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)

PDE3A		location ⇒	5:50415884-50415509		CU463142,CH242-271D14,5:50412364-50416491 (Clone quality: bE271D14 on chr=5; Num_of_Contigs=8; )
PDE3A		location ⇒	5:50425463-50425202		CU463142,CH242-271D14,5:50421461-50434100 (Clone quality: bE271D14 on chr=5; Num_of_Contigs=8; )
PDE3A		location ⇒	5:50469199-50468939		CU463142,CH242-271D14,5:50463398-50471041 (Clone quality: bE271D14 on chr=5; Num_of_Contigs=8; )
PDE3A		location ⇒	5:50723881-50723517		CU407326,CH242-122I24,5:50720698-50895598 (Clone quality: bE122I24 on chr=5; Num_of_Contigs=1; )
PDE3B		ENSSSCG00000013388	2:41398134-41476140
PDE4A		ENSSSCG00000013641	2:52935390-53086202
PDE4A		location ⇒	2:52940290-52940103		CU993813,CH242-86K24,2:52937567-52943390 (Clone quality: bE86K24 on chr=2; Num_of_Contigs=13; )
PDE4A		location ⇒	2:52941105-52941030		CU993813,CH242-86K24,2:52937567-52943390 (Clone quality: bE86K24 on chr=2; Num_of_Contigs=13; )
PDE4A		location ⇒	2:53048825-53048638		CU928523,CH242-307C2,2:53015595-53086293 (Clone quality: bE307C2 on chr=2; Num_of_Contigs=9; )
PDE4A		location ⇒	2:53049640-53049565		CU928523,CH242-307C2,2:53015595-53086293 (Clone quality: bE307C2 on chr=2; Num_of_Contigs=9; )
PDE4B		ENSSSCG00000003805	6:102857699-102900332
PDE4B		location ⇒	6:102890272-102890367		CU929681,CH242-117C23,6:102875270-102928411 (Clone quality: bE117C23 on chr=6; Num_of_Contigs=6; )
PDE4B		location ⇒	6:102890505-102890673		CU929681,CH242-117C23,6:102875270-102928411 (Clone quality: bE117C23 on chr=6; Num_of_Contigs=6; )
PDE4B		location ⇒	6:102892761-102892860		CU929681,CH242-117C23,6:102875270-102928411 (Clone quality: bE117C23 on chr=6; Num_of_Contigs=6; )
PDE4B		location ⇒	6:102895175-102895319		CU929681,CH242-117C23,6:102875270-102928411 (Clone quality: bE117C23 on chr=6; Num_of_Contigs=6; )
PDE4C		ENSSSCG00000013898	2:62369056-62376257
PDE4D		ENSSSCG00000016929	16:35869361-36106905
PDE4DIP		ENSSSCG00000006707	4:104825079-104948365		CU468525,CH242-91D20,4:104823540-104986257 (Clone quality: bE91D20 on chr=4; Num_of_Contigs=8; )
PDE6A		ENSSSCG00000014438	2:136367690-136425357
PDE6C		ENSSSCG00000010480	14:110317141-110402865
PDE6D		ENSSSCG00000016279	15:124682278-124732189
PDE6H		ENSSSCG00000000603	5:54867862-54872405
PDE7A		ENSSSCG00000006218	4:71451501-71475034
PDE7A		location ⇒	4:71462266-71462368		CU151843,CH242-168N12,4:71438791-71467081 (Clone quality: bE168N12 on chr=4; Num_of_Contigs=9; )
PDE7A		location ⇒	4:71466078-71466211		CU151843,CH242-168N12,4:71438791-71467081 (Clone quality: bE168N12 on chr=4; Num_of_Contigs=9; )
PDE7A		location ⇒	4:71466415-71466509		CU151843,CH242-168N12,4:71438791-71467081 (Clone quality: bE168N12 on chr=4; Num_of_Contigs=9; )
PDE7A		location ⇒	4:71469037-71469184		CU207226,CH242-348A19,4:71467082-71544703 (Clone quality: bE348A19 on chr=4; Num_of_Contigs=2; )
PDE7B		ENSSSCG00000004165	1:29372663-29546435
PDE8B		ENSSSCG00000014097	2:75103125-75221059
PDE9A		ENSSSCG00000012085	13:144797613-144911947
PDGFA		ENSSSCG00000007541	3:3109-20763
PDGFA		location ⇒	3:12893-12702		FP102618,CH242-1B21,3:10473-20929 (Clone quality: bE1B21 on chr=3; Num_of_Contigs=5; )
PDGFA		location ⇒	3:20565-20443		FP102618,CH242-1B21,3:10473-20929 (Clone quality: bE1B21 on chr=3; Num_of_Contigs=5; )
PDGFA		location ⇒	3:3895-3659		FP102618,CH242-1B21,3:1-10372 (Clone quality: bE1B21 on chr=3; Num_of_Contigs=5; )
PDGFA		location ⇒	3:6281-6153		FP102618,CH242-1B21,3:1-10372 (Clone quality: bE1B21 on chr=3; Num_of_Contigs=5; )
PDGFB		location ⇒	5:5389135-5388782		CU686742,CH242-39B7,5:5382346-5389411 (Clone quality: bE39B7 on chr=5; Num_of_Contigs=13; )
PDGFC		ENSSSCG00000008871	8:39641095-39655063		CU694633,CH242-50J11,8:39612409-39672403 (Clone quality: bE50J11 on chr=8; Num_of_Contigs=3; )
PDGFD		ENSSSCG00000014994	9:34066339-34352584
PDGFRA		ENSSSCG00000008841	8:35262065-35303473
PDGFRA		location ⇒	8:35279387-35279285		FP015892,CH242-190G10,8:35258950-35279795 (Clone quality: bE190G10 on chr=8; Num_of_Contigs=10; )
PDGFRA		location ⇒	8:35281070-35280965		FP015892,CH242-190G10,8:35279896-35284769 (Clone quality: bE190G10 on chr=8; Num_of_Contigs=10; )
PDGFRA		location ⇒	8:35281827-35281717		FP015892,CH242-190G10,8:35279896-35284769 (Clone quality: bE190G10 on chr=8; Num_of_Contigs=10; )
PDGFRA		location ⇒	8:35282695-35282539		FP015892,CH242-190G10,8:35279896-35284769 (Clone quality: bE190G10 on chr=8; Num_of_Contigs=10; )
PDGFRB		ENSSSCG00000014442	2:136580731-136750284
PDGFRB		location ⇒	2:136529087-136528986		CU681821,CH242-138G12,2:136481055-136539241 (Clone quality: bE138G12 on chr=2; Num_of_Contigs=10; )
PDGFRB		location ⇒	2:136743624-136743426		CU914366,CH242-274B11,2:136737836-136759157 (Clone quality: bE274B11 on chr=2; Num_of_Contigs=10; )
PDGFRB		location ⇒	2:136746553-136746358		CU914366,CH242-274B11,2:136737836-136759157 (Clone quality: bE274B11 on chr=2; Num_of_Contigs=10; )
PDGFRB		location ⇒	2:136747304-136747135		CU914366,CH242-274B11,2:136737836-136759157 (Clone quality: bE274B11 on chr=2; Num_of_Contigs=10; )
PDGFRL		ENSSSCG00000006988	17:5066629-5186685
PDGFRL		location ⇒	17:5075891-5076189		CU682348,CH242-166L11,17:5066629-5083566 (Clone quality: bE166L11 on chr=17; 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, 2201-21

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).