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)

CD97		location ⇒	2:57185884-57186651		FP103015,CH242-135B13,2:57184382-57190924 (Clone quality: bE135B13 on chr=2; Num_of_Contigs=14; )
CD97		location ⇒	2:57534330-57534274		FP102312,CH242-103F14,2:57518208-57627485 (Clone quality: bE103F14 on chr=2; Num_of_Contigs=2; )
CD97		location ⇒	2:57743824-57743882		FP017132,CH242-113D12,2:57735660-57744989 (Clone quality: bE113D12 on chr=2; Num_of_Contigs=10; )
CD99		ENSSSCG00000012744	X:120613640-120723500
CD99L2		ENSSSCG00000012744	X:120613640-120723500
CD99L2		location ⇒	X:120723320-120723234		CU929821,CH242-50C14,X:120654547-120729462 (Clone quality: bE50C14 on chr=X; Num_of_Contigs=4; )
CD99L2		location ⇒	X:120723528-120723393		CU929821,CH242-50C14,X:120654547-120729462 (Clone quality: bE50C14 on chr=X; Num_of_Contigs=4; )
CDA		ENSSSCG00000004719	1:134776546-134786882
CDA		ENSSSCG00000003510	6:54281532-54287189		FP243370,CH242-400E6,6:54279457-54292260 (Clone quality: bE400E6 on chr=6; Num_of_Contigs=4; )
CDA		location ⇒	6:54281542-54281603		FP243370,CH242-400E6,6:54279457-54292260 (Clone quality: bE400E6 on chr=6; Num_of_Contigs=4; )
CDA		location ⇒	6:54286663-54286781		FP243370,CH242-400E6,6:54279457-54292260 (Clone quality: bE400E6 on chr=6; Num_of_Contigs=4; )
CDA		location ⇒	6:54287052-54287164		FP243370,CH242-400E6,6:54279457-54292260 (Clone quality: bE400E6 on chr=6; Num_of_Contigs=4; )
CDADC1		ENSSSCG00000009398	11:18351788-18351979		CU041282,CH242-47L20,11:18346553-18352055 (Clone quality: bE47L20 on chr=11; Num_of_Contigs=10; )
CDAN1		ENSSSCG00000004719	1:134776546-134786882
CDC123		ENSSSCG00000011112	10:56644364-56691682		CU929734,CH242-242C1,10:56589457-56703078 (Clone quality: bE242C1 on chr=10; Num_of_Contigs=3; )
CDC123		location ⇒	10:56644442-56644387		CU929734,CH242-242C1,10:56589457-56703078 (Clone quality: bE242C1 on chr=10; Num_of_Contigs=3; )
CDC123		location ⇒	10:56646000-56645918		CU929734,CH242-242C1,10:56589457-56703078 (Clone quality: bE242C1 on chr=10; Num_of_Contigs=3; )
CDC123		location ⇒	10:56653281-56653158		CU929734,CH242-242C1,10:56589457-56703078 (Clone quality: bE242C1 on chr=10; Num_of_Contigs=3; )
CDC123		location ⇒	10:56678322-56678263		CU929734,CH242-242C1,10:56589457-56703078 (Clone quality: bE242C1 on chr=10; Num_of_Contigs=3; )
CDC14A		ENSSSCG00000006864	4:122529360-122721192
CDC2		ENSSSCG00000015888	15:62431468-62702311
CDC2		ENSSSCG00000017504	12:20737886-20792069
CDC2		ENSSSCG00000010216	14:67060275-67070840
CDC2		ENSSSCG00000004395	1:79254002-79301990
CDC2		ENSSSCG00000005505	1:273948158-273990224
CDC2		ENSSSCG00000010214	14:66845794-66860895		CU468520,CH242-402M7,14:66758226-66885237 (Clone quality: bE402M7 on chr=14; Num_of_Contigs=3; )
CDC2		ENSSSCG00000003216	6:39000770-39015171		FP102476,CH242-133P5,6:39000388-39018494 (Clone quality: bE133P5 on chr=6; Num_of_Contigs=12; )
CDC2		ENSSSCG00000016769	18:53180959-53272992
CDC2		location ⇒	14:66855486-66855661		CU468520,CH242-402M7,14:66758226-66885237 (Clone quality: bE402M7 on chr=14; Num_of_Contigs=3; )
CDC2		location ⇒	14:66860386-66860723		CU468520,CH242-402M7,14:66758226-66885237 (Clone quality: bE402M7 on chr=14; Num_of_Contigs=3; )
CDC2		location ⇒	14:67060784-67060447		CU468495,CH242-39K12,14:67034359-67066370 (Clone quality: bE39K12 on chr=14; Num_of_Contigs=8; )
CDC2		location ⇒	14:67065682-67065507		CU468495,CH242-39K12,14:67034359-67066370 (Clone quality: bE39K12 on chr=14; Num_of_Contigs=8; )
CDC20		ENSSSCG00000003949	6:120243509-120247534		CU694684,CH242-210N13,6:120239819-120247647 (Clone quality: bE210N13 on chr=6; Num_of_Contigs=11; )
CDC20B		ENSSSCG00000016904	16:31721365-31847430
CDC23		ENSSSCG00000014325	2:127173318-127191686		CU928408,CH242-232M5,2:127160377-127220355 (Clone quality: bE232M5 on chr=2; Num_of_Contigs=3; )
CDC25B		ENSSSCG00000007151	17:33603414-33610819		FP236531,CH242-39P18,17:33601318-33612018 (Clone quality: bE39P18 on chr=17; Num_of_Contigs=7; )
CDC25C		ENSSSCG00000014329	2:127265827-127301541		CU928408,CH242-232M5,2:127227830-127327871 (Clone quality: bE232M5 on chr=2; Num_of_Contigs=3; )
CDC27		ENSSSCG00000017308	12:14557060-14672909
CDC2L2		ENSSSCG00000003352	6:43074485-43088851
CDC2L5		ENSSSCG00000016769	18:53180959-53272992
CDC2L6		ENSSSCG00000004395	1:79254002-79301990
CDC37		ENSSSCG00000013647	2:53103702-53113916		CU928523,CH242-307C2,2:53096041-53119307 (Clone quality: bE307C2 on chr=2; Num_of_Contigs=9; )
CDC37L1		ENSSSCG00000005219	1:227366662-227390353		CU467061,CH242-40P15,1:227339625-227392310 (Clone quality: bE40P15 on chr=1; Num_of_Contigs=2; )
CDC40		ENSSSCG00000004403	1:79796035-79848271
CDC42		ENSSSCG00000003520	6:55114231-55133985		CU633957,CH242-4G23,6:55111766-55183249 (Clone quality: bE4G23 on chr=6; Num_of_Contigs=4; )
CDC42		location ⇒	7:35208994-35209434	CT797453,CH242-109D12,7:35137121-35327761 (Clone quality: bE109D12 on chr=7; Num_of_Contigs=2; )
CDC42		location ⇒	7:35208994-35209434	CT797453,CH242-109D12,7:35137121-35327761 (Clone quality: bE109D12 on chr=7; Num_of_Contigs=2; )
CDC42BPA		ENSSSCG00000010862	10:14490153-14686726
CDC42BPB		location ⇒	7:130857855-130856462		CT998550,CH242-445C19,7:130850075-130928536 (Clone quality: bE445C19 on chr=7; Num_of_Contigs=6; )
CDC42BPB		location ⇒	7:130864187-130864116		CT998550,CH242-445C19,7:130850075-130928536 (Clone quality: bE445C19 on chr=7; Num_of_Contigs=6; )

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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).