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)

XRCC1		location ⇒	6:34925467-34925374		FP102604,CH242-184P4,6:34923440-34931069 (No clone quality info on )
XRCC1		location ⇒	6:34926402-34926337		FP102604,CH242-184P4,6:34923440-34931069 (No clone quality info on )
XRCC2		ENSSSCG00000016427	18:3898508-3921406
XRCC2		location ⇒	18:10693727-10693818		CU856469,CH242-395I4,18:10667157-10728997 (Clone quality: bE395I4 on chr=18; Num_of_Contigs=3; )
XRCC2		location ⇒	18:10810042-10810133		CU638822,CH242-106K14,18:10805091-10826049 (Clone quality: bE106K14 on chr=18; Num_of_Contigs=20; )
XRCC2		location ⇒	18:14501900-14501830		CU972378,CH242-113D21,18:14465404-14516857 (Clone quality: bE113D21 on chr=18; Num_of_Contigs=7; )
XRCC2		location ⇒	18:22744839-22744913	CU463091,CH242-443B24,18:22680239-22795810 (Clone quality: bE443B24 on chr=18; Num_of_Contigs=6; )
XRCC3		ENSSSCG00000002546	7:132799815-132807086		CU694215,CH242-506G2,7:132796546-132817357 (Clone quality: bE506G2 on chr=7; Num_of_Contigs=14; )
XRCC4		ENSSSCG00000016205	15:114096821-114184537
XRCC4		ENSSSCG00000014135	2:80765098-81012947
XRCC4		location ⇒	2:104457032-104457102		CU928266,CH242-209C17,2:104442193-104490507 (Clone quality: bE209C17 on chr=2; Num_of_Contigs=4; )
XRCC4		location ⇒	2:105543168-105543111		CU929820,CH242-507P22,2:105531840-105593638 (Clone quality: bE507P22 on chr=2; Num_of_Contigs=6; )
XRCC4		location ⇒	2:60337247-60337299		CU914413,CH242-247L20,2:60301522-60353336 (Clone quality: bE247L20 on chr=2; Num_of_Contigs=8; )
XRCC4		location ⇒	2:91745006-91745058		CU929034,CH242-61I23,2:91729328-91775064 (Clone quality: bE61I23 on chr=2; Num_of_Contigs=7; )
XRCC5		ENSSSCG00000016177	15:111766726-111861668
XRCC6		ENSSSCG00000000453	5:22062455-22105919
XRCC6		ENSSSCG00000000059	5:3448006-3474054
XRCC6BP1		ENSSSCG00000000453	5:22062455-22105919
XRN1		ENSSSCG00000011678	13:67672444-67778431
XRN2		ENSSSCG00000007109	17:30325594-30411250
XRRA1		ENSSSCG00000014845	9:8862549-8871317		CU928552,CH242-149C19,9:8852604-8877808 (Clone quality: bE149C19 on chr=9; Num_of_Contigs=6; )
XTP3TPA		ENSSSCG00000007796	3:16477714-16481604		CU928725,CH242-25P12,3:16471690-16481606 (Clone quality: bE25P12 on chr=3; Num_of_Contigs=8; )
XTP3TPA		location ⇒	3:16478532-16478642		CU928725,CH242-25P12,3:16471690-16481606 (Clone quality: bE25P12 on chr=3; Num_of_Contigs=8; )
XYLB		ENSSSCG00000011254	13:19049838-19099587		CU633398,CH242-322L18,13:19047156-19166830 (Clone quality: bE322L18 on chr=13; Num_of_Contigs=3; )
XYLT1		ENSSSCG00000007872	3:24371453-24518465
XYLT2		ENSSSCG00000017573	12:24329432-24338362

Go to records:
1-49, 50-26

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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).