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)

CEECAM1		location ⇒	1:283514096-283514232		CU467095,CH242-140K13,1:283511446-283514529 (Clone quality: bE140K13 on chr=1; Num_of_Contigs=19; )
CELSR1		ENSSSCG00000000001	5:53223-60881		FP016092,CH242-185O3,5:49191-61348 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
CELSR2		location ⇒	4:115344315-115343420		CU207229,CH242-373I13,4:115343301-115346019 (Clone quality: bE373I13 on chr=4; Num_of_Contigs=14; )
CELSR3		ENSSSCG00000011360	13:26234914-26243599		CU633242,CH242-208G16,13:26234913-26263430 (Clone quality: bE208G16 on chr=13; Num_of_Contigs=5; )
CELSR3		location ⇒	13:26243718-26244285		CU633242,CH242-208G16,13:26234913-26263430 (Clone quality: bE208G16 on chr=13; Num_of_Contigs=5; )
CELSR3		location ⇒	13:26434294-26434861		CU861514,CH242-101J13,13:26433934-26438400 (Clone quality: bE101J13 on chr=13; Num_of_Contigs=18; )
CEND1		ENSSSCG00000012845	2:176014-178780		FP015900,CH242-40P17,2:170992-201722 (Clone quality: bE40P17 on chr=2; Num_of_Contigs=6; )
CEND1		location ⇒	2:177376-177426		FP015900,CH242-40P17,2:170992-201722 (Clone quality: bE40P17 on chr=2; Num_of_Contigs=6; )
CEND1		location ⇒	2:177498-177553		FP015900,CH242-40P17,2:170992-201722 (Clone quality: bE40P17 on chr=2; Num_of_Contigs=6; )
CENPA		ENSSSCG00000008561	3:104727740-104735040		CU914418,CH242-286P5,3:104648755-104742355 (Clone quality: bE286P5 on chr=3; Num_of_Contigs=6; )
CENPB		ENSSSCG00000007150	17:33594699-33595049
CENPF		ENSSSCG00000015581	9:121314064-121377725		CU861557,CH242-325F16,9:121293122-121454748 (Clone quality: bE325F16 on chr=9; Num_of_Contigs=2; )
CENPI		ENSSSCG00000012491	X:76113809-76163285
CENPK		ENSSSCG00000016946	16:41405676-41444158		CU570838,CH242-27G12,16:41378006-41457782 (Clone quality: bE27G12 on chr=16; Num_of_Contigs=3; )
CENPL		ENSSSCG00000015496	9:109016217-109028601
CENPO		ENSSSCG00000008579	3:106194229-106203627		CU929972,CH242-90C18,3:106191128-106234756 (Clone quality: bE90C18 on chr=3; Num_of_Contigs=2; )
CENPP		ENSSSCG00000008070	3:37406146-37638308
CENPT		ENSSSCG00000002768	6:12877620-12883252		FP102672,CH242-302K22,6:12850515-12884873 (Clone quality: bE302K22 on chr=6; Num_of_Contigs=5; )
CENPV		ENSSSCG00000018034	12:56241884-56249787		CU927969,CH242-33C22,12:56240673-56287309 (No clone quality info on )
CEP110		ENSSSCG00000005513	1:274776493-274831166		CU041315,CH242-46J12,1:274774874-274832344 (Clone quality: bE46J12 on chr=1; Num_of_Contigs=10; )
CEP120		ENSSSCG00000014239	2:114829649-114915501
CEP152		ENSSSCG00000004657	1:128242679-128345887		CU656026,CH242-472G9,1:128195008-128383966 (Clone quality: bE472G9 on chr=1; Num_of_Contigs=2; )
CEP164		ENSSSCG00000015080	9:43585532-43665876		CU929872,CH242-154D7,9:43574306-43702015 (Clone quality: bE154D7 on chr=9; Num_of_Contigs=4; )
CEP192		ENSSSCG00000003673	6:66196526-66238548		CU929769,CH242-327I15,6:66087131-66288454 (Clone quality: bE327I15 on chr=6; Num_of_Contigs=2; )
CEP250		ENSSSCG00000007293	17:40668878-40713677		CU606930,CH242-408M19,17:40602020-40753042 (Clone quality: bE408M19 on chr=17; Num_of_Contigs=1; )
CEP290		ENSSSCG00000000928	5:90443338-90457530
CEP350		ENSSSCG00000015531	9:114049933-114207443
CEP55		ENSSSCG00000010477	14:110221404-110243861		CT954211,CH242-292E3,14:110155434-110255067 (Clone quality: bE292E3 on chr=14; Num_of_Contigs=2; )
CEP63		ENSSSCG00000011645	13:62080184-62113698
CEP68		ENSSSCG00000008360	3:70767459-70780996
CEP78		ENSSSCG00000005286	1:241817636-241858211
CEP97		ENSSSCG00000011949	13:115422869-115445761
CER1		ENSSSCG00000005189	1:217235840-217236148		CU469333,CH242-314H4,1:217235114-217241757 (Clone quality: bE314H4 on chr=1; Num_of_Contigs=26; )
CER1		location ⇒	1:217235838-217236334		CU469333,CH242-314H4,1:217235114-217241757 (Clone quality: bE314H4 on chr=1; Num_of_Contigs=26; )
CERCAM		ENSSSCG00000005650	1:283510871-283514231
CERKL		ENSSSCG00000016010	15:81626728-81660526
CES3		location ⇒	6:20604316-20604691		CU694664,CH242-101O9,6:20592879-20606378 (Clone quality: bE101O9 on chr=6; Num_of_Contigs=8; )
CES3		location ⇒	6:20659181-20659554
CES3		location ⇒	6:20660818-20660660		CU694664,CH242-101O9,6:20659655-20726218 (Clone quality: bE101O9 on chr=6; Num_of_Contigs=8; )
CES3		location ⇒	6:20671614-20671407		CU694664,CH242-101O9,6:20659655-20726218 (Clone quality: bE101O9 on chr=6; Num_of_Contigs=8; )
CETN2		ENSSSCG00000012757	X:122072516-122076278	CU468868,CH242-187E18,X:122069416-122115029 (Clone quality: bE187E18 on chr=X; Num_of_Contigs=5; )
CETN3		ENSSSCG00000014151	2:87101101-87120421		CU694873,CH242-282B4,2:87069841-87192752 (Clone quality: bE282B4 on chr=2; Num_of_Contigs=2; )
CFB		location ⇒	7:27858762-27858840	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
CFB		location ⇒	7:27860468-27860560	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
CFB		location ⇒	7:27861107-27861181	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
CFB		location ⇒	7:27861286-27861363	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
CFD		ENSSSCG00000013418	2:46145781-46147980		FP015903,CH242-504E7,2:46128360-46188530 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
CFD		location ⇒	2:46146862-46147002		FP015903,CH242-504E7,2:46128360-46188530 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
CFD		location ⇒	2:46147134-46147788		FP015903,CH242-504E7,2:46128360-46188530 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
CFD		location ⇒	2:46147170-46147347		FP015903,CH242-504E7,2:46128360-46188530 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )

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

Report problems to zhu

iastate.edu

$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).