH242-185B23,1:226537240-226608332 (Clone quality: bE185B23 on chr=1; Num_of_Contigs=9; )
CD274		location ⇒	1:226585323-226584980		CU457399,CH242-185B23,1:226537240-226608332 (Clone quality: bE185B23 on chr=1; Num_of_Contigs=9; )
CD276		ENSSSCG00000001917	7:65153991-65183019		CU137731,CH242-449C4,7:65113175-65198803 (Clone quality: bE449C4 on chr=7; Num_of_Contigs=5; )
CD276		location ⇒	7:1713442-1713345		CU694314,CH242-197B15,7:1595463-1729252 (Clone quality: bE197B15 on chr=7; Num_of_Contigs=3; )
CD276		location ⇒	7:2352329-2352430		CU607065,CH242-35C2,7:2347388-2372804 (Clone quality: bE35C2 on chr=7; Num_of_Contigs=17; )
CD276		location ⇒	7:426416-426296		CU855572,CH242-50N10,7:415676-427685 (Clone quality: bE50N10 on chr=7; Num_of_Contigs=30; )
CD276		location ⇒	7:948629-948516		CU682457,CH242-17I17,7:934292-956861 (Clone quality: bE17I17 on chr=7; Num_of_Contigs=9; )
CD27L		ENSSSCG00000000705	5:60215579-60220962		CU633552,CH242-193I18,5:60186767-60298754 (Clone quality: bE193I18 on chr=5; Num_of_Contigs=2; )
CD28		ENSSSCG00000016121	15:100569241-100576503		CU856435,CH242-89B15,15:100555025-100586764 (Clone quality: bE89B15 on chr=15; Num_of_Contigs=3; )
CD28		ENSSSCG00000016120	15:100516676-100516787		CU927888,CH242-288L12,15:100513346-100517828 (Clone quality: bE288L12 on chr=15; Num_of_Contigs=14; )
CD28		location ⇒	15:100516676-100516787		CU927888,CH242-288L12,15:100513346-100517828 (Clone quality: bE288L12 on chr=15; Num_of_Contigs=14; )
CD28		location ⇒	15:100569652-100569763		CU856435,CH242-89B15,15:100555025-100586764 (Clone quality: bE89B15 on chr=15; Num_of_Contigs=3; )
CD280		ENSSSCG00000017300	12:13713466-13739068
CD283		ENSSSCG00000015801	15:44284517-44293098
CD284		ENSSSCG00000005503	1:271621935-271631702	CR938718,CH242-2F11,1:271517643-271688227 (No clone quality info on bE2F11)
CD289		ENSSSCG00000011436	13:29049282-29052128		CU915558,CH242-407L22,13:29047015-29052186 (Clone quality: bE407L22 on chr=13; Num_of_Contigs=4; )
CD29		ENSSSCG00000011101	10:53172192-53224433		CU570933,CH242-23K17,10:53090393-53282217 (Clone quality: bE23K17 on chr=10; Num_of_Contigs=1; )
CD2AP		ENSSSCG00000001728	7:49649644-49692739
CD2AP		location ⇒	7:49671039-49671142		CU468898,CH242-21M16,7:49629921-49672018 (Clone quality: bE21M16 on chr=7; Num_of_Contigs=3; )
CD2AP		location ⇒	7:49674679-49674801		CU468898,CH242-21M16,7:49672119-49693750 (Clone quality: bE21M16 on chr=7; Num_of_Contigs=3; )
CD2AP		location ⇒	7:49692533-49692728		CU468898,CH242-21M16,7:49672119-49693750 (Clone quality: bE21M16 on chr=7; Num_of_Contigs=3; )
CD2BP2		ENSSSCG00000007791	3:16405822-16544539
CD2BP2		location ⇒	3:16542753-16542593		CU928725,CH242-25P12,3:16542593-16582945 (Clone quality: bE25P12 on chr=3; Num_of_Contigs=8; )
CD2BP2		location ⇒	3:16543018-16542856		CU928725,CH242-25P12,3:16542593-16582945 (Clone quality: bE25P12 on chr=3; Num_of_Contigs=8; )
CD30		ENSSSCG00000003437	6:49086313-49093755		FP102316,CH242-204J17,6:49079436-49098258 (Clone quality: bE204J17 on chr=6; Num_of_Contigs=9; )
CD300A		location ⇒	12:4854532-4854868	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
CD300C		location ⇒	12:4820567-4820495	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
CD300C		location ⇒	12:4849582-4849654	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
CD300C		location ⇒	12:4853592-4853993	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
CD300C		location ⇒	12:4857085-4857395	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
CD300E		location ⇒	12:1642-1731	FP085448,CH242-272C22,12:1-58755 (Clone quality: bE272C22 on chr=12; Num_of_Contigs=8; )
CD300E		location ⇒	12:1665-1789	FP085448,CH242-272C22,12:1-58755 (Clone quality: bE272C22 on chr=12; Num_of_Contigs=8; )
CD300E		location ⇒	12:1668-1769	FP085448,CH242-272C22,12:1-58755 (Clone quality: bE272C22 on chr=12; Num_of_Contigs=8; )
CD300E		location ⇒	12:4781317-4786559	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
CD300LB		ENSSSCG00000017237	12:4859156-4867151	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
CD300LF		location ⇒	12:4733158-4733490	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
CD300LF		location ⇒	12:4813062-4813394	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
CD300LF		location ⇒	12:4824203-4823871	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
CD300LF		location ⇒	12:4830473-4830141	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
CD300LG		location ⇒	12:17194117-17194027		CU914436,CH242-507H4,12:17187863-17209601 (Clone quality: bE507H4 on chr=12; Num_of_Contigs=9; )

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, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-2250, 2251-2300, 2301-2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-2650, 2651-2700, 2701-2750, 2751-2800, 2801-2850, 2851-2900, 2901-2950, 2951-3000, 3001-3050, 3051-3100, 3101-3150, 3151-3200, 3201-3250, 3251-3300, 3301-3350, 3351-3400, 3401-3450, 3451-3500, 3501-3550, 3551-3600, 3601-3650, 3651-3700, 3701-3750, 3751-3800, 3801-3850, 3851-3900, 3901-12

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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).