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)

CCNJ		ENSSSCG00000010502	14:112578014-112596356		CT827825,CH242-216D24,14:112519668-112654753 (Clone quality: bE216D24 on chr=14; Num_of_Contigs=2; )
CCNJL		ENSSSCG00000017036	16:60825530-60851664		CU571129,CH242-2E15,16:60798351-60893351 (Clone quality: bE2E15 on chr=16; Num_of_Contigs=4; )
CCNK		ENSSSCG00000002509	7:129770656-129796927
CCNL2		ENSSSCG00000003354	6:43108898-43111282		FP102593,CH242-171J19,6:43108228-43113471 (Clone quality: bE171J19 on chr=6; Num_of_Contigs=11; )
CCNT1		ENSSSCG00000000173	5:13278670-13312392		CU914692,CH242-143P14,5:13271941-13360701 (Clone quality: bE143P14 on chr=5; Num_of_Contigs=6; )
CCNT2		ENSSSCG00000015697	15:15242559-15285410
CCNY		ENSSSCG00000011107	10:54987099-55021425
CCPG1		ENSSSCG00000004610	1:121174750-121224334
CCPG1		location ⇒	1:121195053-121195129		CU570857,CH242-45M3,1:121148945-121198573 (Clone quality: bE45M3 on chr=1; Num_of_Contigs=5; )
CCPG1		location ⇒	1:121221920-121221982		CU041222,CH242-20A9,1:121203574-121236116 (Clone quality: bE20A9 on chr=1; Num_of_Contigs=5; )
CCPG1		location ⇒	1:121222041-121222105		CU041222,CH242-20A9,1:121203574-121236116 (Clone quality: bE20A9 on chr=1; Num_of_Contigs=5; )
CCPG1		location ⇒	1:61586091-61586015		CU075388,CH242-146I16,1:61439246-61606742 (Clone quality: bE146I16 on chr=1; Num_of_Contigs=1; )
CCR1		ENSSSCG00000011322	13:24637939-24644546
CCR1		location ⇒	13:144115541-144115623		FP085530,CH242-375A3,13:144074550-144121679 (Clone quality: bE375A3 on chr=13; Num_of_Contigs=15; )
CCR1		location ⇒	13:2502072-2501995		CU914425,CH242-36L15,13:2493838-2504612 (Clone quality: bE36L15 on chr=13; Num_of_Contigs=16; )
CCR1		location ⇒	13:26615759-26615699		CU466318,CH242-524L17,13:26606894-26645646 (Clone quality: bE524L17 on chr=13; Num_of_Contigs=16; )
CCR1		location ⇒	13:66426823-66426739		FP016117,CH242-144O2,13:66388884-66544420 (Clone quality: bE144O2 on chr=13; Num_of_Contigs=1; )
CCR10		ENSSSCG00000011289	13:22127196-22128347		CU466505,CH242-515M14,13:22123386-22182273 (Clone quality: bE515M14 on chr=13; Num_of_Contigs=3; )
CCR10		ENSSSCG00000017392	12:17720943-17722854		CU928483,CH242-17I6,12:17706452-17731169 (Clone quality: bE17I6 on chr=12; Num_of_Contigs=8; )
CCR10		location ⇒	12:17722013-17720943		CU928483,CH242-17I6,12:17706452-17731169 (Clone quality: bE17I6 on chr=12; Num_of_Contigs=8; )
CCR2		location ⇒	13:24640139-24640080		CU914332,CH242-66E24,13:24590797-24641499 (Clone quality: bE66E24 on chr=13; Num_of_Contigs=2; )
CCR2		location ⇒	8:21223-21118		FP102972,CH242-47L5,8:17398-21329 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CCR2		location ⇒	8:48273-48212		FP102972,CH242-47L5,8:43508-48739 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CCR2		location ⇒	8:7304-7413		FP102972,CH242-47L5,8:6630-11538 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CCR2		location ⇒	8:79830-79721		FP102972,CH242-47L5,8:79654-82980 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CCR3		location ⇒	13:110319-110392		CU928239,CH242-498F20,13:107367-116558 (Clone quality: bE498F20 on chr=13; Num_of_Contigs=4; )
CCR3		location ⇒	13:128872-128977		CU928239,CH242-498F20,13:116659-148542 (Clone quality: bE498F20 on chr=13; Num_of_Contigs=4; )
CCR3		location ⇒	13:27068-26987		CU928239,CH242-498F20,13:4436-31895 (Clone quality: bE498F20 on chr=13; Num_of_Contigs=4; )
CCR3		location ⇒	13:84307-84210		CU928239,CH242-498F20,13:77539-107266 (Clone quality: bE498F20 on chr=13; Num_of_Contigs=4; )
CCR4		ENSSSCG00000000502	5:33183472-33417601
CCR4		ENSSSCG00000002799	6:19251945-19325733
CCR5		location ⇒	13:24640139-24640080		CU914332,CH242-66E24,13:24590797-24641499 (Clone quality: bE66E24 on chr=13; Num_of_Contigs=2; )
CCR5		location ⇒	8:21223-21118		FP102972,CH242-47L5,8:17398-21329 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CCR5		location ⇒	8:48273-48212		FP102972,CH242-47L5,8:43508-48739 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CCR5		location ⇒	8:7304-7413		FP102972,CH242-47L5,8:6630-11538 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CCR5		location ⇒	8:79830-79721		FP102972,CH242-47L5,8:79654-82980 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
CCR7		ENSSSCG00000017466	12:19577558-19589498		CU856162,CH242-340B15,12:19576351-19592423 (Clone quality: bE340B15 on chr=12; Num_of_Contigs=24; )
CCR7		location ⇒	12:19577562-19577620		CU856162,CH242-340B15,12:19576351-19592423 (Clone quality: bE340B15 on chr=12; Num_of_Contigs=24; )
CCR7		location ⇒	12:19587447-19588569		CU856162,CH242-340B15,12:19576351-19592423 (Clone quality: bE340B15 on chr=12; Num_of_Contigs=24; )
CCR7		location ⇒	12:19588600-19588991		CU856162,CH242-340B15,12:19576351-19592423 (Clone quality: bE340B15 on chr=12; Num_of_Contigs=24; )
CCR7		location ⇒	12:19589046-19589377		CU856162,CH242-340B15,12:19576351-19592423 (Clone quality: bE340B15 on chr=12; Num_of_Contigs=24; )
CCR8-2		location ⇒	9:131944241-131944098		CU655936,CH242-369P7,9:131941408-131957326 (Clone quality: bE369P7 on chr=9; Num_of_Contigs=10; )
CCR8-2		location ⇒	9:131944457-131944397		CU655936,CH242-369P7,9:131941408-131957326 (Clone quality: bE369P7 on chr=9; Num_of_Contigs=10; )
CCR8-2		location ⇒	9:131946802-131946648		CU655936,CH242-369P7,9:131941408-131957326 (Clone quality: bE369P7 on chr=9; Num_of_Contigs=10; )
CCR9		ENSSSCG00000011289	13:22127196-22128347		CU466505,CH242-515M14,13:22123386-22182273 (Clone quality: bE515M14 on chr=13; Num_of_Contigs=3; )
CCR9		ENSSSCG00000011316	13:24444364-24462037		CU469254,CH242-75A24,13:24398824-24519472 (Clone quality: bE75A24 on chr=13; Num_of_Contigs=4; )
CCR9		location ⇒	13:24444402-24444511		CU469254,CH242-75A24,13:24398824-24519472 (Clone quality: bE75A24 on chr=13; Num_of_Contigs=4; )
CCR9		location ⇒	13:24460826-24462020		CU469254,CH242-75A24,13:24398824-24519472 (Clone quality: bE75A24 on chr=13; Num_of_Contigs=4; )
CCRL1		ENSSSCG00000011630	13:60583954-60589111		CU463338,CH242-512O15,13:60561420-60652606 (Clone quality: bE512O15 on chr=13; Num_of_Contigs=4; )
CCRL1		location ⇒	13:60583887-60583942		CU463338,CH242-512O15,13:60561420-60652606 (Clone quality: bE512O15 on chr=13; Num_of_Contigs=4; )

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).