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)

USP43		ENSSSCG00000017995	12:51631115-51687702		CU929537,CH242-329E9,12:51618719-51692234 (Clone quality: bE329E9 on chr=12; Num_of_Contigs=5; )
USP44		ENSSSCG00000000898	5:82940763-82952801
USP45		ENSSSCG00000004351	1:69751812-69809611		CU041276,CH242-402K9,1:69742747-69847842 (Clone quality: bE402K9 on chr=1; Num_of_Contigs=3; )
USP47		ENSSSCG00000013402	2:44020814-44083938
USP48		ENSSSCG00000003516	6:54976002-54986824		CU915824,CH242-56H10,6:54974452-54991615 (Clone quality: bE56H10 on chr=6; Num_of_Contigs=9; )
USP49		ENSSSCG00000001629	7:42569363-42581335
USP5		ENSSSCG00000000684	5:59892529-59904370
USP50		ENSSSCG00000004638	1:126227376-126397134
USP54		ENSSSCG00000010302	14:79609218-79678282
USP7		ENSSSCG00000007907	3:29792405-29848926
USP8		ENSSSCG00000004639	1:126262882-126330434
USP9X		ENSSSCG00000012251	X:36384105-36584255
USPL1		ENSSSCG00000009328	11:6761822-6773482	CU062617,CH242-96H3,11:6637457-6779643 (Clone quality: bE96H3 on chr=11; Num_of_Contigs=1; )
UST		ENSSSCG00000004111	1:17812596-17863104
UTF1		ENSSSCG00000010771	14:147937297-147938633
UTP11L		ENSSSCG00000003645	6:63569864-63583222
UTP18		ENSSSCG00000017593	12:25170730-25209079
UTP20		ENSSSCG00000000869	5:78226281-78452363
UTP23		ENSSSCG00000006017	4:21884676-21890861		CU914669,CH242-39F16,4:21869776-21892202 (Clone quality: bE39F16 on chr=4; Num_of_Contigs=8; )
UTP6		ENSSSCG00000017745	12:40849798-40876524		FP089481,CH242-212P22,12:40732922-40899579 (Clone quality: bE212P22 on chr=12; Num_of_Contigs=1; )
UTP6		location ⇒	12:40849811-40849991		FP089481,CH242-212P22,12:40732922-40899579 (Clone quality: bE212P22 on chr=12; Num_of_Contigs=1; )
UTP6		location ⇒	12:40855261-40855354		FP089481,CH242-212P22,12:40732922-40899579 (Clone quality: bE212P22 on chr=12; Num_of_Contigs=1; )
UTP6		location ⇒	12:40859039-40859160		FP089481,CH242-212P22,12:40732922-40899579 (Clone quality: bE212P22 on chr=12; Num_of_Contigs=1; )
UTP6		location ⇒	12:40862343-40862393		FP089481,CH242-212P22,12:40732922-40899579 (Clone quality: bE212P22 on chr=12; Num_of_Contigs=1; )
UTRN		ENSSSCG00000004123	1:21499955-21561156		FP102247,CH242-291A23,1:21437550-21569411 (Clone quality: bE291A23 on chr=1; Num_of_Contigs=2; )
UTS2D		ENSSSCG00000011816	13:96843385-96851240
UTX		ENSSSCG00000012262	X:39996571-40050956
UTX		location ⇒	X:39951865-39951975		CU468333,CH242-231F21,X:39872093-39967050 (Clone quality: bE231F21 on chr=X; Num_of_Contigs=4; )
UTX		location ⇒	X:40042400-40042328		FP102540,CH242-107L17,X:40032293-40048687 (Clone quality: bE107L17 on chr=X; Num_of_Contigs=9; )
UTX		location ⇒	X:40089849-40089970		FP102540,CH242-107L17,X:40081845-40091384 (Clone quality: bE107L17 on chr=X; Num_of_Contigs=9; )
UTX		location ⇒	X:40100772-40100828		FP102540,CH242-107L17,X:40091485-40110606 (Clone quality: bE107L17 on chr=X; Num_of_Contigs=9; )
UXS1		ENSSSCG00000008143	3:44005314-44096991
UXT		ENSSSCG00000012280	X:42144196-42152068		FP015952,CH242-69I19,X:42126488-42205335 (Clone quality: bE69I19 on chr=X; Num_of_Contigs=6; )

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, 1001-33

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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).