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)

RNF149		location ⇒	3:48762541-48762139		CU407202,CH242-326N21,3:48761349-48764661 (Clone quality: bE326N21 on chr=3; Num_of_Contigs=9; )
RNF150		ENSSSCG00000009053	8:74130179-74159441
RNF152		ENSSSCG00000004902	1:166473622-166474230		CU582901,CH242-60C21,1:166458737-166474760 (Clone quality: bE60C21 on chr=1; Num_of_Contigs=9; )
RNF157		ENSSSCG00000017186	12:3584864-3653790
RNF165		ENSSSCG00000004502	1:100160368-100169355		FP015922,CH242-123E15,1:100135794-100174246 (Clone quality: bE123E15 on chr=1; Num_of_Contigs=7; )
RNF167		ENSSSCG00000017906	12:49161853-49166076		FP015831,CH242-271O18,12:49076321-49169107 (Clone quality: bE271O18 on chr=12; Num_of_Contigs=4; )
RNF168		ENSSSCG00000012183	X:19539505-19540474		CU207412,CH242-477E15,X:19481709-19550329 (Clone quality: bE477E15 on chr=X; Num_of_Contigs=9; )
RNF169		ENSSSCG00000014844	9:8794070-8821474		CU928552,CH242-149C19,9:8793625-8828371 (Clone quality: bE149C19 on chr=9; Num_of_Contigs=6; )
RNF17		ENSSSCG00000009572	11:79542828-79575422		CU928666,CH242-357O8,11:79538144-79577126 (Clone quality: bE357O8 on chr=11; Num_of_Contigs=11; )
RNF180		ENSSSCG00000016941	16:40448530-40682573
RNF181		ENSSSCG00000008232	3:54049028-54050862		CU928286,CH242-219K12,3:54043219-54085564 (Clone quality: bE219K12 on chr=3; Num_of_Contigs=4; )
RNF182		ENSSSCG00000001058	7:10459627-10460370		CT827871,CH242-258D4,7:10406331-10519128 (Clone quality: bE258D4 on chr=7; Num_of_Contigs=3; )
RNF187		ENSSSCG00000013996	2:66946179-66949552	FP015983,CH242-74L12,2:66907442-67096474 (Clone quality: bE74L12 on chr=2; Num_of_Contigs=3; )
RNF19A		ENSSSCG00000006066	4:37036762-37071876
RNF2		ENSSSCG00000015568	9:118615386-118729631
RNF20		ENSSSCG00000005399	1:254840045-254867407
RNF207		ENSSSCG00000003368	6:45407326-45416334		FP102454,CH242-79J15,6:45387357-45440384 (Clone quality: bE79J15 on chr=6; Num_of_Contigs=7; )
RNF208		ENSSSCG00000005858	1:294439810-294440604		CU928955,CH242-34I15,1:294431557-294452171 (Clone quality: bE34I15 on chr=1; Num_of_Contigs=4; )
RNF213		ENSSSCG00000017146	12:1061906-1115819
RNF214		ENSSSCG00000015077	9:43513158-43556330
RNF215		ENSSSCG00000010005	14:48160497-48166215		CT956025,CH242-69C12,14:48142322-48239134 (Clone quality: bE69C12 on chr=14; Num_of_Contigs=15; )
RNF216		ENSSSCG00000007587	3:3952543-3969567		FP102569,CH242-151E19,3:3887357-3971939 (Clone quality: bE151E19 on chr=3; Num_of_Contigs=3; )
RNF217		ENSSSCG00000004227	1:39434595-39531471
RNF222		ENSSSCG00000017985	12:50620228-50620857		CU672254,CH242-41G13,12:50613728-50681703 (Clone quality: bE41G13 on chr=12; Num_of_Contigs=3; )
RNF24		ENSSSCG00000007141	17:33370314-33394494
RNF25		ENSSSCG00000016202	15:113891615-113893622		CU914509,CH242-30J4,15:113890521-113893812 (Clone quality: bE30J4 on chr=15; Num_of_Contigs=25; )
RNF26		ENSSSCG00000015117	9:45155745-45157046		CU915638,CH242-115L13,9:45139059-45168315 (Clone quality: bE115L13 on chr=9; Num_of_Contigs=6; )
RNF31		ENSSSCG00000002003	7:81481033-81499734		CT961055,CH242-32K2,7:81442434-81553552 (Clone quality: bE32K2 on chr=7; Num_of_Contigs=2; )
RNF32		ENSSSCG00000016414	18:1142696-1169728
RNF38		ENSSSCG00000005343	1:248307859-248424441
RNF39		ENSSSCG00000001244	7:24826735-24831445	CT737425,CH242-47O8,7:24783186-24956885 (Clone quality: bE47O8 on chr=7; Num_of_Contigs=3; )
RNF4		ENSSSCG00000008690	8:752967-762300		CU640885,CH242-239A2,8:750365-768182 (Clone quality: bE239A2 on chr=8; Num_of_Contigs=14; )
RNF40		location ⇒	3:16100126-16100181		FP102303,CH242-232B18,3:16093731-16104652 (Clone quality: bE232B18 on chr=3; Num_of_Contigs=7; )
RNF40		location ⇒	3:16112426-16112519		FP102303,CH242-232B18,3:16104753-16142778 (Clone quality: bE232B18 on chr=3; Num_of_Contigs=7; )
RNF40		location ⇒	3:16254592-16254499		FP102572,CH242-151L13,3:16242831-16259477 (Clone quality: bE151L13 on chr=3; Num_of_Contigs=14; )
RNF40		location ⇒	3:16268295-16268240		FP102572,CH242-151L13,3:16259578-16299350 (Clone quality: bE151L13 on chr=3; Num_of_Contigs=14; )
RNF41		ENSSSCG00000000383	5:20521051-20546739		CU694915,CH242-453C18,5:20512361-20554936 (Clone quality: bE453C18 on chr=5; Num_of_Contigs=10; )
RNF43		ENSSSCG00000017640	12:32653791-32668228
RNF44		ENSSSCG00000014056	2:70391204-70406754	FP101981,CH242-191F5,2:70304317-70501298 (Clone quality: bE191F5 on chr=2; Num_of_Contigs=3; )
RNF5		ENSSSCG00000001436	7:28054882-28057372	CT954269,CH242-404E7,7:27953077-28153182 (Clone quality: bE404E7 on chr=7; Num_of_Contigs=12; )
RNF6		ENSSSCG00000009299	11:3165368-3174969		CU633808,CH242-519P8,11:3156619-3186937 (Clone quality: bE519P8 on chr=11; Num_of_Contigs=11; )
RNF7		ENSSSCG00000011674	13:67333892-67340309		CU914638,CH242-182J3,13:67262584-67431184 (Clone quality: bE182J3 on chr=13; Num_of_Contigs=1; )
RNFT1		ENSSSCG00000017671	12:34299118-34311135
RNFT2		ENSSSCG00000009862	14:35901619-35974348
RNGTT		ENSSSCG00000004311	1:59723829-59871609
RNH1		ENSSSCG00000003313	6:41814425-41815804		FP236123,CH242-107C1,6:41810249-41839566 (Clone quality: bE107C1 on chr=6; Num_of_Contigs=14; )
RNLS		ENSSSCG00000010441	14:105217467-105289830
RNMTL1		ENSSSCG00000017806	12:44994313-45000453		CU928997,CH242-26C19,12:44982217-45011842 (Clone quality: bE26C19 on chr=12; Num_of_Contigs=2; )
RNPC3		ENSSSCG00000006856	4:120126062-120311261
RNPC3		location ⇒	4:120132102-120132040		CU469487,CH242-504I2,4:120110516-120179418 (Clone quality: bE504I2 on chr=4; Num_of_Contigs=16; )

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, 1001-16

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).