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)

BTN2A3		location ⇒	7:22065007-22065212		CU466447,CH242-214G3,7:22003876-22069073 (Clone quality: bE214G3 on chr=7; Num_of_Contigs=15; )
BTN3A1		location ⇒	7:22087050-22087103		CU466447,CH242-214G3,7:22084194-22088434 (Clone quality: bE214G3 on chr=7; Num_of_Contigs=15; )
BTN3A3		location ⇒	17:7112882-7112687		CU606978,CH242-286D19,17:7097366-7120140 (Clone quality: bE286D19 on chr=17; Num_of_Contigs=12; )
BTN3A3		location ⇒	17:7114247-7114148		CU606978,CH242-286D19,17:7097366-7120140 (Clone quality: bE286D19 on chr=17; Num_of_Contigs=12; )
BTN3A3		location ⇒	17:7115968-7115730		CU606978,CH242-286D19,17:7097366-7120140 (Clone quality: bE286D19 on chr=17; Num_of_Contigs=12; )
BTNL2		location ⇒	7:28977248-28977128	CT797454,CH242-173D7,7:28821097-28994356 (Clone quality: bE173D7 on chr=7; Num_of_Contigs=2; )
BTNL2		location ⇒	7:28978658-28978317	CT797454,CH242-173D7,7:28821097-28994356 (Clone quality: bE173D7 on chr=7; Num_of_Contigs=2; )
BTNL2		location ⇒	7:29013364-29013705	BX323846,PigI-43B6,7:28994357-29074505 (No clone quality info on bS43B6)
BTNL2		location ⇒	7:29014774-29014894	BX323846,PigI-43B6,7:28994357-29074505 (No clone quality info on bS43B6)
BTNL6I8		location ⇒	7:28124967-28124155	CT954269,CH242-404E7,7:27953077-28153182 (Clone quality: bE404E7 on chr=7; Num_of_Contigs=12; )
BTNL6I8		location ⇒	7:28172984-28172171	CU468018,CH242-108B7,7:28153183-28303468 (Clone quality: bE108B7 on chr=7; Num_of_Contigs=39; )
BTRC		ENSSSCG00000010563	14:117246780-117447356
BUB1B		ENSSSCG00000004782	1:137623107-137749862
BUB3		ENSSSCG00000010726	14:139147449-139159629		CU468341,CH242-268H7,14:139020351-139163532 (Clone quality: bE268H7 on chr=14; Num_of_Contigs=2; )
BUD13		ENSSSCG00000015065	9:42932652-42962942
BVES		ENSSSCG00000004366	1:74857601-74900588
BVES		location ⇒	1:74880170-74880049		CU407220,CH242-377A23,1:74870742-74935498 (Clone quality: bE377A23 on chr=1; Num_of_Contigs=2; )
BVES		location ⇒	1:74881591-74881421		CU407220,CH242-377A23,1:74870742-74935498 (Clone quality: bE377A23 on chr=1; Num_of_Contigs=2; )
BVES		location ⇒	1:74889516-74889406		CU407220,CH242-377A23,1:74870742-74935498 (Clone quality: bE377A23 on chr=1; Num_of_Contigs=2; )
BVES		location ⇒	1:74890549-74890389		CU407220,CH242-377A23,1:74870742-74935498 (Clone quality: bE377A23 on chr=1; Num_of_Contigs=2; )
BXDC1		ENSSSCG00000004394	1:79185934-79226104
BYSL		ENSSSCG00000001631	7:42654242-42663929
BYSL		location ⇒	7:42654183-42654511		CU468691,CH242-161L14,7:42653403-42658821 (Clone quality: bE161L14 on chr=7; Num_of_Contigs=22; )
BYSL		location ⇒	7:42662048-42662191		CU468691,CH242-161L14,7:42658922-42663434 (Clone quality: bE161L14 on chr=7; Num_of_Contigs=22; )
BYSL		location ⇒	7:42662490-42662626		CU468691,CH242-161L14,7:42658922-42663434 (Clone quality: bE161L14 on chr=7; Num_of_Contigs=22; )
BYSL		location ⇒	7:42663580-42664250		CU468691,CH242-161L14,7:42663535-42670478 (Clone quality: bE161L14 on chr=7; Num_of_Contigs=22; )
BZRAP1		ENSSSCG00000017638	12:32600742-32626704		CU571372,CH242-73D9,12:32562317-32656104 (Clone quality: bE73D9 on chr=12; Num_of_Contigs=4; )
BZW1		ENSSSCG00000016094	15:98214259-98229896		CU468511,CH242-98M12,15:98176186-98278835 (Clone quality: bE98M12 on chr=15; 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, 651-28

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).