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)

CATHL9		location ⇒	13:26044977-26044870		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL9		location ⇒	13:26045592-26045381		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL9		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CATL1_PIG		ENSSSCG00000011170	10:65264634-65269060		CU928815,CH242-240P16,10:65259062-65274763 (Clone quality: bE240P16 on chr=10; Num_of_Contigs=8; )
CATL1_PIG		ENSSSCG00000011171	10:65320862-65326580		CU972490,CH242-226K16,10:65315474-65345255 (Clone quality: bE226K16 on chr=10; Num_of_Contigs=8; )
CATSPER1		ENSSSCG00000012959	2:4686131-4694266
CATSPER2		ENSSSCG00000004701	1:133890106-133904423		CU861634,CH242-463N18,1:133885270-133939793 (Clone quality: bE463N18 on chr=1; Num_of_Contigs=7; )
CATSPERB		ENSSSCG00000002442	7:121114470-121206370
CAV1		ENSSSCG00000016634	18:28433047-28467889
CAV1		ENSSSCG00000000763	5:65002112-65141065
CAV1		ENSSSCG00000011455	13:29986203-30144848
CAV1		ENSSSCG00000012298	X:42760501-42794033
CAV1		location ⇒	18:28433483-28433051		CU855654,CH242-299F11,18:28431875-28464856 (Clone quality: bE299F11 on chr=18; Num_of_Contigs=4; )
CAV1		location ⇒	18:28435263-28433523		CU855654,CH242-299F11,18:28431875-28464856 (Clone quality: bE299F11 on chr=18; Num_of_Contigs=4; )
CAV1		location ⇒	18:28466393-28466227		CU855654,CH242-299F11,18:28464957-28514429 (Clone quality: bE299F11 on chr=18; Num_of_Contigs=4; )
CAV1		location ⇒	18:28467882-28467811		CU855654,CH242-299F11,18:28464957-28514429 (Clone quality: bE299F11 on chr=18; Num_of_Contigs=4; )
CAV2		ENSSSCG00000016635	18:28484473-28492739		CU855654,CH242-299F11,18:28464957-28514429 (Clone quality: bE299F11 on chr=18; Num_of_Contigs=4; )
CAZA2_PIG		ENSSSCG00000016631	18:27975412-28025463		CU694968,CH242-18F23,18:27960681-28051031 (Clone quality: bE18F23 on chr=18; Num_of_Contigs=3; )
CAZA2_PIG		ENSSSCG00000016632	18:28099833-28149896		CU694675,CH242-150K23,18:28081367-28216058 (Clone quality: bE150K23 on chr=18; Num_of_Contigs=2; )
CBARA1		ENSSSCG00000010289	14:78429785-78706911
CBFA2T2		ENSSSCG00000007266	17:39066076-39078886
CBFA2T2		location ⇒	17:38991721-38991955		CU075927,CH242-92I13,17:38979590-38998177 (Clone quality: bE92I13 on chr=17; Num_of_Contigs=16; )
CBFA2T2		location ⇒	17:39073038-39072979		CU075927,CH242-92I13,17:39069049-39079900 (Clone quality: bE92I13 on chr=17; Num_of_Contigs=16; )
CBFA2T2		location ⇒	17:39077893-39077689		CU075927,CH242-92I13,17:39069049-39079900 (Clone quality: bE92I13 on chr=17; Num_of_Contigs=16; )
CBFA2T2		location ⇒	17:39078882-39078796		CU075927,CH242-92I13,17:39069049-39079900 (Clone quality: bE92I13 on chr=17; Num_of_Contigs=16; )
CBFA2T3		ENSSSCG00000002648	6:396805-408185		FP102571,CH242-151H1,6:395325-411339 (Clone quality: bE151H1 on chr=6; Num_of_Contigs=15; )
CBFA2T3		location ⇒	6:398625-398484		FP102571,CH242-151H1,6:395325-411339 (Clone quality: bE151H1 on chr=6; Num_of_Contigs=15; )
CBFA2T3		location ⇒	6:398941-398871		FP102571,CH242-151H1,6:395325-411339 (Clone quality: bE151H1 on chr=6; Num_of_Contigs=15; )
CBFA2T3		location ⇒	6:399548-399353		FP102571,CH242-151H1,6:395325-411339 (Clone quality: bE151H1 on chr=6; Num_of_Contigs=15; )
CBFA2T3		location ⇒	6:400203-400117		FP102571,CH242-151H1,6:395325-411339 (Clone quality: bE151H1 on chr=6; Num_of_Contigs=15; )
CBL		ENSSSCG00000010494	14:111954319-112193346
CBL		ENSSSCG00000003083	6:35768919-35784680		CU459172,CH242-480J10,6:35756411-35818672 (Clone quality: bE480J10 on chr=6; Num_of_Contigs=12; )
CBL		ENSSSCG00000012160	X:15098687-15256316
CBL		ENSSSCG00000015115	9:45017359-45118067
CBL		location ⇒	9:45122674-45125113		CU915638,CH242-115L13,9:45114077-45138958 (Clone quality: bE115L13 on chr=9; Num_of_Contigs=6; )
CBLB		ENSSSCG00000009932	14:41586464-41599398		CT737283,CH242-112F16,14:41491728-41660145 (Clone quality: bE112F16 on chr=14; Num_of_Contigs=1; )
CBLC		ENSSSCG00000003083	6:35768919-35784680		CU459172,CH242-480J10,6:35756411-35818672 (Clone quality: bE480J10 on chr=6; Num_of_Contigs=12; )
CBLL1		location ⇒	X:17165334-17165207	CU463994,CH242-77J21,X:17136648-17199246 (Clone quality: bE77J21 on chr=X; Num_of_Contigs=3; )
CBLL1		location ⇒	X:17233579-17233706		CU582972,CH242-312D13,X:17229649-17234970 (Clone quality: bE312D13 on chr=X; Num_of_Contigs=3; )
CBLN2		ENSSSCG00000004877	1:158165345-158168994		CU062561,CH242-394J16,1:158142954-158237595 (Clone quality: bE394J16 on chr=1; Num_of_Contigs=4; )
CBLN3		ENSSSCG00000001985	7:81206829-81209341		CT997804,CH242-280B15,7:81187212-81281808 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
CBLN4		ENSSSCG00000007490	17:59209904-59218285	CR956373,CH242-69F10,17:59033051-59220949 (No clone quality info on bE69F10)
CBR3		ENSSSCG00000012053	13:140242206-140251911		CU915666,CH242-280H1,13:140230630-140261298 (Clone quality: bE280H1 on chr=13; Num_of_Contigs=9; )
CBR4		ENSSSCG00000009717	14:20642776-20662060		CU062559,CH242-374J1,14:20564388-20702379 (Clone quality: bE374J1 on chr=14; Num_of_Contigs=3; )
CBX1		ENSSSCG00000017529	12:21912862-21939181
CBX2		location ⇒	12:1632660-1632712	CU464073,CH242-396G1,12:1427255-1662757 (Clone quality: bE396G1 on chr=3; Num_of_Contigs=9; )
CBX2		location ⇒	12:1758015-1758121		FP236795,CH242-62A6,12:1755627-1764457 (Clone quality: bE62A6 on chr=12; Num_of_Contigs=13; )
CBX2		location ⇒	12:1759869-1761105		FP236795,CH242-62A6,12:1755627-1764457 (Clone quality: bE62A6 on chr=12; Num_of_Contigs=13; )
CBX2		location ⇒	12:1762940-1763077		FP236795,CH242-62A6,12:1755627-1764457 (Clone quality: bE62A6 on chr=12; Num_of_Contigs=13; )
CBX3		ENSSSCG00000016711	18:45087736-45095271		FP236743,CH242-201O19,18:45085661-45097060 (Clone quality: bE201O19 on chr=18; Num_of_Contigs=8; )

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).