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)

CCK		location ⇒	13:21637965-21637912		CU928734,CH242-406G23,13:21635443-21658475 (Clone quality: bE406G23 on chr=13; Num_of_Contigs=4; )
CCKBR		ENSSSCG00000014631	9:2721407-2831787
CCL1		ENSSSCG00000017720	12:38293074-38296197		CU928660,CH242-280M5,12:38285912-38302748 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
CCL11		ENSSSCG00000017722	12:38323663-38326296
CCL11		location ⇒	12:38307115-38307039		CU928660,CH242-280M5,12:38302849-38308872 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
CCL11		location ⇒	12:38323764-38323663		CU928660,CH242-280M5,12:38319495-38324697 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
CCL11		location ⇒	12:38324169-38324055		CU928660,CH242-280M5,12:38319495-38324697 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
CCL11		location ⇒	12:38326296-38326173		CU928660,CH242-280M5,12:38324798-38339122 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
CCL13		location ⇒	12:38372943-38372901		CU928660,CH242-280M5,12:38371176-38373405 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
CCL14		ENSSSCG00000017703	12:37379355-37380010		CU929934,CH242-43L9,12:37376518-37382841 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL14		location ⇒	12:37355967-37356028		CU929934,CH242-43L9,12:37292599-37376417 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL15		location ⇒	12:37376305-37376408		CU929934,CH242-43L9,12:37292599-37376417 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL15		location ⇒	12:37379375-37379494		CU929934,CH242-43L9,12:37376518-37382841 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL15		location ⇒	12:37379929-37380406		CU929934,CH242-43L9,12:37376518-37382841 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL16		ENSSSCG00000017704	12:37382438-37385815
CCL16		location ⇒	12:37382611-37382746		CU929934,CH242-43L9,12:37376518-37382841 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL16		location ⇒	12:37384963-37385081		CU896616,CH242-206O9,12:37382842-37393080 (Clone quality: bE206O9 on chr=12; Num_of_Contigs=7; )
CCL16		location ⇒	12:37385502-37385813		CU896616,CH242-206O9,12:37382842-37393080 (Clone quality: bE206O9 on chr=12; Num_of_Contigs=7; )
CCL18		location ⇒	12:37257333-37257219		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL18		location ⇒	12:37258166-37257711		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL18		location ⇒	12:37286510-37286614		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL19		ENSSSCG00000010966	10:30554414-30557010		FP236727,CH242-511I17,10:30551839-30567954 (Clone quality: bE511I17 on chr=10; Num_of_Contigs=7; )
CCL19		location ⇒	10:30554636-30554696		FP236727,CH242-511I17,10:30551839-30567954 (Clone quality: bE511I17 on chr=10; Num_of_Contigs=7; )
CCL19		location ⇒	10:30555731-30555829		FP236727,CH242-511I17,10:30551839-30567954 (Clone quality: bE511I17 on chr=10; Num_of_Contigs=7; )
CCL2		ENSSSCG00000017723	12:38372460-38374364
CCL2		location ⇒	12:38372958-38372856		CU928660,CH242-280M5,12:38371176-38373405 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
CCL2		location ⇒	12:38373407-38373343		CU928660,CH242-280M5,12:38371176-38373405 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; ) CU571289,CH242-352D21,12:38373406-38427513 (Clone quality: bE352D21 on chr=12; Num_of_Contigs=4; )
CCL20		ENSSSCG00000016254	15:121877745-121880971		CU861588,CH242-174G17,15:121858065-121882478 (Clone quality: bE174G17 on chr=15; Num_of_Contigs=11; )
CCL20		location ⇒	15:121878146-121878054		CU861588,CH242-174G17,15:121858065-121882478 (Clone quality: bE174G17 on chr=15; Num_of_Contigs=11; )
CCL20		location ⇒	15:121878887-121878810		CU861588,CH242-174G17,15:121858065-121882478 (Clone quality: bE174G17 on chr=15; Num_of_Contigs=11; )
CCL20		location ⇒	15:121879722-121879606		CU861588,CH242-174G17,15:121858065-121882478 (Clone quality: bE174G17 on chr=15; Num_of_Contigs=11; )
CCL20		location ⇒	15:121880956-121880844		CU861588,CH242-174G17,15:121858065-121882478 (Clone quality: bE174G17 on chr=15; Num_of_Contigs=11; )
CCL21		ENSSSCG00000010965	10:30537652-30538765		FP236727,CH242-511I17,10:30537395-30548503 (Clone quality: bE511I17 on chr=10; Num_of_Contigs=7; )
CCL21		location ⇒	10:30537673-30537774		FP236727,CH242-511I17,10:30537395-30548503 (Clone quality: bE511I17 on chr=10; Num_of_Contigs=7; )
CCL21		location ⇒	10:30537872-30537996		FP236727,CH242-511I17,10:30537395-30548503 (Clone quality: bE511I17 on chr=10; Num_of_Contigs=7; )
CCL21		location ⇒	10:30538076-30538259		FP236727,CH242-511I17,10:30537395-30548503 (Clone quality: bE511I17 on chr=10; Num_of_Contigs=7; )
CCL22		ENSSSCG00000002821	6:20120622-20125581		FP102873,CH242-277I7,6:20115234-20170472 (Clone quality: bE277I7 on chr=6; Num_of_Contigs=4; )
CCL22		location ⇒	6:20121244-20120688		FP102873,CH242-277I7,6:20115234-20170472 (Clone quality: bE277I7 on chr=6; Num_of_Contigs=4; )
CCL22		location ⇒	6:20124159-20124033		FP102873,CH242-277I7,6:20115234-20170472 (Clone quality: bE277I7 on chr=6; Num_of_Contigs=4; )
CCL22		location ⇒	6:20125577-20125471		FP102873,CH242-277I7,6:20115234-20170472 (Clone quality: bE277I7 on chr=6; Num_of_Contigs=4; )
CCL23		location ⇒	12:50061745-50061588	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
CCL23		location ⇒	12:50062438-50062316	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
CCL23		location ⇒	12:50062874-50062596	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
CCL23		location ⇒	12:50062989-50062919	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
CCL24		ENSSSCG00000007699	3:8750352-8750749		CU855597,CH242-327P3,3:8749498-8751811 (Clone quality: bE327P3 on chr=3; Num_of_Contigs=27; )
CCL24		location ⇒	3:8750215-8750391		CU855597,CH242-327P3,3:8749498-8751811 (Clone quality: bE327P3 on chr=3; Num_of_Contigs=27; )
CCL24		location ⇒	3:8750626-8750745		CU855597,CH242-327P3,3:8749498-8751811 (Clone quality: bE327P3 on chr=3; Num_of_Contigs=27; )
CCL25		ENSSSCG00000013593	2:51407278-51410741		CU929699,CH242-182L23,2:51289316-51437705 (Clone quality: bE182L23 on chr=2; Num_of_Contigs=2; )
CCL25		location ⇒	2:51407554-51407628		CU929699,CH242-182L23,2:51289316-51437705 (Clone quality: bE182L23 on chr=2; Num_of_Contigs=2; )
CCL25		location ⇒	2:51409342-51409461		CU929699,CH242-182L23,2:51289316-51437705 (Clone quality: bE182L23 on chr=2; Num_of_Contigs=2; )

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).