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)

FREM2		location ⇒	11:13836821-13836970		CU633806,CH242-181G7,11:13829398-13853087 (Clone quality: bE181G7 on chr=11; Num_of_Contigs=20; )
FREM2		location ⇒	11:13838603-13838917		CU633806,CH242-181G7,11:13829398-13853087 (Clone quality: bE181G7 on chr=11; Num_of_Contigs=20; )
FREM3		location ⇒	8:72617237-72617406		CU463195,CH242-292M11,8:72617185-72646958 (Clone quality: bE292M11 on chr=8; Num_of_Contigs=4; )
FREM3		location ⇒	8:72619313-72619441		CU463195,CH242-292M11,8:72617185-72646958 (Clone quality: bE292M11 on chr=8; Num_of_Contigs=4; )
FREM3		location ⇒	8:72626702-72626876		CU463195,CH242-292M11,8:72617185-72646958 (Clone quality: bE292M11 on chr=8; Num_of_Contigs=4; )
FRIL_PIG		ENSSSCG00000003153	6:37763537-37765040
FRK		ENSSSCG00000004434	1:85584900-85690472
FRMD1		ENSSSCG00000004017	1:2065306-2077209
FRMD3		ENSSSCG00000010962	10:30134896-30250964
FRMD4A		ENSSSCG00000011056	10:45936689-45987183
FRMD4B		ENSSSCG00000011511	13:42482409-42891844
FRMD5		ENSSSCG00000004694	1:133677750-133724354
FRMD6		ENSSSCG00000005027	1:189644114-189683528		CU074297,CH242-138I16,1:189617322-189754881 (Clone quality: bE138I16 on chr=1; Num_of_Contigs=2; )
FRMD8		ENSSSCG00000012992	2:5225537-5245030
FRMPD1		ENSSSCG00000005352	1:249751186-250068011
FRMPD2		ENSSSCG00000010379	14:92681015-92755183
FRMPD3		ENSSSCG00000012561	X:86220839-86355120
FRMPD4		ENSSSCG00000012115	X:8379484-8390537		CU861900,CH242-165J7,X:8379459-8406130 (Clone quality: bE165J7 on chr=X; Num_of_Contigs=11; )
FRRS1		ENSSSCG00000006873	4:123162141-123207542		CU138489,CH242-35K22,4:123073624-123215352 (Clone quality: bE35K22 on chr=4; Num_of_Contigs=3; )
FRS2		ENSSSCG00000000493	5:32562653-32569247		CU915502,CH242-413F24,5:32561645-32572972 (Clone quality: bE413F24 on chr=5; Num_of_Contigs=17; )
FRS3		ENSSSCG00000001624	7:42432315-42441949		CU914409,CH242-204N15,7:42432150-42476753 (Clone quality: bE204N15 on chr=7; Num_of_Contigs=9; )
FRY		ENSSSCG00000009337	11:8070256-8300751
FRZB		ENSSSCG00000016018	15:82951048-83003871
FSCB		ENSSSCG00000004992	1:183150307-183152610		CU062654,CH242-133L1,1:183093947-183272442 (Clone quality: bE133L1 on chr=1; Num_of_Contigs=1; )
FSCN1		ENSSSCG00000007586	3:3925881-3934358		FP102569,CH242-151E19,3:3887357-3971939 (Clone quality: bE151E19 on chr=3; Num_of_Contigs=3; )
FSCN3		ENSSSCG00000016592	18:18809698-18818633		CU861978,CH242-2M6,18:18763764-18883603 (Clone quality: bE2M6 on chr=18; Num_of_Contigs=4; )
FSCN3		location ⇒	18:18812033-18811825		CU861978,CH242-2M6,18:18763764-18883603 (Clone quality: bE2M6 on chr=18; Num_of_Contigs=4; )
FSCN3		location ⇒	18:18812682-18812509		CU861978,CH242-2M6,18:18763764-18883603 (Clone quality: bE2M6 on chr=18; Num_of_Contigs=4; )
FSCN3		location ⇒	18:18817369-18816670		CU861978,CH242-2M6,18:18763764-18883603 (Clone quality: bE2M6 on chr=18; Num_of_Contigs=4; )
FSCN3		location ⇒	18:18818633-18818389		CU861978,CH242-2M6,18:18763764-18883603 (Clone quality: bE2M6 on chr=18; Num_of_Contigs=4; )
FSD1		ENSSSCG00000013505	2:48543630-48557636		CU972396,CH242-401E10,2:48541506-48658119 (Clone quality: bE401E10 on chr=2; Num_of_Contigs=4; )
FSD1L		ENSSSCG00000005426	1:258823643-258882151
FSD2		ENSSSCG00000001806	7:58209987-58236433
FSHB		ENSSSCG00000013328	2:28321515-28325023
FSIP1		ENSSSCG00000004788	1:137935295-138098298
FSIP2		ENSSSCG00000016025	15:85146797-85148905		CU582971,CH242-30F24,15:85144015-85150566 (Clone quality: bE30F24 on chr=15; Num_of_Contigs=15; )
FST		ENSSSCG00000016892	16:30062130-30068461
FST		location ⇒	16:30064567-30064759		CU929814,CH242-47A14,16:30036507-30067623 (Clone quality: bE47A14 on chr=16; Num_of_Contigs=10; )
FST		location ⇒	16:30065195-30065415		CU929814,CH242-47A14,16:30036507-30067623 (Clone quality: bE47A14 on chr=16; Num_of_Contigs=10; )
FST		location ⇒	16:30065718-30065942		CU929814,CH242-47A14,16:30036507-30067623 (Clone quality: bE47A14 on chr=16; Num_of_Contigs=10; )
FST		location ⇒	16:30066593-30066823		CU929814,CH242-47A14,16:30036507-30067623 (Clone quality: bE47A14 on chr=16; Num_of_Contigs=10; )
FSTL4		ENSSSCG00000014293	2:123399835-123427148
FSTL4		location ⇒	2:123418694-123418843		CU467508,CH242-144E17,2:123398810-123423968 (Clone quality: bE144E17 on chr=2; Num_of_Contigs=8; )
FSTL4		location ⇒	2:123426481-123426617		CU467508,CH242-144E17,2:123424069-123428199 (Clone quality: bE144E17 on chr=2; Num_of_Contigs=8; )
FSTL4		location ⇒	2:123443826-123443690		CU582906,CH242-112N12,2:123442687-123471682 (Clone quality: bE112N12 on chr=2; Num_of_Contigs=9; )
FSTL4		location ⇒	2:123451610-123451461		CU582906,CH242-112N12,2:123442687-123471682 (Clone quality: bE112N12 on chr=2; Num_of_Contigs=9; )
FSTL5		ENSSSCG00000008885	8:43842027-43842272		CU929912,CH242-300A18,8:43772919-43898894 (Clone quality: bE300A18 on chr=8; Num_of_Contigs=2; )
FSTL5		location ⇒	2:123426617-123426481		CU467508,CH242-144E17,2:123424069-123428199 (Clone quality: bE144E17 on chr=2; Num_of_Contigs=8; )
FSTL5		location ⇒	2:123427145-123426983		CU467508,CH242-144E17,2:123424069-123428199 (Clone quality: bE144E17 on chr=2; Num_of_Contigs=8; )
FSTL5		location ⇒	2:123443162-123443324		CU582906,CH242-112N12,2:123442687-123471682 (Clone quality: bE112N12 on chr=2; Num_of_Contigs=9; )

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, 1001-22

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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).