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)

AFP		ENSSSCG00000008949	8:58963626-58970709		FP104530,CH242-172E18,8:58958180-58971352 (Clone quality: bE172E18 on chr=8; Num_of_Contigs=16; )
AFP		location ⇒	8:58965736-58965871		FP104530,CH242-172E18,8:58958180-58971352 (Clone quality: bE172E18 on chr=8; Num_of_Contigs=16; )
AFP		location ⇒	8:58967838-58968054		FP104530,CH242-172E18,8:58958180-58971352 (Clone quality: bE172E18 on chr=8; Num_of_Contigs=16; )
AFP		location ⇒	8:58969151-58969287		FP104530,CH242-172E18,8:58958180-58971352 (Clone quality: bE172E18 on chr=8; Num_of_Contigs=16; )
AFP		location ⇒	8:58970606-58970705		FP104530,CH242-172E18,8:58958180-58971352 (Clone quality: bE172E18 on chr=8; Num_of_Contigs=16; )
AFTPH		ENSSSCG00000008363	3:71275784-71313011		CU856569,CH242-196D3,3:71266093-71351057 (Clone quality: bE196D3 on chr=3; Num_of_Contigs=1; )
AGA		ENSSSCG00000015772	15:36757153-36767717		CU582769,CH242-12O16,15:36746707-36833020 (Clone quality: bE12O16 on chr=15; Num_of_Contigs=2; )
AGA		location ⇒	15:36757426-36757155		CU582769,CH242-12O16,15:36746707-36833020 (Clone quality: bE12O16 on chr=15; Num_of_Contigs=2; )
AGA		location ⇒	15:36758965-36758828		CU582769,CH242-12O16,15:36746707-36833020 (Clone quality: bE12O16 on chr=15; Num_of_Contigs=2; )
AGA		location ⇒	15:36765237-36765081		CU582769,CH242-12O16,15:36746707-36833020 (Clone quality: bE12O16 on chr=15; Num_of_Contigs=2; )
AGA		location ⇒	15:36767720-36767502		CU582769,CH242-12O16,15:36746707-36833020 (Clone quality: bE12O16 on chr=15; Num_of_Contigs=2; )
AGAP1		ENSSSCG00000016317	15:128178456-128325862
AGAP2		ENSSSCG00000000451	5:21974411-21975865		CU914582,CH242-235E14,5:21973900-21976069 (Clone quality: bE235E14 on chr=5; Num_of_Contigs=33; )
AGBL2		ENSSSCG00000013225	2:12949347-12982287
AGBL3		ENSSSCG00000016529	18:12283467-12342301
AGBL4		ENSSSCG00000005108	1:202336756-202420022
AGBL5		ENSSSCG00000008558	3:104484023-104502027
AGC1		ENSSSCG00000001832	7:59854877-59894917
AGC1		location ⇒	7:59879278-59879652		CU407101,CH242-73C15,7:59871259-59894932 (Clone quality: bE73C15 on chr=7; Num_of_Contigs=17; )
AGC1		location ⇒	7:59891834-59891996		CU407101,CH242-73C15,7:59871259-59894932 (Clone quality: bE73C15 on chr=7; Num_of_Contigs=17; )
AGC1		location ⇒	7:59894014-59894199		CU407101,CH242-73C15,7:59871259-59894932 (Clone quality: bE73C15 on chr=7; Num_of_Contigs=17; )
AGC1		location ⇒	7:59894615-59894800		CU407101,CH242-73C15,7:59871259-59894932 (Clone quality: bE73C15 on chr=7; Num_of_Contigs=17; )
AGER		ENSSSCG00000001437	7:28057509-28060556	CT954269,CH242-404E7,7:27953077-28153182 (Clone quality: bE404E7 on chr=7; Num_of_Contigs=12; )
AGFG2		ENSSSCG00000007664	3:6800956-6822787		CU928563,CH242-369L8,3:6786261-6837493 (Clone quality: bE369L8 on chr=3; Num_of_Contigs=1; )
AGGF1		ENSSSCG00000014094	2:74787965-74831832		CU467996,CH242-497E12,2:74761261-74940301 (Clone quality: bE497E12 on chr=2; Num_of_Contigs=1; )
AGGF1		location ⇒	2:74814430-74814698		CU467996,CH242-497E12,2:74761261-74940301 (Clone quality: bE497E12 on chr=2; Num_of_Contigs=1; )
AGGF1		location ⇒	2:74815545-74815658		CU467996,CH242-497E12,2:74761261-74940301 (Clone quality: bE497E12 on chr=2; Num_of_Contigs=1; )
AGGF1		location ⇒	2:74823239-74823344		CU467996,CH242-497E12,2:74761261-74940301 (Clone quality: bE497E12 on chr=2; Num_of_Contigs=1; )
AGGF1		location ⇒	2:74824333-74824446		CU467996,CH242-497E12,2:74761261-74940301 (Clone quality: bE497E12 on chr=2; Num_of_Contigs=1; )
AGK		ENSSSCG00000016492	18:6748359-6866858
AGL		ENSSSCG00000006872	4:123030364-123100430
AGMAT		ENSSSCG00000003463	6:51359158-51368806
AGPAT1		ENSSSCG00000001435	7:28044279-28049284	CT954269,CH242-404E7,7:27953077-28153182 (Clone quality: bE404E7 on chr=7; Num_of_Contigs=12; )
AGPAT2		ENSSSCG00000005829	1:294115116-294118823
AGPAT4		ENSSSCG00000004033	1:7552878-7674727
AGPAT5		ENSSSCG00000015755	15:34944024-34961079
AGPAT9		ENSSSCG00000009233	8:116033227-116095009
AGPHD1		ENSSSCG00000001755	7:53570574-53593306
AGPS		ENSSSCG00000015993	15:78273894-78274013		FP236699,CH242-196C8,15:78273589-78276404 (Clone quality: bE196C8 on chr=15; Num_of_Contigs=11; )
AGPS		location ⇒	15:78271396-78271331		FP236699,CH242-196C8,15:78270411-78273488 (Clone quality: bE196C8 on chr=15; Num_of_Contigs=11; )
AGPT		ENSSSCG00000006035	4:30187582-30312928
AGPT		location ⇒	4:30025559-30025833
AGPT		location ⇒	4:30213556-30213790		CU179712,CH242-318L17,4:30124198-30292499 (Clone quality: bE318L17 on chr=4; Num_of_Contigs=1; )
AGPT		location ⇒	4:30256105-30256274		CU179712,CH242-318L17,4:30124198-30292499 (Clone quality: bE318L17 on chr=4; Num_of_Contigs=1; )
AGPT		location ⇒	4:30312766-30313461		CU467718,CH242-27F1,4:30302193-30380282 (Clone quality: bE27F1 on chr=4; Num_of_Contigs=6; )
AGR2		ENSSSCG00000015363	9:80488684-80496544
AGRIN		ENSSSCG00000004266	1:47303611-47335932		CU928313,CH242-267E23,1:47302416-47347966 (Clone quality: bE267E23 on chr=1; Num_of_Contigs=5; )
AGRN		ENSSSCG00000004266	1:47303611-47335932		CU928313,CH242-267E23,1:47302416-47347966 (Clone quality: bE267E23 on chr=1; Num_of_Contigs=5; )
AGRP		ENSSSCG00000002775	6:13080838-13081885		CU929737,CH242-250E5,6:13062455-13202086 (Clone quality: bE250E5 on chr=6; Num_of_Contigs=3; )
AGT		ENSSSCG00000006148	4:53464180-53503315		CU468596,CH242-179L8,4:53420974-53607412 (Clone quality: bE179L8 on chr=4; 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, 651-700, 701-750, 751-800, 801-850, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-32

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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).