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)

CCL25		location ⇒	2:51409545-51409682		CU929699,CH242-182L23,2:51289316-51437705 (Clone quality: bE182L23 on chr=2; Num_of_Contigs=2; )
CCL25		location ⇒	2:51410013-51410135		CU929699,CH242-182L23,2:51289316-51437705 (Clone quality: bE182L23 on chr=2; Num_of_Contigs=2; )
CCL26		ENSSSCG00000007697	3:8642289-8643021		CU855597,CH242-327P3,3:8640694-8644150 (Clone quality: bE327P3 on chr=3; Num_of_Contigs=27; )
CCL26		location ⇒	3:8642859-8642745		CU855597,CH242-327P3,3:8640694-8644150 (Clone quality: bE327P3 on chr=3; Num_of_Contigs=27; )
CCL26		location ⇒	3:8643149-8642947		CU855597,CH242-327P3,3:8640694-8644150 (Clone quality: bE327P3 on chr=3; Num_of_Contigs=27; )
CCL27		ENSSSCG00000010967	10:30582407-30583155		CU928717,CH242-142N10,10:30573702-30613538 (Clone quality: bE142N10 on chr=10; Num_of_Contigs=7; )
CCL27		location ⇒	10:30582407-30582500		CU928717,CH242-142N10,10:30573702-30613538 (Clone quality: bE142N10 on chr=10; Num_of_Contigs=7; )
CCL27		location ⇒	10:30582643-30582778		CU928717,CH242-142N10,10:30573702-30613538 (Clone quality: bE142N10 on chr=10; Num_of_Contigs=7; )
CCL27		location ⇒	10:30582980-30583154		CU928717,CH242-142N10,10:30573702-30613538 (Clone quality: bE142N10 on chr=10; Num_of_Contigs=7; )
CCL28		ENSSSCG00000016871	16:25072581-25094252
CCL28		location ⇒	16:25073277-25072585		CU655897,CH242-147C10,16:25061785-25079567 (Clone quality: bE147C10 on chr=16; Num_of_Contigs=7; )
CCL28		location ⇒	16:25076371-25076243		CU655897,CH242-147C10,16:25061785-25079567 (Clone quality: bE147C10 on chr=16; Num_of_Contigs=7; )
CCL28		location ⇒	16:25094252-25094182		CU655897,CH242-147C10,16:25079668-25113134 (Clone quality: bE147C10 on chr=16; Num_of_Contigs=7; )
CCL3		location ⇒	12:37256370-37256530		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL3		location ⇒	12:37257219-37257333		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL3		location ⇒	12:37257711-37258061		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL3		location ⇒	12:37286614-37286510		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL3L1		ENSSSCG00000017700	12:37256341-37258243		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL3L1		location ⇒	12:37256455-37256530		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL3L1		location ⇒	12:37257219-37257333		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL3L1		location ⇒	12:37257711-37257801		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL3L1		location ⇒	12:37286614-37286524		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL3L2		location ⇒	12:37286248-37286112		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL3L2		location ⇒	12:37286614-37286300		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL3L2		location ⇒	12:37287080-37286966		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL3L2		location ⇒	12:37317034-37316932		CU929934,CH242-43L9,12:37292599-37376417 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL4		ENSSSCG00000017698	12:37243337-37245115		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL4		location ⇒	12:37243739-37243650		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL4		location ⇒	12:37244409-37244295		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL4		location ⇒	12:37244971-37244878		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL4L1		ENSSSCG00000017698	12:37243337-37245115		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL4L2		location ⇒	12:37243447-37243355		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL4L2		location ⇒	12:37243739-37243645		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL4L2		location ⇒	12:37244409-37244295		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL4L2		location ⇒	12:37244961-37244878		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
CCL5		ENSSSCG00000017705	12:37417187-37423594		CU896616,CH242-206O9,12:37393181-37445015 (Clone quality: bE206O9 on chr=12; Num_of_Contigs=7; )
CCL5		location ⇒	12:37413059-37413241		CU896616,CH242-206O9,12:37393181-37445015 (Clone quality: bE206O9 on chr=12; Num_of_Contigs=7; )
CCL5		location ⇒	12:37417090-37417323		CU896616,CH242-206O9,12:37393181-37445015 (Clone quality: bE206O9 on chr=12; Num_of_Contigs=7; )
CCL5		location ⇒	12:37418685-37418801		CU896616,CH242-206O9,12:37393181-37445015 (Clone quality: bE206O9 on chr=12; Num_of_Contigs=7; )
CCL5		location ⇒	12:37423098-37423591		CU896616,CH242-206O9,12:37393181-37445015 (Clone quality: bE206O9 on chr=12; Num_of_Contigs=7; )
CCL7		location ⇒	12:38307102-38307039		CU928660,CH242-280M5,12:38302849-38308872 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
CCL7		location ⇒	12:38326236-38326173		CU928660,CH242-280M5,12:38324798-38339122 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
CCL7		location ⇒	12:38372940-38372852		CU928660,CH242-280M5,12:38371176-38373405 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
CCL8		ENSSSCG00000017721	12:38305186-38307206		CU928660,CH242-280M5,12:38302849-38308872 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
CCL8		location ⇒	12:38305764-38305452		CU928660,CH242-280M5,12:38302849-38308872 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
CCL8		location ⇒	12:38306184-38306132		CU928660,CH242-280M5,12:38302849-38308872 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
CCL8		location ⇒	12:38306252-38306132		CU928660,CH242-280M5,12:38302849-38308872 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
CCL8		location ⇒	12:38307179-38307039		CU928660,CH242-280M5,12:38302849-38308872 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
Ccl9		location ⇒	4:114630382-114630276		CU606863,CH242-71K19,4:114596843-114641017 (Clone quality: bE71K19 on chr=4; Num_of_Contigs=8; )
Ccl9		location ⇒	4:114630522-114630476		CU606863,CH242-71K19,4:114596843-114641017 (Clone quality: bE71K19 on chr=4; 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).