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)

CD61		location ⇒	12:1600022-1599945	CU464073,CH242-396G1,12:1427255-1662757 (Clone quality: bE396G1 on chr=3; Num_of_Contigs=9; )
CD61		location ⇒	12:1743568-1743491		FP236795,CH242-62A6,12:1741855-1746830 (Clone quality: bE62A6 on chr=12; Num_of_Contigs=13; )
CD61		location ⇒	12:1915140-1915016	CU942393,CH242-200M2,12:1864056-2044534 (Clone quality: bE200M2 on chr=14; Num_of_Contigs=6; )
CD62		ENSSSCG00000006286	4:84377739-84387530		CU407291,CH242-513E17,4:84329694-84430611 (Clone quality: bE513E17 on chr=4; Num_of_Contigs=7; )
CD62		ENSSSCG00000006288	4:84453836-84489355	CU179726,CH242-320P15,4:84431793-84627616 (Clone quality: bE320P15 on chr=4; Num_of_Contigs=2; )
CD62E		ENSSSCG00000006286	4:84377739-84387530		CU407291,CH242-513E17,4:84329694-84430611 (Clone quality: bE513E17 on chr=4; Num_of_Contigs=7; )
CD63		ENSSSCG00000000361	5:20079426-20127422
CD63		location ⇒	5:20079597-20079442		CU855487,CH242-124H13,5:20045739-20096880 (Clone quality: bE124H13 on chr=5; Num_of_Contigs=8; )
CD63		location ⇒	5:20081180-20080992		CU855487,CH242-124H13,5:20045739-20096880 (Clone quality: bE124H13 on chr=5; Num_of_Contigs=8; )
CD63		location ⇒	5:20123626-20123471	CU606916,CH242-141C7,5:20096881-20252808 (Clone quality: bE141C7 on chr=5; Num_of_Contigs=1; )
CD63		location ⇒	5:20125211-20125023	CU606916,CH242-141C7,5:20096881-20252808 (Clone quality: bE141C7 on chr=5; Num_of_Contigs=1; )
CD64		ENSSSCG00000006678	4:103242867-103251849		CU462833,CH242-167L20,4:103208937-103337851 (Clone quality: bE167L20 on chr=4; Num_of_Contigs=2; )
CD68		ENSSSCG00000008769	8:23617243-23619485		CU406992,CH242-305H5,8:23609474-23775679 (Clone quality: bE305H5 on chr=8; Num_of_Contigs=1; )
CD68		ENSSSCG00000008769	8:23617243-23619485		CU406992,CH242-305H5,8:23609474-23775679 (Clone quality: bE305H5 on chr=8; Num_of_Contigs=1; )
CD68		location ⇒	12:50061038-50060708	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
CD68		location ⇒	12:50061745-50061588	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
CD68		location ⇒	12:50062438-50062316	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
CD68		location ⇒	12:50062874-50062596	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
CD69		ENSSSCG00000000653	5:58693397-58700536		CU633551,CH242-192N12,5:58674281-58796136 (Clone quality: bE192N12 on chr=5; Num_of_Contigs=4; )
CD69		location ⇒	5:58697154-58697276		CU633551,CH242-192N12,5:58674281-58796136 (Clone quality: bE192N12 on chr=5; Num_of_Contigs=4; )
CD69		location ⇒	5:58698328-58698535		CU633551,CH242-192N12,5:58674281-58796136 (Clone quality: bE192N12 on chr=5; Num_of_Contigs=4; )
CD69		location ⇒	5:58698881-58698987		CU633551,CH242-192N12,5:58674281-58796136 (Clone quality: bE192N12 on chr=5; Num_of_Contigs=4; )
CD69		location ⇒	5:58700075-58700242		CU633551,CH242-192N12,5:58674281-58796136 (Clone quality: bE192N12 on chr=5; Num_of_Contigs=4; )
CD70		ENSSSCG00000013543	2:49855557-49858531		CU929921,CH242-352E11,2:49850244-49867632 (Clone quality: bE352E11 on chr=2; Num_of_Contigs=12; )
CD70		ENSSSCG00000013548	2:49988613-49991587		CU694937,CH242-71B7,2:49979846-50046985 (Clone quality: bE71B7 on chr=2; Num_of_Contigs=4; )
CD71		ENSSSCG00000011848	13:100772881-100799950	CU695181,CH242-182C12,13:100594044-100802412 (Clone quality: bE182C12 on chr=13; Num_of_Contigs=21; )
CD72		ENSSSCG00000005311	1:247438251-247445894		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
CD72		location ⇒	1:247438584-247438253		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
CD72		location ⇒	1:247440598-247440448		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
CD72		location ⇒	1:247443879-247443544		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
CD72		location ⇒	1:247445894-247445683		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
CD74		location ⇒	2:14237-14322		CU928976,CH242-144M19,2:1-32533 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
CD74		location ⇒	2:20343-20274		CU928976,CH242-144M19,2:1-32533 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
CD74		location ⇒	2:45152-45031		CU928976,CH242-144M19,2:43742-170991 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
CD74		location ⇒	2:52581-52686		CU928976,CH242-144M19,2:43742-170991 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
CD79a		ENSSSCG00000003041	6:34616593-34620152		FP015926,CH242-183C8,6:34614693-34644455 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
CD79A		ENSSSCG00000003041	6:34616593-34620152		FP015926,CH242-183C8,6:34614693-34644455 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
CD79A		location ⇒	6:34617065-34616598		FP015926,CH242-183C8,6:34614693-34644455 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
CD79A		location ⇒	6:34618181-34618061		FP015926,CH242-183C8,6:34614693-34644455 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
CD79A		location ⇒	6:34618732-34618437		FP015926,CH242-183C8,6:34614693-34644455 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
CD79A		location ⇒	6:34621548-34621368		FP015926,CH242-183C8,6:34614693-34644455 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
CD79B		ENSSSCG00000017283	12:12626857-12630260		CU466386,CH242-271O11,12:12583385-12667411 (Clone quality: bE271O11 on chr=12; Num_of_Contigs=5; )
CD79b		ENSSSCG00000017283	12:12626857-12630260		CU466386,CH242-271O11,12:12583385-12667411 (Clone quality: bE271O11 on chr=12; Num_of_Contigs=5; )
CD79B		location ⇒	12:12626877-12627010		CU466386,CH242-271O11,12:12583385-12667411 (Clone quality: bE271O11 on chr=12; Num_of_Contigs=5; )
CD79B		location ⇒	12:12628633-12628952		CU466386,CH242-271O11,12:12583385-12667411 (Clone quality: bE271O11 on chr=12; Num_of_Contigs=5; )
CD79B		location ⇒	12:12629181-12629301		CU466386,CH242-271O11,12:12583385-12667411 (Clone quality: bE271O11 on chr=12; Num_of_Contigs=5; )
CD79B		location ⇒	12:12629719-12630311		CU466386,CH242-271O11,12:12583385-12667411 (Clone quality: bE271O11 on chr=12; Num_of_Contigs=5; )
CD80		ENSSSCG00000011899	13:105493732-105503556
CD80		location ⇒	13:20034416-20034320		CU633654,CH242-199D16,13:20011264-20171682 (Clone quality: bE199D16 on chr=13; Num_of_Contigs=1; )
CD80		location ⇒	13:22292280-22292183		CU466505,CH242-515M14,13:22221042-22333039 (Clone quality: bE515M14 on chr=13; 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).