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)

COP1		location ⇒	9:111016284-111016213		CU638728,CH242-5J14,9:111000901-111067851 (Clone quality: bE5J14 on chr=9; Num_of_Contigs=2; )
COP1		location ⇒	9:111025596-111025508		CU638728,CH242-5J14,9:111000901-111067851 (Clone quality: bE5J14 on chr=9; Num_of_Contigs=2; )
COPA		ENSSSCG00000006386	4:93590711-93639478	CU207285,CH242-406N12,4:93542791-93708820 (Clone quality: bE406N12 on chr=4; Num_of_Contigs=3; )
COPB1		ENSSSCG00000013392	2:41778183-41800993		CU487223,CH242-352O9,2:41664838-41804442 (Clone quality: bE352O9 on chr=2; Num_of_Contigs=2; )
COPB2		ENSSSCG00000011662	13:65334771-65364543		CU582855,CH242-31D16,13:65319701-65366964 (Clone quality: bE31D16 on chr=13; Num_of_Contigs=9; )
COPEB		location ⇒	15:103141035-103140927		FP236702,CH242-211J1,15:103135223-103142851 (Clone quality: bE211J1 on chr=15; Num_of_Contigs=17; )
COPG		ENSSSCG00000011616	13:59316487-59327249		CU928115,CH242-63I22,13:59314044-59329072 (Clone quality: bE63I22 on chr=13; Num_of_Contigs=9; )
COPG		location ⇒	13:59316555-59316492		CU928115,CH242-63I22,13:59314044-59329072 (Clone quality: bE63I22 on chr=13; Num_of_Contigs=9; )
COPG		location ⇒	13:59322376-59322207		CU928115,CH242-63I22,13:59314044-59329072 (Clone quality: bE63I22 on chr=13; Num_of_Contigs=9; )
COPG		location ⇒	13:59325540-59325414		CU928115,CH242-63I22,13:59314044-59329072 (Clone quality: bE63I22 on chr=13; Num_of_Contigs=9; )
COPG		location ⇒	13:59327239-59326991		CU928115,CH242-63I22,13:59314044-59329072 (Clone quality: bE63I22 on chr=13; Num_of_Contigs=9; )
COPG2		ENSSSCG00000016553	18:16419268-16458562		CU915599,CH242-89E18,18:16414600-16459325 (Clone quality: bE89E18 on chr=18; Num_of_Contigs=5; )
COPS2		ENSSSCG00000004652	1:127891421-127920084
COPS3		ENSSSCG00000018051	12:56897388-56920055		CU927962,CH242-273I13,12:56891060-57001521 (Clone quality: bE273I13 on chr=12; Num_of_Contigs=8; )
COPS4		ENSSSCG00000009241	8:116394181-116428053		CU694671,CH242-135K3,8:116354156-116447271 (Clone quality: bE135K3 on chr=8; Num_of_Contigs=3; )
COPS5		ENSSSCG00000006203	4:70234750-70252180		CU582915,CH242-248L23,4:70219330-70272096 (Clone quality: bE248L23 on chr=4; Num_of_Contigs=6; )
COPS7A		ENSSSCG00000000691	5:60007931-60014112		CU914489,CH242-100M5,5:60003877-60023417 (Clone quality: bE100M5 on chr=5; Num_of_Contigs=13; )
COPS7B		ENSSSCG00000016280	15:124737803-124839293
COPZ1		ENSSSCG00000000290	5:18080339-18099538		CU466514,CH242-63P24,5:18071192-18111791 (Clone quality: bE63P24 on chr=5; Num_of_Contigs=10; )
COPZ2		ENSSSCG00000017526	12:21743509-21754904		FP016123,CH242-397L8,12:21742773-21757011 (Clone quality: bE397L8 on chr=12; Num_of_Contigs=6; )
COQ10A		ENSSSCG00000000387	5:20587725-20591158		CU694915,CH242-453C18,5:20582151-20599340 (Clone quality: bE453C18 on chr=5; Num_of_Contigs=10; )
COQ10B		ENSSSCG00000016076	15:94877804-94893752
COQ2		ENSSSCG00000009238	8:116245643-116265218
COQ3		ENSSSCG00000004349	1:69709810-69720545
COQ4		ENSSSCG00000005646	1:283391431-283403146		CU234126,CH242-282L14,1:283270038-283452033 (Clone quality: bE282L14 on chr=1; Num_of_Contigs=4; )
COQ5		ENSSSCG00000009903	14:40486327-40503205
COQ6		ENSSSCG00000002354	7:105272680-105284626		CT797481,CH242-31K14,7:105227853-105414617 (Clone quality: bE31K14 on chr=7; Num_of_Contigs=1; )
COQ7		ENSSSCG00000007867	3:23810641-23818256		FP236408,CH242-138D10,3:23801628-23819313 (Clone quality: bE138D10 on chr=3; Num_of_Contigs=11; )
CORIN		ENSSSCG00000008813	8:32202800-32326615
CORO1B		ENSSSCG00000012908	2:3461819-3467096		CU633429,CH242-6G2,2:3461790-3468357 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
CORO1C		ENSSSCG00000009944	14:42321730-42402815	CT827801,CH242-209H21,14:42218746-42424391 (Clone quality: bE209H21 on chr=14; Num_of_Contigs=7; )
CORO2A		ENSSSCG00000005375	1:251500327-251550387
CORO2B		ENSSSCG00000004962	1:173869663-174010754
CORO6		ENSSSCG00000017792	12:43726847-43728374		CU463908,CH242-174P20,12:43725664-43729480 (Clone quality: bE174P20 on chr=12; Num_of_Contigs=11; )
CORO7		ENSSSCG00000007944	3:33934482-33940154
CORT		location ⇒	6:47525937-47525990		CU929886,CH242-214O13,6:47459319-47565046 (Clone quality: bE214O13 on chr=6; Num_of_Contigs=3; )
CORT		location ⇒	6:47526129-47526185		CU929886,CH242-214O13,6:47459319-47565046 (Clone quality: bE214O13 on chr=6; Num_of_Contigs=3; )
COTL1		location ⇒	4:9169535-9169610		CU151862,CH242-258D7,4:9094720-9198868 (Clone quality: bE258D7 on chr=4; Num_of_Contigs=3; )
COX15		ENSSSCG00000010541	14:115642282-115656226		CT868685,CH242-211E15,14:115597313-115736638 (Clone quality: bE211E15 on chr=14; Num_of_Contigs=2; )
COX16		ENSSSCG00000002316	7:102245985-102267209		CU695063,CH242-376L7,7:102238342-102373323 (Clone quality: bE376L7 on chr=7; Num_of_Contigs=1; )
COX17		ENSSSCG00000011893	13:105345992-105356336		CU607003,CH242-303J2,13:105344285-105449516 (Clone quality: bE303J2 on chr=13; Num_of_Contigs=5; )
COX18		ENSSSCG00000008947	8:58841175-58853929
COX19		ENSSSCG00000007550	3:438581-442694		CU928365,CH242-185G1,3:433477-444832 (Clone quality: bE185G1 on chr=3; Num_of_Contigs=21; )
COX1_PIG		ENSSSCG00000018075	MT:6511-8055
COX3_PIG		ENSSSCG00000018082	MT:9800-10583
COX5B		ENSSSCG00000008195	3:51944585-51946674		FP102542,CH242-108N5,3:51931376-51962356 (Clone quality: bE108N5 on chr=3; Num_of_Contigs=4; )
COX5B		ENSSSCG00000008195	3:51944585-51946674		FP102542,CH242-108N5,3:51931376-51962356 (Clone quality: bE108N5 on chr=3; Num_of_Contigs=4; )
COX6B1		ENSSSCG00000002834	6:22094163-22094444		FP102989,CH242-160M21,6:22059920-22102882 (Clone quality: bE160M21 on chr=6; Num_of_Contigs=4; )
COX6B2		ENSSSCG00000003296	6:41352216-41353364		FP245423,CH242-507H20,6:41345089-41360674 (Clone quality: bE507H20 on chr=6; Num_of_Contigs=16; )
COX6CP4		ENSSSCG00000006070	4:37514403-37515234		CU138567,CH242-256I17,4:37482749-37585273 (Clone quality: bE256I17 on chr=4; Num_of_Contigs=5; )

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).