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)

C1orf38		location ⇒	6:58593038-58592627		CU928393,CH242-274K17,6:58588142-58594217 (Clone quality: bE274K17 on chr=6; Num_of_Contigs=5; )
C1orf38		location ⇒	6:58597176-58597033		CU928393,CH242-274K17,6:58594318-58604352 (Clone quality: bE274K17 on chr=6; Num_of_Contigs=5; )
C1orf38		location ⇒	6:58600128-58600004		CU928393,CH242-274K17,6:58594318-58604352 (Clone quality: bE274K17 on chr=6; Num_of_Contigs=5; )
C1orf43		ENSSSCG00000006554	4:99563879-99574374		CU856218,CH242-277E7,4:99509313-99581754 (Clone quality: bE277E7 on chr=4; Num_of_Contigs=4; )
C1orf51		ENSSSCG00000006655	4:102758916-102762666		CU468675,CH242-4P3,4:102748159-102770887 (Clone quality: bE4P3 on chr=4; Num_of_Contigs=11; )
C1orf53		ENSSSCG00000010902	10:21977168-21982340		FP236725,CH242-493N13,10:21969497-21996611 (Clone quality: bE493N13 on chr=10; Num_of_Contigs=8; )
C1orf54		ENSSSCG00000006656	4:102763901-102772625
C1orf55		ENSSSCG00000010858	10:14082742-14101503		CU914379,CH242-206B3,10:14068855-14118456 (Clone quality: bE206B3 on chr=10; Num_of_Contigs=3; )
C1orf56		ENSSSCG00000006639	4:102135560-102137756		CU459198,CH242-258B14,4:102107604-102144873 (Clone quality: bE258B14 on chr=4; Num_of_Contigs=7; )
C1orf57		ENSSSCG00000010166	14:59284032-59314620		CU468618,CH242-93C11,14:59270264-59356752 (Clone quality: bE93C11 on chr=14; Num_of_Contigs=8; )
C1orf58		ENSSSCG00000010836	10:11596786-11611124		CU571292,CH242-3B15,10:11566469-11612398 (Clone quality: bE3B15 on chr=10; Num_of_Contigs=7; )
C1orf59		ENSSSCG00000006846	4:115878957-115896919		CU326386,CH242-265P14,4:115841878-115922954 (Clone quality: bE265P14 on chr=4; Num_of_Contigs=5; )
C1orf62		ENSSSCG00000006842	4:115707755-115737227		CU468439,CH242-5D18,4:115697042-115796952 (Clone quality: bE5D18 on chr=4; Num_of_Contigs=3; )
C1orf65		ENSSSCG00000010888	10:19101299-19103143		CU571220,CH242-283B3,10:19068991-19106113 (Clone quality: bE283B3 on chr=10; Num_of_Contigs=3; )
C1orf66		ENSSSCG00000006470	4:97050852-97058759		CU582900,CH242-5K23,4:96992487-97070807 (Clone quality: bE5K23 on chr=4; Num_of_Contigs=3; )
C1orf68		ENSSSCG00000006599	4:100633671-100634474		CU210949,CH242-471G17,4:100629419-100634936 (Clone quality: bE471G17 on chr=4; Num_of_Contigs=4; )
C1orf69		ENSSSCG00000013988	2:66514930-66525375	FP085478,CH242-132B19,2:66476472-66645587 (Clone quality: bE132B19 on chr=2; Num_of_Contigs=3; )
C1orf70		ENSSSCG00000003335	6:42859945-42948778
C1orf71		ENSSSCG00000010882	10:18731790-18740732		FP089501,CH242-45D18,10:18727254-18743409 (Clone quality: bE45D18 on chr=10; Num_of_Contigs=15; )
C1orf74		ENSSSCG00000015613	9:125542108-125542899		CU855559,CH242-186K8,9:125498250-125543189 (Clone quality: bE186K8 on chr=9; Num_of_Contigs=10; )
C1orf84		ENSSSCG00000003942	6:120079562-120089739
C1orf85		ENSSSCG00000006488	4:97662587-97665559		CU468654,CH242-228K10,4:97649767-97712830 (Clone quality: bE228K10 on chr=4; Num_of_Contigs=7; )
C1orf87		ENSSSCG00000003823	6:107497003-107576824
C1orf88		ENSSSCG00000006795	4:113449993-113455307		CU468595,CH242-175A23,4:113445124-113550429 (Clone quality: bE175A23 on chr=4; Num_of_Contigs=4; )
C1orf89		ENSSSCG00000003473	6:51748324-51752754
C1orf9		ENSSSCG00000015485	9:108044428-108088797
C1orf91		ENSSSCG00000003611	6:60838843-60841434
C1orf92		ENSSSCG00000006462	4:96855525-96869043
C1orf94		ENSSSCG00000003623	6:61580932-61622167		FP236311,CH242-237A14,6:61568621-61637443 (Clone quality: bE237A14 on chr=6; Num_of_Contigs=7; )
C1orf96		ENSSSCG00000010193	14:63023545-63040302
C1QA		ENSSSCG00000003524	6:55586559-55589474
C1QA		location ⇒	6:55587559-55587738		FP245426,CH242-91I16,6:55586971-55606438 (Clone quality: bE91I16 on chr=6; Num_of_Contigs=7; )
C1QA		location ⇒	6:55588827-55589474		FP245426,CH242-91I16,6:55586971-55606438 (Clone quality: bE91I16 on chr=6; Num_of_Contigs=7; )
C1QB		ENSSSCG00000003528	6:55781457-55783226		FP236753,CH242-42H7,6:55774673-55785389 (Clone quality: bE42H7 on chr=6; Num_of_Contigs=7; )
C1QB		ENSSSCG00000003526	6:55605785-55606300		FP245426,CH242-91I16,6:55586971-55606438 (Clone quality: bE91I16 on chr=6; Num_of_Contigs=7; )
C1QB		location ⇒	6:55605785-55606300		FP245426,CH242-91I16,6:55586971-55606438 (Clone quality: bE91I16 on chr=6; Num_of_Contigs=7; )
C1QB		location ⇒	6:55782140-55781625		FP236753,CH242-42H7,6:55774673-55785389 (Clone quality: bE42H7 on chr=6; Num_of_Contigs=7; )
C1QBP		location ⇒	13:8119973-8120396		CU464160,CH242-393A15,13:8077051-8120399 (Clone quality: bE393A15 on chr=13; Num_of_Contigs=5; )
C1QBP		location ⇒	13:8281521-8282637		CU914790,CH242-105N22,13:8259410-8289623 (Clone quality: bE105N22 on chr=13; Num_of_Contigs=17; )
C1QC		ENSSSCG00000003525	6:55592968-55597855		FP245426,CH242-91I16,6:55586971-55606438 (Clone quality: bE91I16 on chr=6; Num_of_Contigs=7; )
C1QDC1		location ⇒	14:11729206-11729439		CU468329,CH242-220E13,14:11669700-11856557 (Clone quality: bE220E13 on chr=14; Num_of_Contigs=1; )
C1QG		location ⇒	6:55593149-55593239		FP245426,CH242-91I16,6:55586971-55606438 (Clone quality: bE91I16 on chr=6; Num_of_Contigs=7; )
C1QG		location ⇒	6:55593479-55593676		FP245426,CH242-91I16,6:55586971-55606438 (Clone quality: bE91I16 on chr=6; Num_of_Contigs=7; )
C1QG		location ⇒	6:55597006-55597850		FP245426,CH242-91I16,6:55586971-55606438 (Clone quality: bE91I16 on chr=6; Num_of_Contigs=7; )
C1QL1		ENSSSCG00000011043	10:43502285-43508918		CU694240,CH242-232P13,10:43502230-43519179 (Clone quality: bE232P13 on chr=10; Num_of_Contigs=2; )
C1QL2		ENSSSCG00000015717	15:23378708-23379920
C1QL4		ENSSSCG00000000197	5:14056294-14059028		CU633660,CH242-20J14,5:13996651-14067250 (Clone quality: bE20J14 on chr=5; Num_of_Contigs=3; )
C1qR(P)		ENSSSCG00000007116	17:31744235-31746961		CU606974,CH242-23K16,17:31739767-31793889 (Clone quality: bE23K16 on chr=17; Num_of_Contigs=5; )
C1QR1		ENSSSCG00000007116	17:31744235-31746961		CU606974,CH242-23K16,17:31739767-31793889 (Clone quality: bE23K16 on chr=17; Num_of_Contigs=5; )
C1QR1		location ⇒	17:31704572-31704311		CU407182,CH242-263H13,17:31698231-31705569 (Clone quality: bE263H13 on chr=17; Num_of_Contigs=6; )

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).