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)

DYNLT1		ENSSSCG00000004056	1:9618269-9624790		CU498836,CH242-100E21,1:9618267-9651855 (Clone quality: bE100E21 on chr=1; Num_of_Contigs=11; )
DYNLT3		ENSSSCG00000012230	X:33167393-33178648	CU207398,CH242-388N8,X:33096810-33201162 (Clone quality: bE388N8 on chr=X; Num_of_Contigs=2; )
DYNLT3		location ⇒	X:110145956-110145877		CU210850,CH242-390L19,X:110145180-110147367 (Clone quality: bE390L19 on chr=X; Num_of_Contigs=8; )
DYNLT3		location ⇒	X:110146738-110146613		CU210850,CH242-390L19,X:110145180-110147367 (Clone quality: bE390L19 on chr=X; Num_of_Contigs=8; )
DYNLT3		location ⇒	X:33168228-33168149	CU207398,CH242-388N8,X:33096810-33201162 (Clone quality: bE388N8 on chr=X; Num_of_Contigs=2; )
DYNLT3		location ⇒	X:33169010-33168885	CU207398,CH242-388N8,X:33096810-33201162 (Clone quality: bE388N8 on chr=X; Num_of_Contigs=2; )
DYRK1A		ENSSSCG00000012064	13:141570659-141606292		CU856387,CH242-199M12,13:141531550-141622593 (Clone quality: bE199M12 on chr=13; Num_of_Contigs=4; )
DYRK2		ENSSSCG00000000958	5:99345545-99355323		CU855993,CH242-182P2,5:99345136-99376115 (Clone quality: bE182P2 on chr=5; Num_of_Contigs=5; )
DYRK3		ENSSSCG00000015649	9:131811356-131812312		CU633844,CH242-3I15,9:131789716-131812465 (Clone quality: bE3I15 on chr=9; Num_of_Contigs=8; )
DYRK4		ENSSSCG00000000721	5:61559896-61585013		CU915392,CH242-243A6,5:61547954-61596935 (Clone quality: bE243A6 on chr=5; Num_of_Contigs=1; )
DYR_PIG		ENSSSCG00000014125	2:78544871-78569098
DYSF		ENSSSCG00000008312	3:65123672-65405136
DYTN		ENSSSCG00000016132	15:102699099-102874327
DYX1C1		ENSSSCG00000004608	1:121059674-121155639
DZIP1		ENSSSCG00000009501	11:65934727-65988799
DZIP3		ENSSSCG00000011940	13:112200178-112289785

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, 751-16

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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).