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)

C0LU84_PIG		ENSSSCG00000007756	3:15672130-15672631		CU915579,CH242-114I19,3:15670698-15675401 (Clone quality: bE114I19 on chr=3; Num_of_Contigs=28; )
C10orf104		ENSSSCG00000010286	14:78310507-78320584		CU607002,CH242-299J16,14:78303074-78368436 (Clone quality: bE299J16 on chr=14; Num_of_Contigs=5; )
C10orf105		ENSSSCG00000010279	14:77816157-77816495		CT954215,CH242-341I21,14:77695739-77877008 (Clone quality: bE341I21 on chr=14; Num_of_Contigs=1; )
C10orf107		ENSSSCG00000010218	14:67690434-67813348		CT827818,CH242-129G17,14:67672390-67864024 (Clone quality: bE129G17 on chr=14; Num_of_Contigs=1; )
C10orf11		ENSSSCG00000010324	14:81722863-81734006		CT827804,CH242-237N19,14:81718473-81852205 (Clone quality: bE237N19 on chr=14; Num_of_Contigs=2; )
C10orf112		ENSSSCG00000011092	10:52524430-52738790
C10orf114		ENSSSCG00000011086	10:50831689-50831865		FP017142,CH242-258E5,10:50801302-50836873 (Clone quality: bE258E5 on chr=10; Num_of_Contigs=9; )
C10orf116		ENSSSCG00000010366	14:91822270-91824454		CU633355,CH242-179A13,14:91776156-91937562 (Clone quality: bE179A13 on chr=14; Num_of_Contigs=3; )
C10orf118		ENSSSCG00000010648	14:130342093-130380210		CU019667,CH242-264H11,14:130338198-130508081 (Clone quality: bE264H11 on chr=14; Num_of_Contigs=1; )
C10orf119		ENSSSCG00000010688	14:135656765-135728297
C10orf12		ENSSSCG00000010513	14:113549671-113553402		CU469002,CH242-26D9,14:113519783-113560977 (Clone quality: bE26D9 on chr=14; Num_of_Contigs=6; )
C10orf122		ENSSSCG00000010740	14:141987973-142003290		CT867966,CH242-516H10,14:141912618-142053899 (Clone quality: bE516H10 on chr=14; Num_of_Contigs=5; )
C10orf125		ENSSSCG00000010791	14:148497020-148500641
C10orf128		ENSSSCG00000010388	14:93591875-93624943		CU407084,CH242-470M16,14:93581650-93651336 (Clone quality: bE470M16 on chr=14; Num_of_Contigs=10; )
C10orf131		ENSSSCG00000008739	8:8029635-8031893		CU928759,CH242-80M6,8:8014454-8034149 (Clone quality: bE80M6 on chr=8; Num_of_Contigs=5; )
C10orf134		ENSSSCG00000010664	14:132909113-132935594	CT737198,CH242-101L9,14:132896369-133092131 (Clone quality: bE101L9 on chr=14; Num_of_Contigs=2; )
C10orf137		ENSSSCG00000010741	14:142036154-142079891
C10orf140		ENSSSCG00000011087	10:50850772-50853492		FP017142,CH242-258E5,10:50836974-50860894 (Clone quality: bE258E5 on chr=10; Num_of_Contigs=9; )
C10orf26		ENSSSCG00000010590	14:118861339-118874214
C10orf27		ENSSSCG00000010273	14:76834332-76848520	CT737289,CH242-133B3,14:76783692-76995335 (Clone quality: bE133B3 on chr=14; Num_of_Contigs=4; )
C10orf28		ENSSSCG00000010531	14:114230784-114269355
C10orf41		ENSSSCG00000010323	14:81145889-81150190		CT963087,CH242-248M4,14:81141948-81199702 (Clone quality: bE248M4 on chr=14; Num_of_Contigs=10; )
C10orf46		ENSSSCG00000010676	14:134583898-134730413
C10orf53		ENSSSCG00000010393	14:94018187-94027763		CT990602,CH242-369H2,14:94016627-94077443 (Clone quality: bE369H2 on chr=14; Num_of_Contigs=4; )
C10orf54		ENSSSCG00000010280	14:77849910-77875448		CT954215,CH242-341I21,14:77695739-77877008 (Clone quality: bE341I21 on chr=14; Num_of_Contigs=1; )
C10orf57		ENSSSCG00000010340	14:85731576-85753309		CU633299,CH242-455F21,14:85695530-85783710 (Clone quality: bE455F21 on chr=14; Num_of_Contigs=5; )
C10orf68		ENSSSCG00000011099	10:53094149-53122096		CU570933,CH242-23K17,10:53090393-53282217 (Clone quality: bE23K17 on chr=10; Num_of_Contigs=1; )
C10orf71		ENSSSCG00000010389	14:93753249-93757532		CT990615,CH242-381G23,14:93705455-93805867 (Clone quality: bE381G23 on chr=14; Num_of_Contigs=5; )
C10orf72		ENSSSCG00000010385	14:93472678-93560161
C10orf76		ENSSSCG00000010571	14:117746799-118042799
C10orf78		ENSSSCG00000010608	14:120171544-120175306		CT737413,CH242-152J3,14:120085580-120213865 (Clone quality: bE152J3 on chr=14; Num_of_Contigs=2; )
C10orf79		ENSSSCG00000010609	14:120180244-120282055
C10orf81		ENSSSCG00000010643	14:129939581-129974466		CU012038,CH242-328H13,14:129818796-130012065 (Clone quality: bE328H13 on chr=14; Num_of_Contigs=2; )
C10orf82		ENSSSCG00000010663	14:132881428-132888803		CT943652,CH242-275L8,14:132846566-132896368 (Clone quality: bE275L8 on chr=14; Num_of_Contigs=2; )
C10orf84		ENSSSCG00000010674	14:134266795-134302267		CT737313,CH242-140B3,14:134257823-134423168 (Clone quality: bE140B3 on chr=14; Num_of_Contigs=2; )
C10orf90		ENSSSCG00000010747	14:142814977-142907368
C10orf92		ENSSSCG00000010768	14:147689228-147732584
C10orf96		ENSSSCG00000010656	14:132368461-132418098
C10orf97		ENSSSCG00000011045	10:43909512-43991296
C10orf99		ENSSSCG00000010346	14:88748258-88866537
C11orf1		ENSSSCG00000015024	9:38482060-38487219
C11orf10		location ⇒	2:7806307-7806174		CU914654,CH242-267E20,2:7800942-7832178 (Clone quality: bE267E20 on chr=2; Num_of_Contigs=5; )
C11orf10		location ⇒	2:7807275-7807165		CU914654,CH242-267E20,2:7800942-7832178 (Clone quality: bE267E20 on chr=2; Num_of_Contigs=5; )
C11orf10		location ⇒	2:8010107-8010217		CU914494,CH242-176B17,2:7952685-8028591 (Clone quality: bE176B17 on chr=2; Num_of_Contigs=9; )
C11orf10		location ⇒	2:8011075-8011208		CU914494,CH242-176B17,2:7952685-8028591 (Clone quality: bE176B17 on chr=2; Num_of_Contigs=9; )
C11orf17		ENSSSCG00000014574	9:281017-287153		FP102436,CH242-219P18,9:279164-310715 (Clone quality: bE219P18 on chr=9; Num_of_Contigs=6; )
C11orf2		ENSSSCG00000013005	2:5482078-5495295	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
C11orf20		ENSSSCG00000013027	2:6156279-6159332		CU861533,CH242-1H13,2:6154184-6159926 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
C11orf24		ENSSSCG00000012886	2:2964562-2974104		CU928939,CH242-69C7,2:2938457-2993112 (Clone quality: bE69C7 on chr=2; Num_of_Contigs=5; )

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).