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)

COL1A1		location ⇒	12:27460058-27460151		CU655872,CH242-181D5,12:27364235-27545652 (Clone quality: bE181D5 on chr=12; Num_of_Contigs=1; )
COL1A1		location ⇒	12:27598511-27598604		CU915595,CH242-32B14,12:27593205-27703476 (Clone quality: bE32B14 on chr=12; Num_of_Contigs=7; )
COL1A2		ENSSSCG00000015326	9:69420740-69456361		CU915372,CH242-63A14,9:69407843-69460209 (Clone quality: bE63A14 on chr=9; Num_of_Contigs=2; )
COL1A2		location ⇒	9:69453287-69453547		CU915372,CH242-63A14,9:69407843-69460209 (Clone quality: bE63A14 on chr=9; Num_of_Contigs=2; )
COL1A2		location ⇒	9:69453957-69454142		CU915372,CH242-63A14,9:69407843-69460209 (Clone quality: bE63A14 on chr=9; Num_of_Contigs=2; )
COL1A2		location ⇒	9:69454736-69454980		CU915372,CH242-63A14,9:69407843-69460209 (Clone quality: bE63A14 on chr=9; Num_of_Contigs=2; )
COL1A2		location ⇒	9:69455761-69455941		CU915372,CH242-63A14,9:69407843-69460209 (Clone quality: bE63A14 on chr=9; Num_of_Contigs=2; )
COL21A1		ENSSSCG00000001500	7:33879858-34015941
COL21A1		location ⇒	7:34009292-34009441	CU607018,CH242-138E20,7:33930957-34116846 (Clone quality: bE138E20 on chr=7; Num_of_Contigs=1; )
COL21A1		location ⇒	7:34010464-34010668	CU607018,CH242-138E20,7:33930957-34116846 (Clone quality: bE138E20 on chr=7; Num_of_Contigs=1; )
COL21A1		location ⇒	7:34012132-34012213	CU607018,CH242-138E20,7:33930957-34116846 (Clone quality: bE138E20 on chr=7; Num_of_Contigs=1; )
COL21A1		location ⇒	7:34015123-34015279	CU607018,CH242-138E20,7:33930957-34116846 (Clone quality: bE138E20 on chr=7; Num_of_Contigs=1; )
COL22A1		ENSSSCG00000005938	4:2882316-3017566		CU861599,CH242-1G3,4:2882085-3037908 (Clone quality: bE1G3 on chr=4; Num_of_Contigs=2; )
COL23A1		ENSSSCG00000014029	2:69293091-69313246		CU468334,CH242-242B23,2:69292765-69313870 (Clone quality: bE242B23 on chr=2; Num_of_Contigs=5; )
COL24A1		location ⇒	4:135117962-135118072		CU469075,CH242-29N15,4:135117912-135121227 (Clone quality: bE29N15 on chr=4; Num_of_Contigs=28; )
COL24A1		location ⇒	4:135120403-135120507		CU469075,CH242-29N15,4:135117912-135121227 (Clone quality: bE29N15 on chr=4; Num_of_Contigs=28; )
COL24A1		location ⇒	4:135224996-135224825		CU469075,CH242-29N15,4:135220681-135230239 (Clone quality: bE29N15 on chr=4; Num_of_Contigs=28; )
COL24A1		location ⇒	4:135225705-135225640		CU469075,CH242-29N15,4:135220681-135230239 (Clone quality: bE29N15 on chr=4; Num_of_Contigs=28; )
COL25A1		ENSSSCG00000009143	8:97178019-97309782
COL27A1		ENSSSCG00000005487	1:267801206-267956630
COL28A1		ENSSSCG00000015342	9:73100202-73186451
COL29A1		ENSSSCG00000011186	13:1592435-1681709		CU633554,CH242-199A15,13:1536369-1697112 (Clone quality: bE199A15 on chr=13; Num_of_Contigs=1; )
COL2A1		location ⇒	5:73640869-73640814		CU582786,CH242-499H9,5:73638675-73642202 (Clone quality: bE499H9 on chr=5; Num_of_Contigs=8; )
COL2A1		location ⇒	5:73641217-73641109		CU582786,CH242-499H9,5:73638675-73642202 (Clone quality: bE499H9 on chr=5; Num_of_Contigs=8; )
COL2A1		location ⇒	5:73641504-73641404		CU582786,CH242-499H9,5:73638675-73642202 (Clone quality: bE499H9 on chr=5; Num_of_Contigs=8; )
COL2A1		location ⇒	5:73642011-73641948		CU582786,CH242-499H9,5:73638675-73642202 (Clone quality: bE499H9 on chr=5; Num_of_Contigs=8; )
COL3A1		ENSSSCG00000016034	15:88061419-88080791		CU467671,CH242-14N12,15:88029080-88150714 (Clone quality: bE14N12 on chr=15; Num_of_Contigs=4; )
COL3A1		location ⇒	15:88077212-88077509		CU467671,CH242-14N12,15:88029080-88150714 (Clone quality: bE14N12 on chr=15; Num_of_Contigs=4; )
COL3A1		location ⇒	15:88078552-88078740		CU467671,CH242-14N12,15:88029080-88150714 (Clone quality: bE14N12 on chr=15; Num_of_Contigs=4; )
COL3A1		location ⇒	15:88079077-88079322		CU467671,CH242-14N12,15:88029080-88150714 (Clone quality: bE14N12 on chr=15; Num_of_Contigs=4; )
COL3A1		location ⇒	15:88080060-88080474		CU467671,CH242-14N12,15:88029080-88150714 (Clone quality: bE14N12 on chr=15; Num_of_Contigs=4; )
COL4A1		ENSSSCG00000009544	11:77165233-77248332
COL4A1		location ⇒	11:77177011-77176925		CT954225,CH242-194N14,11:77139033-77195541 (Clone quality: bE194N14 on chr=11; Num_of_Contigs=6; )
COL4A1		location ⇒	11:77184366-77184311		CT954225,CH242-194N14,11:77139033-77195541 (Clone quality: bE194N14 on chr=11; Num_of_Contigs=6; )
COL4A1		location ⇒	11:77187188-77187075		CT954225,CH242-194N14,11:77139033-77195541 (Clone quality: bE194N14 on chr=11; Num_of_Contigs=6; )
COL4A1		location ⇒	11:77202647-77202560		CT954225,CH242-194N14,11:77195642-77219260 (Clone quality: bE194N14 on chr=11; Num_of_Contigs=6; )
COL4A2		ENSSSCG00000009545	11:77349261-77462386
COL4A3		ENSSSCG00000016245	15:121142895-121208597
COL4A3		location ⇒	15:121169967-121170062		CU627997,CH242-426G1,15:121163159-121174050 (Clone quality: bE426G1 on chr=15; Num_of_Contigs=13; )
COL4A3		location ⇒	15:121173458-121173532		CU627997,CH242-426G1,15:121163159-121174050 (Clone quality: bE426G1 on chr=15; Num_of_Contigs=13; )
COL4A3		location ⇒	15:121194449-121194545		CU627997,CH242-426G1,15:121179204-121204678 (Clone quality: bE426G1 on chr=15; Num_of_Contigs=13; )
COL4A3		location ⇒	15:121208505-121208590		CU627997,CH242-426G1,15:121204779-121208794 (Clone quality: bE426G1 on chr=15; Num_of_Contigs=13; )
COL4A3BP		ENSSSCG00000014081	2:73269381-73394394
COL4A3BP		location ⇒	2:73273984-73273847		CU694556,CH242-177D18,2:73227715-73368035 (Clone quality: bE177D18 on chr=2; Num_of_Contigs=2; )
COL4A3BP		location ⇒	2:73276834-73276705		CU694556,CH242-177D18,2:73227715-73368035 (Clone quality: bE177D18 on chr=2; Num_of_Contigs=2; )
COL4A3BP		location ⇒	2:73277685-73277555		CU694556,CH242-177D18,2:73227715-73368035 (Clone quality: bE177D18 on chr=2; Num_of_Contigs=2; )
COL4A3BP		location ⇒	2:73286383-73286249		CU694556,CH242-177D18,2:73227715-73368035 (Clone quality: bE177D18 on chr=2; Num_of_Contigs=2; )
COL4A4		ENSSSCG00000016244	15:121001105-121048187
COL4A5		ENSSSCG00000012572	X:87207370-87429414
COL4A6		ENSSSCG00000012571	X:86907578-86942811		CU856296,CH242-222M23,X:86872658-86944935 (Clone quality: bE222M23 on chr=X; Num_of_Contigs=3; )

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).